Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

27 Apr '20

External Email - Use Caution for example, here is the lh.gyrification.gii file from CAT calculation. I want a mgh file called lh.gyrification.mgh. My mris_convert command line is as followings: mris_convert lh.gyrification.gii lh.gyrification.mgh But this mgh file seemed failed. I do not know whether my command line is right or not. You should use mris_convert. What is your command line and terminal output? On 4/27/2020 11:05 AM, 肖伏龙 wrote: External Email - Use Caution Dear professor: I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much! I am looking forwards to hear from you. Sincerely, Fulong Xiao

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Dear professor
by 肖伏龙 27 Apr '20

27 Apr '20

External Email - Use Caution Dear professor: I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much! I am looking forwards to hear from you. Sincerely, Fulong Xiao

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correcting fsaverage surface area by eICV
by Paul 27 Apr '20

27 Apr '20

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How is Total cortical gray matter volume calculated
by Ian Hardingham 27 Apr '20

27 Apr '20

External Email - Use Caution Morning Freesurfers. Can you describe how the FS stat Total cortical gray matter volume is calculated from the files in the freesurfer subject directory? Is there an mgz file where each voxel has an estimated percentage grey matter here as the value... or is the volume between the surfaces calculated somehow? Thanks, Ian

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Freeview surface loading error : MRISread failed
by Sezer, Idil 27 Apr '20

27 Apr '20

Hello FreeSurfer developers, I am having an issue viewing a .mgh file I created. Using an output from the fmriprep pipeline, I converted an nii.gz to a .mgh surface : mri_vol2surf --src <participant_ID>_desc-preproc_T1w.nii.gz --<participant_ID> --regheader <participant_ID> --hemi lh I am trying to visualize this surface on an inflated brain using: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=/Users/idilsezer/Desktop/fmriprep_outputs/test/lh.<participant_ID>.mgh I get an error message saying : MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated): could not open file No such file or directory MRISread failed MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated): could not open file And Freeview’s GUI says : Failed to load Surface /Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated I also tried loading it directly from the GUI instead of the command line, it also doesn’t seem to work unfortunately. FreeSurfer version : freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform : mac OS Catalina version 10.15.4 (19E287) Thanks in advance for your help, Best regards, Idil

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Mri_segstats for PET data: Reviewer question
by Shane Schofield 27 Apr '20

27 Apr '20

External Email - Use Caution Hi Freesurfer Team, I have used mri_segstats to get ythe mean PET uptake across all the parcellations in the WMPARC space. These values were calculated in the native PET space (following the DTI tutorial). A reviewer asked what is the grey matter probability of the ROI and I am not sure how to address this. Any help is kindly appreciated. Thanks.

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Contrast file to be used in mri_glimfit
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 27 Apr '20

27 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am a little bit confused on how I should construct my .mtx file to be used in mri_glmfit. The following variables are what I have used in my fsgd file: GroupDescriptorFile 1,,,, Title Study,,,, Class B,,,, Class NB,,,, Variables ,,,Gender,Age Input, Sub_ID,NB,F,71 Input, Sub_ID, B, F, 80 Please let me know if you need more information on my work. Thank you! All the best, Alex Job

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Overlapping Treatments and fsgd files
by Matthew Peverill 27 Apr '20

27 Apr '20

External Email - Use Caution Hello all, I hope everyone is staying safe and sane out there. I'm running an analysis looking at brain structure differences associated with two separate environmental exposures in children (both dichotomous variables). I am controlling for sex and age, and I'm not interested in interaction effects. My go-to strategy does not match the documentation, but I'm not sure the documented solution using fsgd files will meet my needs. I was hoping I could check with the list about best practices. Because some participants have both exposures, my intuition was to use dummy coded variables so that the design matrix looks like this: +1.00000 +3.11124 -0.48322 -0.51007 -0.53020 +1.00000 -0.20820 +0.51678 -0.51007 -0.53020 +1.00000 -2.06654 -0.48322 -0.51007 -0.53020 ... Where the columns are (mean, mean centered age, mean centered sex, mean centered exposure 1, mean centered exposure 2). A contrast for exposure 1 - exposure 2 would then look like this: [0, 0, 0, 1, -1] However, it's clear from the documentation that, given 3, 2 level factors, the recommended approach is to specify 8 classes (one for every combination of factors) and the covariate in an fsgd file. I can remove the interaction terms from the resulting matrix, but even so it looks very different than what I had above: +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +3.11124 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 -2.06654 ... With a contrast with all classes with exposure 1 set to '1', and all classes with exposure 2 set to '-1' - with the order of the classes in the fsgd file it comes out as [-1 -1 1 1 1 1 -1 -1 0]. I'm not positive that this is the right way to model differences associated with each exposure given unequal #s of participants with neither/both/just one exposure, but I certainly don't have the expertise to be certain. Could someone give me some guidance on the best approach here? Thank you, -Matt -- Matthew Peverill 857-277-9083 mrpeverill(a)gmail.com (preferred) pronouns: he/his

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Threshold values changed/modified before display.
by Devavrat Vartak PhD 26 Apr '20

26 Apr '20

External Email - Use Caution Hi freesurfer developers!, I am using Freesurfer 6.0 and the latest (freeview -beta) to display overlays on my flat surfaces. I am a novice user of freesurfer and I am a bit confused with how the overlays are displayed / thresholds calculated. My overlay of rsquare values ranges from 0.2 to 1.0 (i.e all are positive values.). When the overlay is loaded, the threshold histogram depicts values that are negative and positive (centered around zero). 1) Does freeview recaluate/modify the values before they are displayed? 2) Is it possible to display the values of the overlay as they are? Thank you. Stay healthy and safe! Best, Devavrat

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exporting segmented mgz file
by atira gan-zvi bick 26 Apr '20

26 Apr '20

External Email - Use Caution Hi I'm new to freesurfer. I used freesurfer to preform Thalamus segmentation, and can see the segmented volume in freeview. I would like to export the segmented volume to nii to continue analysis in MRvista. I was able to do this using mri_convert - however the values in the nifti are not those on the label list (as seen in freeview). The number of different values is similar but not the same, and the values themselves are totally different (8103-8233 in freeview, 16384 - 32767). It is possible to compare regions based on visual inspection - however that is tedious and might lead to mistakes. How can I export the labels of each region in the segmented mgz? Any suggestions? I'd appreciate to learn fro your experience Thanks Atira -- ד"ר עתירה גן-צבי ביק יחידת ההדמיה התפקודית הדסה עין-כרם האוניברסיטה העברית Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem

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Freesurfer April 2020