Home

file - BioMed Central

1. Feedback e008 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Have you experienced any difficulties in coding your paper Please provide your comments on this program Please use this window to record any questions or comments you may have on the paper Save BrainMap Database Submission After all experiments have been entered save the BrainMap functional database submission by clicking on the top left program menu File gt Save As This saves the information in an ent file Enter the file name in the following format Author_Journal_Year Journal names should be abbreviated and years listed as the last two digits of the published year for example Lee HBM_0O2 ent When you are finished email your ent file and a pdf of the original article to the BrainMap Research Assistant http brainmap org contact html for review and insertion into the database Scribe User Manual page 36 Voxel Based Morphometry Neuroimaging Submissions The interface for VBM submissions is very similar to that for functional submissions Here we highlight the differences e The Citation and Submitter panels are identical to those previously described e Due to the reduced complexity of VBM papers there is no Prose Description Instead we ask that you paste in the published abstract for your submission e The Subjects
2. click the box to the left of Group and all other boxes would remain unchecked Example 5 Session Contrast If all of the conditions of an experiment were identical and were endured by only one group but during more than one session this would be considered a Session contrast Select the Session box and all other boxes would remain unchecked Example 6 External Variable Contrast If an experiment included an external variable with which to conduct a correlation with brain activity and this was the means for cultivating brain images choose the box for External Variable This contrast type must be selected for all experiments that investigated the accuracy of the responses Example 7 Experience Dependent Change If the experimental results could have been affected by experience for example learning order priming repetition or training select the box for Experience Dependent Change Scribe User Manual page 30 Experiments Paradigm Class __BrainMap Scribe Adler_AA_97 ent_ 808 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Locations Select classes appropriate for your experiment Possible Classes Selected Classes Action Observation Pain Monitor Discrimination Acupuncture Anti Saccades Braille Reading Classical Conditioning Counting Calculation Cued Explicit Reca
3. Class Behavioral Domain Locations O Activations Deactivations High Level Control Low Level Control Select conditions used in this experiment Possible Conditions Selected Conditions Warm Painful Painful Warm Select Remove Experiment Saved Close J Save p T Check the box to indicate whether this experiment reports activations increases or deactivations decreases and whether a high or low level of control was used to contrast with the activation condition Only select Low Level Control for rest or fixation control conditions Select Conditions This panel contains the names of the conditions you provided previously on the Conditions panel Choose the conditions included in this experiment After selecting a condition from the menu click the Select button Scribe User Manual page 27 Experiments Sessions A000 BrainMap Scribe Adler_AA_97 ent e088 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions _ Contrast Paradigm Class Behavioral Domain Locations Select sessions used in this experiment Possible Sessions Selected Sessions Placebo Injection Placebo Injection Fentanyl Injection Fentanyl Injection Select Co Remove Experiment Saved Select Sessions This panel contains the names of the sessions previously provided on the Sessions p
4. Drug Effects Disease Effects Drug Effects Experimental Design Effects Gender Effects Handedness Effects Learning Linguistic Effects f Select 3 Remove If Drug Effects then select the corresponding pharmacology domain E Pharmacology sa Pharmacology Opioids Alcohol gt C Amphetamines Caffeine j Capsaicin Cocaine Ketamine Marijuana Select Remove Experiment Saved _ I Provide a brief name for the experiment The names entered here must be the same as those used in the Prose Panel Select contexts appropriate for the experiment Context refers to the broadest category to which an experiment belongs within the realm of brain imaging Most frequently the context of Normal Mapping will be selected Experimental Design Effects is ONLY selected for studies in which a technical aspect of the paradigm is being manipulated such as when comparing the effect of the rate of presentation of the stimuli Self Paced n back vs Fixed Paced n back or Slow Words vs Fast Words This is NOT the appropriate context when simply contrasting two or more conditions that is Normal Mapping Pharmacology If Drug Effects is selected as a context then you will be prompted to enter a corresponding pharmacological domain from the available list of options Scribe User Manual page 24 Experiments Functional Imaging A000 BrainMap Scribe
5. External Assessments This menu is primarily intended for studies wherein an external assessment Test Score Physical Characteristic etc was correlated with brain morphometry If an experiment correlated an external assessment with the volume of brain matter and provided x y z locations enter it here After selecting the desired option from the menu click the Select button If the exact external assessment from your paper is not in the list provided try your best to fit it into one of the provided categories and then provide the exact test name characteristic etc in the short description Do not add your own external assessment other to the list unless absolutely necessary Click Ok when complete with the subjects panel to save your information Scribe User Manual page 39 VBM Analysis AOO Schmidt Wilcke_Ceph_08 vbm Citation Submitter Abstract Subjects j Sessions MBM Analysis Experiments F Feedback VBM Software SPM2 Brain Template MNI SPM2 If Talairach 1967 Choose Origin MRI Field Strength Resolution mm Smoothing Kernel mm Optimized Provide Short Description VBM Software Click on the drop down menu provided and choose the software used to analyze VBM data Brain Template Click on the drop down menu provided and choose the brain template used to report the stereotactic coordinates MRI Field Strength Click on the drop down menu provided and c
6. Invalid gt Valid Cueing Example 2 Subjects underwent 4 conditions in which they performed the n back task Condition 1 Zero Back subjects responded to a single pre specified target Condition 2 One Back subjects responded if the target was any letter identical to the one immediately preceding it Condition 3 Two Scribe User Manual page 9 Back subjects responded if the target was any letter identical to the one presented 2 trials back Condition 4 Three Back subjects responded if the target was any letter identical to the one presented 3 trials back Experiment 1 Load Experiment 2 Time Example 3 Depressed subjects underwent 2 sessions and 1 condition Session 1 Baseline Session 2 8 Week Paroxetine Treatment Condition 1 Rest Experiment 1 8 Week Paroxetine Treatment vs Baseline Example 4 Schizophrenic bipolar and control patients underwent 4 conditions in which they were presented with auditory and visual stimuli Condition 1 Verbal Fluency subjects were presented with a letter aurally and asked to generate a word beginning with that letter internally Condition 2 Verbal Fluency Control subjects were cued by the auditory presentation of the word rest and asked to internally articulate the word Condition 3 Semantic Decision subjects were cued by visual presentation of a noun and asked to decide internally if the word represented a living or non living object Condition 4 Semantic Decision Control subject
7. K J e List authors in the order of appearance on the paper e Do not hyphenate first names of authors Example Marie Claude Antoinette should be entered as Antoinette M C not as Antoinette M C Scribe User Manual page 6 Submitter 00e BrainMap Scribe Adler_AA_97 ent l _Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback C Check if you are an author Name Karl Li Coding Author Institution and Address The University of Texas Health Science Center at San Antonio Email farmers uthscsa edu _ Research Imaging Center M C 6240 7703 Floyd Curl Drive Phone 210 567 8172 Type Undergraduate Student San Antonio TX 78229 3900 Save As Defaults Enter the requested information about the submitter you Check the appropriate box if you are an author on the paper By clicking the Save as Defaults button you can save your submitter information so that you will not have to re type it on subsequent submissions Scribe User Manual page 7 Prose Description e208 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Enter your prose description here see the Scribe User s Manual Subjects underwent 2 sessions and 2 conditions in which they experienced either awarm ora hot painful thermal stimulus
8. Verify and Close Provide a Name for this Condition Painful Stimulus Choose Stimulus Modality Tactile 4 Tactile Heat Painful heat Choose Stimulus Type Heat D Provide Short Description Painful heat Add Stimulus 3 Remove Stimulu Response Choose Response Modality lt 4 None None Choose Response Type ra X Provide Short Description Add Response 7 Remove Response rinstruction Choose Instructions Passive Rest 4 Passive Rest Provide Short Description Add Instruction Remove Instruction Provide a Name for this Condition Use the same naming system as defined in the prose description Again try to keep the naming convention of the paper but use your best judgment Sometimes authors can be confusing and will invent a very long condition name for a simple task If in the interest of brevity it is necessary to formulate your own condition names then do so Choose a Stimulus Modality Choose the sensory mechanism through which the subject was stimulated That is what was used to stimulate one of their five senses while they were in the scanner Choose Stimulus Type Select the specific stimulus from the drop down menu If these choices do not match the stimulus exactly choose Other then click the Add button Scribe User Manual page 15 Provide Short Description Fill in any
9. e g eye movement heart rate accuracy temperature etc In order to be listed here the external variable must be specifically stated in the study When there is no external variable select None Many studies record accuracy and response time Do not forget to include these external variables Scribe User Manual page 18 Conditions Verify and Close Edit Condition Warm Condition Properties External Variable Verify and Close When you are finished with editing click Verify and Close to verify information and update the paper or Cancel to close this dialog Cancel and Close Verify and Close this dialog Once all condition information has been entered click on the Verify and Close this dialog button To discard the changes select Cancel and Close Scribe User Manual page 19 Sessions e088 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Session refers to the period of time between the scanning recording set up and the release of the subject _ Single Session wi Multiple Sessions Placebo Injection Add Session Fentanyl Injection Edit Session Remove Session Sessions refers to the period of time between the scanning recording set up and the release of a subject Most studies occur during only one session If a subject is set up r
10. menu provided If the journal name does not appear choose Other and enter the journal name without abbreviations Do not list sections Institution List the name of the institution where the data was acquired Enter the university name not the department Enter Institute of Psychiatry King s College of London as University of London Enter Wellcome Department of Cognitive Neurology as University College London Medline Num The Medline Number can be located at the PubMed or Medline website If a paper is not archived in PubMed leave this field blank Citation Keywords Scribe User Manual page 5 Click on the desired keywords from the list published with the paper and then click the Select button The chosen keyword will appear in the box to the right Use the Up Down buttons to reorganize the keywords as needed If the appropriate keywords used in your paper are not included in the list provided click the Other button and type in the keyword in the window provided e Enter the exact keyword listed for example fMRI and functional MRI are two different keywords e Do not use capital letters except for proper names nouns e Enter only the keywords published with the paper If there are no keywords listed leave this field blank Authors Enter all authors listed on the paper e Do not add another version of an author s name that already appears in the database e g Friston K and Friston
11. of activation are extracted from the SPls and are entered into the database Initially the BrainMap database archived only functional neuroimaging experiments In 2007 the BrainMap team initiated efforts to expand into archiving structural neuroimaging data Specifically voxel based morphometry VBM which is a statistical analysis for investigating structural differences between two groups of subjects e g areas of increased gray matter density for patients vs healthy controls also had achieved community standardization such that results reported in the form of stereotactic coordinates had become the norm in the same form as for functional neuroimaging data Formal integration by meta analyses on structural neuroimaging findings has thus become possible Following multiple years of data entry as well as database serviet and software programming and development the BrainMap VBM database has been released to the public and is now live June 2011 The Scribe software application is used to code data and meta data from a functional or voxel based neuroimaging paper so that this information can be submitted and inserted into the BrainMap database When Scribe is launched a dialog window asks users to select which type of paper they wish to code functional or VBM Following this the main application window is configured to match the user s selection Functional submissions are created as ent files while the VBM database archives vbm files
12. to their left forearm Session 1 Placebo Injection Session 2 Fentanyl Injection Condition 1 Warm Condition 2 Painful Experiment 1 Painful vs Warm Activations Experiment 2 Painful vs Warm Deactivations Experiment 3 Fentanyl vs Placebo Activations Experiment 4 Fentanyl vs Placebo Deactivations When entering a paper into BrainMap special care should be taken when writing the Prose Description The prose description should e Describe only the experimental design no background results or discussion e Be illustrative but as succinct as possible e Be written in the past tense Include sufficient specific information for each condition and experiment so that a reader will fully understand the experimental design in the paper Correct Format Subjects underwent 2 conditions Condition 1 Name C1 description Condition 2 Name C2 description Experiment 1 Name E1 Experiment 2 Name E2 Sample Prose Description Subjects underwent 2 conditions Condition 1 Verb Generation subjects viewed pictures and generated semantically related verbs of the objects Condition 2 Rest Experiment 1 Verb Generation Rest e Beas brief as possible when describing conditions Scribe User Manual page 8 e Describe the conditions in a chronological sense For example subjects viewed a series of letters after a delay subjects viewed a probe letter and recalled if the probe letter had been one of the encoded lette
13. Adler_AA_97 ent e088 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Locations Select the functional imaging modality rer A Provide a short description Experiment Saved Close Save Functional Imaging Modality Select the functional modality from the pull down menu Short Description If the imaging modality if MRI please provide the magnet strength in the short description if available e g 3T Scribe User Manual page 25 Experiments Subjects A000 BrainMap Scribe Adler_AA_97 ent e088 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Locations Select subject group s for this experiment Possible Subject Group s Selected Subject Group s Normals Normals EEE EEO EE Experiment Saved This panel contains the list of groups entered on the previous Subjects panel Click on the group used for the experiment you are presently entering and then click Select Scribe User Manual page 26 Experiments Conditions gt IO 2 BrainMap Scribe Adler_AA_97 ent Edit Experiment Painful vs Warm Deactivations _ ENS Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm
14. BrainMap Scribe 2 0 http www brainmap org Copyright 2003 2011 Research Imaging Institute UTHSCSA User Manual for Scribe 2 0 http brainmap org Angela R Laird Ph D Research Imaging Institute UT Health Science Center San Antonio BrainMap Development Team Peter T Fox M D Angela R Laird Ph D Simon B Eickhoff M D Jack L Lancaster Ph D Mick Fox Programmer Analyst Angela M Uecker Programmer Analyst Kimberly L Ray Research Assistant Juan J Saenz Jr Research Assistant Updated 20 May 2011 Scribe User Manual page 2 Introduction BrainMap has been in step wise development since 1988 and actively in use since 1992 Its purpose is to facilitate the retrieval and understanding of the literature on functional mapping of the human brain and to enable meta analysis of this literature The structure of BrainMap data entry involves three levels of information paper experiment and locations coordinates Paper level information contains fields such as authors year of publication and age of subjects In the BrainMap database experiments are defined as the comparison of two or more imaged conditions that result in a statistical parametric image SPI Papers containing multiple experiments require information for each experiment to be entered separately this includes fields such as the paradigm class At the location level Talairach or MNI x y z coordinates i e centers of mass of sites
15. Ratio Provide the number of right handed and left handed people ex 5 5 Scribe User Manual page 38 Gender Select the gender from the pull down menu If Mixed gender is selected indicate the number of male and female subjects in the short description Male Female Provide the number of males and females ex 5 5 Sex Matched Controls Select Yes if the non control patient group and control group have the same similar ratio of males to females ICD Code Most diseases are listed in the International Classification of Diseases ICD If the ICD number is unknown usually the case then leave this blank Duration of Illness Provide the mean amount of time the patients have been experiencing symptoms specify days months years Medication If subjects are medicated provide all of the names of the medications Specify the number of subjects taking each medication in the short description Native Language Choose the native language or languages of the subjects or add a new language to the list by choosing Other and typing into the window that appears Min Age Fillin Min Age if reported Only integers are allowed Max Age Fill in Max Age if reported Only integers are allowed Mean Age Fillin Mean Age if reported Only integers are allowed Age Matched Controls Select Yes if the non control patient group and control group have the same similar mean age
16. a given experiment If External Variable is selected please provide the corresponding external variable in this window Example 1 Upon entering descriptions for the stimulus instruction and response used in each condition in an experiment you notice that even though the stimulus used in Condition 1 was different from the stimulus used in Condition 2 the given choices for describing the instruction do not indicate that there is indeed any difference For instance an experiment might involve the following Condition 1 the subject focused on a fixation point while a checkerboard wedge stimulated one part of the visual field There was no response Condition 2 the subject focused on a fixation point while a checkerboard wedge stimulated a more peripheral part of the visual field There was no response In entering the descriptions for these conditions you notice that both are described as Stimulus Modality Visual Stimulus Type Checkerboard Response Modality None Response Type None Instruction Attend The Scribe User Manual page 29 point of interest of this experiment is not indicated by the condition descriptions For the Contrast field however you have the opportunity to indicate which aspects of the conditions differed In this experiment the choice of contrast selected would be Stimulus Type because it was the stimulus that differed between conditions All other fields would remain unchecked Example 2 If the experim
17. additional details about the stimulus that are necessary for a firm understanding of the paper or that add interest to the study This might include information about the exact type of stimulus not apparent from the Stimulus Type selected for example Letter Strings or Spanish Nouns Choose Overt Response Modality Enter measurable responses only for example imagined movement and silent verb generation are covert responses and should not be entered If the response was a button press choose Hand for the modality Choose Overt Response Type Select the appropriate response type Use the Overt Response Type Ocular for saccades or eye movement only not for simply looking at something Don t forget to click on Add Provide Short Description Fill in any additional details about the response that are truly necessary for a firm understanding of the study Choose Instructions Choose the instruction that best describes those used in the study If a subject was instructed to read words aloud choose Read as the instruction and Speech as the subject s response rather than choosing Speak as the instruction If the instructions were to attend and then press a button upon perceiving a target it is only necessary that you enter the instruction to Attend Button Press should be entered only as a response Don t forget to click on Add Please use a complete sentence to
18. anel If the paper included more than one session choose the session used in this experiment If not ignore this panel Scribe User Manual page 28 Experiments Contrast BrainMap Scribe Adler_AA_97 ent eoe Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions l Sessions Contrast Paradigm Class Behavioral Domain l Locations Contrast refers to any and all possible sources of activation in a functional image comparing scans from two conditions between levels of a parametric design effect of correlating a regressor or the main effects and interactions in a factorial design L Stimulus Modality C External Variable wv Stimulus Type l Experience Dependent Change _ Response Modality C Group Response Type Vv Session Instruction Experiment Not Saved Close Contrast The purpose of contrast is to identify the key aspect of the study In a given experiment the contrast fields indicates how the conditions being compared in an experiment are different To choose the source of contrast in the experiment click on the box to the left of the description Make as many choices as appropriate for each experiment To help identify the contrast refer to the Conditions panel and look at the differences in condition stimulus response and instructions Provide a short description Use the blank window in the lower half of this panel to summarize and clarify the contrast of
19. ap voxel based morphometry submission Scribe User Manual page 4 Functional Neuroimaging Submissions Citation e098 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Title Regional brain activity changes associated with fentanyl analgesia elucidated by positron emission tomography Journal Institution Anesthesia and Analgesia ka University of Pittsburgh Date City Jan R 1997 EE Pittsburgh Medline Num Volume 8989012 84 Country United States Page From Page To 120 126 Citation Keywords Authors limbic structures 0 Select Abbott D F Select Adler LJ lhz Abdallah S p Gyulai F E 6 18F fluoro L dopa FDOPA PET Abel K M Diehl D J 99mtc hexamethylpyleneamine oximi Remove Abelson J L Remove Mintun MA 99mtc hmpao spect Abend NS Winter P M 150 H20 PET Other Abercrombie H C _ Other Firestone LL 18f fluorodeoxyglucose positron emis Abler B abstract acc Abplanalp B Abrahams S accumbens Abramoff A acoustic communications Abrams MT acoustic startle Aburano T Abutalebi J Arhim A M Title Capitalize the initial word and those used to capitalize proper names use lowercase for all other words Also capitalize the first letter after a colon Do not leave a period at the end of the title Journal Select the journal name from the pull down
20. describe the instructions e g Subjects were instructed to generate verbs in response to the presented nouns Also please use the past tense e Do not confuse detect and discriminate Detect is to discover the presence of i e does target exist while discriminate is to distinguish from another like object by discerning differences i e choosing a target e Do not use attend every time the subjects pay attention to the stimulus otherwise it will be coded in every paper Only use attend in studies where the subjects only instruction is to pay attention to the stimuli Provide Short Description Any additional details about instructions that are necessary for a firm understanding of the study should be entered in this field Short Description Bottom Window Use this space to enter any summary or clarifying information that pertains to the condition as a whole i e that cannot be broken into one of the three components stimulus response instructions If the description CAN be classified as one of the three components then enter the desired information into one of the short description fields listed above Also making a mental note of the differences in various conditions of your paper during entry will assist in identifying the contrast when entering experiment information later on Scribe User Manual page 16 Before exiting this panel make sure that the way this condition differs fro
21. e Description If relevant specify the external assessment as you did in the Subjects panel If corrected for multiple comparisons include the method of correction e g Family wise Error Correction etc here Threshold P value Provide the p value used for this experiment e g lt 0 01 lt 0 001 lt 0 05 etc Thresholding Select the method of thresholding If information not provided select Unknown Corrected for Multiple Comparisons Select the answer from the pull down menu Observed Changes Scribe User Manual page 42 If there is greater brain matter volume in controls Normals gt Patients then this would be Increases in Controls if great brain matter volume in patients Patients gt Normals then you would select Increases in Patients If the experiment contrasts two patient groups or two healthy control groups choose Neither ROI Based Analysis Select Yes for ROI based analyses that analyzed a small fixed number of a priori brain regions Select No for whole brain analyses Coordinates State whether the published x y z coordinates were extracted from the Center of Mass or Peak Voxel of the observed cluster Save VBM BrainMap Database Submission After all information has been entered save the BrainMap database submission by clicking on the top left program menu File gt Save As This saves the information in an vb
22. eleased and then set up again the second set up marks the beginning of a second session Before and after treatment studies and before and after practice studies would involve multiple sessions For one session studies no entries are required on this panel e For multiple sessions check on Multiple Sessions and click the Add Session button A message box will then appear prompting you to enter at least two sessions If your paper includes multiple sessions be sure to include this design in the prose description Sessions Session Name Scribe User Manual page 20 f A000 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Session refers to the period of time between the scanning recording set up and the release of the subject C Single Session V iiien 2 000 Edit Session Fentanyl Injection Placebo Injection Session Name Fentanyl Injection Fentanyl Injection Add Session Description Subjects were injected with fentany just prior to scanning Cancel OK o C Edit Session Remove Session Give the session a brief name for example Before Treatment or After Therapy Description of this Session Describe the session including sufficient detail to distinguish this session from other sessions and to give a firm understanding of the s
23. elected indicate the number of male and female subjects in the short description Handedness Choose one option from the menu to describe the handedness of the subject group Use the Mixed option if the subjects had different handedness Native Language Choose the native language or languages of the subjects or add a new language to the list by choosing Other and typing into the window that appears Ages of Subjects Fill in Min Age Max Age and Mean Age if reported Only integers are allowed Scribe User Manual page 13 Conditions 00e BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Each stimulation or control state would be considered a condition Please provide the names of your conditions Warm Add Condition 9 Painful Edit Condition Remove Condition 3 Duplicate Condition 4 Shift Up gt Shift Down J Enter all conditions used in the paper including the control conditions e g Rest or Baseline To change the order listed to better reflect the order used in the experiment click the Shift Up or Shift Down button at the bottom of the window Scribe User Manual page 14 Conditions Stimulus Response and Instructions Edit Condition Painful Condition Properties External Variable
24. ent involved Condition 1 subject viewed nouns on a screen and was asked to generate verbs aloud which pertain to the nouns on the screen and Condition 2 subject viewed nouns on a screen and was asked to read the words aloud the only difference here is in the instructions For both conditions the stimulus is visual words and the response is speech In this case the instructions for Condition 1 would be Generate and the instructions for Condition 2 would be Read It is implied that during Condition 1 the subject had to read the nouns first in order to generate verbs Therefore the contrast between the conditions is only in Instructions All other fields would remain unchecked Example 3 If the experiment involved Condition 1 subject listened to nouns presented aurally one at a time with instructions to generate verbs which pertain to the nouns and Condition 2 subject listened to nouns presented one at a time and was instructed to generate words that rhyme with the nouns then in this case all three fields stimulus response instructions would be entered identically for the two conditions However the generation performed in each condition was indeed different Therefore enter again the contrast as Instructions All other fields would remain unchecked Example 4 Group Contrast If the conditions of an experiment are identical but were endured by two different groups this would be considered a Group contrast In this case
25. hoose the strength of the MRI magnet used to acquire data in Tesla Resolution mm Provide the final voxel size resolution in mm e g 1x1x1 If this parameter is not provided in the paper provide the Field of View FOV and the slice thickness in mm Smoothing Kernel mm Provide the Gaussian smoothing kernel used in mm Optimized State whether the authors used an optimized VBM protocol If the paper states they used the protocol described in Good et al 2001 or Asburner and Friston 2000 then this is optimized Also if images were modulated by the Jacobian determinant then this is also considered optimized Short Description Enter the software used for spatial normalization Scribe User Manual page 40 Experiments Schmidt Wilcke_Ceph_08 vbm Edit Experiment Controls gt Migraine Patients Context Imaging Modality Subjects Sessions VBM Analysis Locations Provide a brief name for the experiment It should indicate the source of contrast in the image e g Read vs Rest see Submit User s Manual Controls gt Migraine Patients Select contexts appropriate for your experiment Age Effects Disease Effects Disease Effects Drug Effects Gender Effects Genotype Effects Handedness Effects Learning Linguistic Effects Normal Mapping Treatment Effects C Remove Experiment Saved Close Save In the Experiments panel the options for Con
26. ll Deductive Reasoning Delayed Match To Sample Divided Auditory Attention Drawing Eating Encoding Episodic Recall Face Monitor Discrimination Film Viewing Finger Tapping Fixation Flanker Task Flashing Checkerboard Flexion Extension Free Word List Recall Go No Go Imanina A Mauamanr Select Remove Experiment Not Saved Close gt Save J Paradigm Class Paradigm Class refers to those experimental paradigms that have been used repeatedly by different researchers Some have become widely known and accepted by brain imagers and have acquired informal or formal names This list is not intended to include a fitting description of every experimental paradigm imaginable but evolves with the field Select only the Paradigm Class that fits the Activation condition For example if the Activation condition is the Stroop task and the Control condition is Fixation then for Activation Control select Stroop only not Stroop AND Fixation Scribe User Manual page 31 Experiments Behavioral Domain Adler_AA_97 ent ANO Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class BehavioraDomain Locations Select the behavioral domain s Possible Behavioral Domain s Selected Behavioral Domain s Action Perception Somesthesis Pain L Cognition L Emotion __ Interoception Perception Audition Gu
27. m file Enter the file name in the following format Author_Journal_Year Journal names should be abbreviated and years listed as the last two digits of the published year for example Lee HBM_02 vbm When you are finished email your vbm file and a pdf of the original article to the BrainMap Research Assistant http brainmap org contact html for review and insertion into the database Scribe User Manual page 43 Troubleshooting Scribe says that I m missing an essential file Data file missing Unable to find an essential file SearchList xml Try checking your internet connection or 2y configuring your proxy server settings under Options Okay This can indicate one of two things First the BrainMap web server may be down for maintenance In this case try restarting Scribe in an hour or so Alternatively there may be a firewall blocking communication to the BrainMap web server If a successful connection to BrainMap has been made previously then please contact BrainMap technical support to check the web server If you are behind a restrictive firewall and have a known proxy server Scribe can use it to access our BrainMap web server Under File Options there is a menu item called Proxy Settings You will need to know the IP and valid port of the proxy server A Scribe 1 2 Preferences Use HTTP Proxy Host 129 111 249 38 Port 3128
28. m the other condition s in your paper can be determined by looking at the Conditions panel i e don t duplicate conditions To edit existing conditions simply double click on the selected field entry This will populate the condition information back into the drop down menus so that you may edit the details If necessary use the Up Down buttons to organize the condition information to reference time dependent stimuli responses or instructions stimuli presented first listed first while stimuli presented later listed second Scribe User Manual page 17 Conditions External Variable 8 08 Edit Condition Warm l Condition Properties External Variable Verify and Close Choose External Variables non imaging variables obtained during imaging Possible External Variables Selected External Variables Unknown Blood Pressure None Heart Rate Accuracy Respiratory Data Blood Pressure ECG EEG Electrooculogram EMG Grip Force Heart Rate Pain Rating Penile Tumescence Respiratory Data Response Time Chins Candhi iren nen Select Provide Short Description This menu is primarily intended for studies wherein an external variable was correlated with brain activity If a correlation included an external variable enter the variable here After selecting the desired option from the menu click the Select button The external variable is any measurement taken during the scan
29. ng the results synopsis of the paper Significant differences in regional cerebral blood flow rCBF between the placebo and the fentanyl conditions during nonpainful and painful stimuli were identified using statistical parametric mapping It was found that pain increased rCBF in the anterior cingulate ipsilateral thalamus prefrontal cortex and contralateral supplementary motor area Fentanyl increased rCBF in the anterior cingulate and contralateral motor cortices and decreased rCBF in the thalamus bilaterally and posterior cingulate during both stimuli During combined pain stimulation and fentanyl administration fentanyl significantly augmented pain related rCBF increases in the supplementary motor area and prefrontal cortex This activation pattern was associated with decreased pain perception as measured on a visual analog scale In contrast to our hypothesis these data indicate that fentanyl analgesia involves augmentation of pain evoked cerebral responses in certain areas as well as both activation and inhibition in other brain regions unresponsive to pain stimulation alone To enter the results synopsis of a paper copy the published abstract from Medline or PubMed Delete the first sentences that deal with the introduction methods and design of the study and leave only the sentences concerning the results and conclusions DO NOT edit the synopsis to include your own interpretation of the study Scribe User Manual page 35
30. or individual subjects as opposed to group mean data Hemisphere Adhere to the standard that left is negative Inspect your table carefully to be sure that all coordinates listed from the left hemisphere have x values that are negative and those from the right hemisphere are positive If not switch the signs of your x values before entering them into the table X mm Y mm Z mm Enter the x y and z values as printed in the table with the exception as noted above SPI Value Enter the SPI value statistic reported in the paper for example z t or r The z score or t statistic can be the mean or the maximum value for the cluster SPI Unit Indicate the variable z t r entered in the SPI Value column Do not enter voxel wise P values in the SPI columns Extent mm Scribe User Manual page 33 Report the extent also referred to as volume or size of the activation recorded in cubic millimeters This number usually ranges from the low hundreds to 1000 or 2000 Do not record the number of voxels not in units of mm e 1ml 1cc 1cm 1000 mm e 1ul 1mm For other conversions please see http www onlineconversion com volume htm Scribe User Manual page 34 Results Synopsis e088 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Enter in a brief prose explaini
31. panel has a few minor modifications based on the details for the subject groups e The Sessions panel is the same as previously described e Anew panel VBM Analysis has been added for VBM submissions e The Experiments panel is greatly simplified in comparison to functional submissions e The Feedback panel is the same as previously described Schmidt Wilcke_Ceph_08 vbm Citation Submitter Abstract Subjects Sessions VBM Analysis Experiments Feedback Title Subtle grey matter changes between migraine patients and healthy controls Journal Institution Cephalalgia a University of Regensburg Date City Jan Ea 2008 Regensburg Medline Num Volume Country 17986275 28 T Germany Page From Page To 1 Citation Keywords Authors where pathway A select cingulate cortex Ss Select Schmidt Wilcke T 18F FDG PET f imaging Aarsland D Gansbauer S 22q11 e migraine Aasen I a Neuner T 22q11 2 deletion syndrome 22qD AORTNE a Abbott D F Bogdahn U 5 HT Abe M TRO 5 HT 1A receptor __ Other Abe O _ Other 5 HT2A receptor Abele M S HTT Aberg L E K1 DC WAY100635 Absinta M 18F FDG PET Acker J D a MTrp brain trapping Acosta Cabronero J Abstinence p Acton P D E l C Down fadali T Scribe User Manual page 37 Subjects Subject Group A O Edit Subjects Migraine Patients Subject D escription External Assessments En
32. rs e Capitalize the first letter in all words in the names of conditions and the names of experiments e The names of experiments should be taken directly from the coordinate tables in the papers Some experiment names explicitly state the conditions in them Finger Tapping Rest or Finger Tapping vs Rest or Finger Tapping gt Rest and some do not Motor Directed Attention or Conjunction Analysis Use the convention of naming adopted in the paper For conjunction and disjunction analyses normally all conditions are used in all experiments unless the experiment indicates which conditions were used in each experiment See Thierry_HBM 03 ent for an example e Avoid use of the word task in the condition and experiment name For example Finger Tapping Task should be named Finger Tapping e When possible combine like instructions for more than one condition in the first sentence of the prose description Example Subjects underwent 5 conditions in which they silently read words immediately after presentation Then list each condition When one condition is different from the others list this condition last e If Rest is used as a control condition list it last The conditions Rest and Fixation do not require a description e Some papers report increases and decreases in activation Be sure to inspect the coordinate tables carefully as authors frequently pre
33. s fixated on an isoluminant screen Experiment 1 Verbal Fluency Bipolar Patients Experiment 2 Verbal Fluency Control Bipolar Patients Experiment 3 Semantic Decision Bipolar Patients Experiment 4 Semantic Decision Control Bipolar Patients Experiment 5 Bipolar vs Control Verbal Fluency Experiment 6 Bipolar vs Schizophrenic Verbal Fluency Experiment 7 Bipolar vs Control Semantic Decision Experiment 8 Bipolar vs Schizophrenic Semantic Decision Scribe User Manual page 10 Subjects 00e BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Describe your subject groups Normals Add Group Edit Group Remove Group Duplicate Group Shift Down Click the Add Group button to enter subject information in the Subjects panel that appears as a blank window To enter several similar subject groups enter the first set of data and then click on the group name Next click the Duplicate Group button Data entered for the first group will be copied into a new subject group window Rename the duplicate subject group and change the data as appropriate If coordinates reported are for individual subjects as opposed to group mean data enter each subject s information as an individual group Subjects Subject Group Scribe User Manual page 11 Adler_AA_97 en
34. sent each in the same table Increases and decreases should be coded and named as separate experiments For example a study may investigate motor function and acquire data on two conditions Finger Tapping and Rest The coordinate table may be titled Increases and Decreases and the paper should be coded with two experiments not one e If the paper includes normal subjects and a patient group begin by stating this in the first line of the prose description For example Epilepsy patients and normal subjects underwent 3 conditions Examples of properly formatted prose descriptions are provided below Example 1 Subjects completed a variant of the Posner spatial cueing task The target was an X or an O and the subjects pressed one of 2 buttons to indicate the target s identity as quickly as possible Condition 1 Location Based Valid Cueing attention was cued by an arrow pointing in the direction of the target positions Condition 2 Location Based Invalid Cueing attention was cued by an arrow pointing in the incorrect direction of the target positions Condition 3 Object Based Valid Cueing attention was cued by a geometric shape drawn to contain the target positions within its boundaries Condition 4 Object Based Invalid Cueing attention was cued by a geometric shape drawn to contain the target positions within its boundaries and the shape did not contain the target Experiment 1 Object gt Location Based Cueing Experiment 2
35. ser Manual page 3 Rest The names used here should be entered on the Experiments panel Experiments should be listed here and in the order in which they were published Do not enter conditions that do not result in activations or were not used in experiments Save BrainMap Database Submission It is a good idea to save your changes to file after completing each major panel To do so click on the top left program menu File gt Save As This saves the information in an ent file or a vbm file depending on your choice Enter the file name in the following format Author_Journal_Year ent If you are on a PC be sure and type in file extension Journal names should be abbreviated and years listed as the last two digits of the published year for example Lee_HBM_02 ent Functional or VBM Database Submissions When Scribe is launched you will see the following dialog window BrainMap Scribe 1 2 BrainMap Paper Type Please choose which type of BrainMap paper to code Functional or VBM C veM C Functional Copyright 2003 2010 Research Imaging Center UTHSCSA Selecting VBM takes you to the interface for a VBM submission while selecting Functional will take you to the interface for a functional submission In this manual we will first describe how to generate a submission for the BrainMap functional neuroimaging database On page 36 we address the modifications necessary to generate a BrainM
36. station Olfaction Y E Somesthesis gt 0 vision Remove Experiment Saved Close SY Behavioral Domain The categories on the left provide several subcategories as drop down menus Double click on the categories to see the related subcategories These categories and subcategories classify the mental operations likely to be isolated by the experimental contrast Select only the Behavioral Domain that fits the Activation condition For example if the Activation condition is semantic in nature and the Control condition is phonological in nature then for Activation Control select Semantics only not Semantics AND Phonology e Use both Behavioral Domains of Cognition Language Speech and Action Execution Speech with overt speech production but with covert speech production use only the Behavioral Domain of Cognition Language Speech Scribe User Manual page 32 Experiments Locations y BrainMap Scribe Adler_AA_9 7 ent e098 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Locations Check if entering individual subject s data Hemisphere x mm Y mm Zmm SPI Value SPI Unit Extent mm3 T 10 68 20 3 0 Left Remove Row Experiment Not Saved Close Save TA Check if entering individual subject s data Check this box if the coordinates entered are f
37. t Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Describe your subject groups Normals Enter a brief name for your subject group Edit Subjects Normals Normals Provide Diagnosis If applicable please provide concurrent diagnosis Provide Short Description Normals ICD code 5 men 4 women Total subjects Gender Handedness Native Language Mixed Min Age Max Age Unknown Mean Age Unknown Cancel Shift Up Shift Down Name of Subject Group Provide a brief name for the subject group for example Normals Provide Diagnosis Select from the list any medical or psychological conditions Concurrent Diagnosis If applicable please select a concurrent diagnosis from the list Generally this is left blank ICD Code Most diseases are listed in the International Classification of Diseases ICD If the ICD number is not known usually the case then leave this blank Provide Short Description Enter the ratio of male to female subjects e g 4 women 5 men Also enter the ratio of right handed and left handed subjects e g 6 right handed 4 left handed Total Subjects Enter a number into the space provided Only integers are allowed Gender Scribe User Manual page 12 Select the gender from the pull down menu If Mixed gender is s
38. ter a brief name for your subject group Migraine Patients Provide Diagnosis ICD code Migraines Age of Onset 0 Duration of Illness Treatment Status Mixed Medication NSAID Total Number of Subjects 35 Native Language Unknown Handedness Ages of Subjects Unknown Right Handed Left Handed Ratio Min Age 18 Gender Max Age 49 Male Female Ratio Mean Age 32 Sex Matched Controls No O unknown Age Matched Controls O Yes No Unknown Provide Short Description 35 migraine patients 3 male 32 female 19 patients with menstrual migraine 16 patients without menstrual migraine Cancel Name of Subject Group Provide a brief name for the subject group for example Normals Provide Diagnosis Select from the list any medical or psychological conditions Age of Onset Provide the age in years when patients began to experience symptoms of disease condition Only integers are allowed Treatment Status Select the treatment Medicated or Unmedicated from the pull down list If Mixed provide the number of subjects unmedicated and medicated in the short description Total Number of Subjects Enter the number of subjects studied into the space provided Only integers are allowed Handedness Choose one option from the menu to describe the handedness of the subject group Use the Mixed option if the subjects had different handedness Right Handed Left Handed
39. text Imaging Modality Subjects Sessions and Locations are the same as for functional submissions A new panel for VBM Analysis has been added Due to the simplicity of VBM protocols there is no panel for Conditions Paradigm Class or Behavioral Domain When naming VBM experiments please specific if the locations are Grey Matter or White Matter and Increases or Decreases Scribe User Manual page 41 Experiments VBM Analysis Schmidt Wilcke_Ceph_08 vbm ANO Edit Experiment Controls gt Migraine Patients Context Imaging Modality Subjects Sessions VBM Analysis Locations Contrast Gray Matter White Matter csi C Unknown External Assessment Significant grey matter increase in controls versus patients Description g grey p Threshold P value lt 0 05 Thresholding O Voxel wise O Cluster wise Unknown Corrected for Multiple Comparisons Yes ry Observed Changes Increases in Controls B ROI Based Analysis O Yes No O Unknown Coordinates O Center of Mass O Peak Voxel Unknown Experiment Saved Close Save Contrast Select the tissue contrast for the given experiment External Assessment This panel contains the names of the external assessments previously provided on the Subjects panel If the paper included more than one external assessment choose the one correlated in the given experiment If no external assessment was correlated then you should select Non
40. tivations Fentanyl vs Placebo Deactivations Edit Experiment Remove Experiment Duplicate Experiment Shift Up Shift Down Enter experiments according to the names and order entered in the Prose panel To enter several similar experiments enter the information for the first experiment and verify and close it Then click on its name and click the Duplicate Experiment button The experiment data will be copied into a new experiment Enter a new name for the new experiment making changes to the existing data as needed Shortcut Many experiments are very similar within a paper so it can save time if you enter in all the information for the first experiment EXCEPT for the coordinates Then save the experiment duplicate it and edit the duplication s for the additional experiment s The final step is to go back and enter in the coordinates for all the experiments once they have been created Scribe User Manual page 23 Experiments Context Adler_AA_97 ent 6 0 8 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Locations Provide a brief name for the experiment It should indicate the source of contrast in the image e g Read vs Rest see Scribe User s Manual Painful vs Warm Deactivations Select contexts appropriate for your experiment Age Effects
41. tudy Please use a complete sentence to describe the session Scribe User Manual page 21 Brain Template e008 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Brain Template Talairach 1988 iz If Talairach 1967 Choose Origin ac B Provide Short Description Click on the drop down menu provided and choose the brain template used Short Description Enter the software used for spatial normalization e g SPM96 FSL SPM99 then converted to Talairach space using the Brett transform etc All MNI coordinates will be automatically converted to Talairach space using the icbm2tal transform Lancaster et al 2007 All MNI coordinates converted to Talairach space via the Brett transform in the original publication will be subject to 2 transforms 1 reverse Brett to convert back to MNI space and 2 icbm2tal for correct transformation from MNI to Talairach space Scribe User Manual page 22 Experiments e068 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback An experiment is anything that produces an SP Statistical Parametric Image Please enter your experiment s Painful vs Warm Activations New Experiment Painful vs Warm Deactivations Fentanyl vs Placebo Ac
42. which allows each type of submission to be easily identified Regardless of the type of submission the first panel of the BrainMap Scribe interface is entitled Citation and the last is entitled Feedback The interface is designed to enter data from the left to right Some entry panels will not accept information until previous panels have been completed Furthermore all panels except Experiment require paper level information Some fields provide drop down menus and some provide windows for free form entry The words from the drop down menus are all keywords that users may use to conduct searches using BrainMap Sleuth www brainmap org sleuth According to BrainMap s system of describing a paper studies are broken down into Conditions and Experiments Conditions Subjects perform tasks under certain conditions and these conditions are contrasted in an experiment Each condition used in a BrainMap defined experiment should be briefly described and named by simple terms such as Read Finger Tapping Rest or Word Generation For example in a simple motor study subjects performed two conditions Finger Tapping and Rest Conditions are worded in the past tense Experiments An experiment is the result of comparing two or more conditions Each experiment name should indicate which conditions were contrasted In the preceding example the experiment would be named Finger Tapping Scribe U

file - BioMed Central

Contents

Download Pdf Manuals

Related Search

Related Contents