Freesurfer

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30084 discussions

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

2 1

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

2 1

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

2 1

Infant freesurfer
by COLLEEN PLETCHER 26 Apr '20

26 Apr '20

External Email - Use Caution Hello. I am working with the infant Freesurfer pipeline. I have noticed that some of our subjects may need to be manually edited, and then run through the pipeline again. However, when I try to do an infant_recon_all command combined with something like autorecon2-wm, I am getting an error that says the command cannot be found. Are there any commands specific to infant Freesurfer that can be used in combination with manual edits? Thanks!

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Re: [Freesurfer] How is Total cortical gray matter volume calculated
by Xiaojiang Yang 25 Apr '20

25 Apr '20

External Email - Use Caution Ian, You can use the mris_anatomical_stats command with the -b option. E.g., mris_anatomical_stats -b subjectid lh will give you a tabular output containing the total gray matter volume in the 3rd column: 128449 86239 *243375 *2.588 0.876 0.123 0.026 1496 133.3 /xxx./subjects/QEN001/surf/lh.white See https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats for more information. Xiaojiang

1 0

Generating Surfaces Meshes
by Peter, Jonah 24 Apr '20

24 Apr '20

Hello, I'm trying to generate surface meshes for different brain regions that can be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, etc.). I ran recon-all on my T1 images, and the parcellation/segmentation looks fine. However, I noticed that when I imported this data into 3DSlicer, the volumes of these regions did not match the volumes in the aseg.stats file. In some cases, the differences were quite substantial. I tried removing all smoothing filters in 3DSlicer but the outcome was the same. Do you know what could be going wrong here? Alternatively, is there an easier way to generate surface meshes from the aparc or aseg atlases? I'm using the ICBM 2009c Nonlinear Asymmetric template ( http://nist.mni.mcgill.ca/?p=904) as a generic brain volume (though alternative suggestions are welcome). Thanks! Jonah -- Jonah Peter Graduate Student in The Biophysics Program Harvard University P: 646-306-0848 E: jonahpeter(a)g.harvard.edu

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matlab runtime error - Hippocampal subfield segmentation
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 24 Apr '20

24 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am having trouble installing matlab runtime to be used for hippocampal subfield segmentation. I run the code following the instructions on the website, but nothing is installed. This is what happens: /home/alex/Documents/freesurfer/bin# cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_inst… -o fs_install_mcr && chmod +x fs_install_mcr % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1801 100 1801 0 0 17485 0 --:--:-- --:--:-- --:--:-- 17485 Any ideas why this isn't loading? Thanks, Alex Job

2 1

creating label from volume mask in MNI space
by Tammi Kral 24 Apr '20

24 Apr '20

External Email - Use Caution Hello, I have tried multiple strategies to create labels in subject space from a couple subcortical (brainstem and cerebellum) volume-based ROIs (masks) defined from a thresholded statistical map. The ROI file is a simple binary mask in MNI space. However, the results are misaligned and appear as a grid of dots. First I tried using mri_vol2vol to go from MNI space to FS space (I tried using both the fsaverage brain and the mni205 brain). I previously ran the MNI152 brain through recon_all, per advice I found in the archives. For example, using the below command: mri_vol2vol --mov ${ROI_DIR}${roi}.nii.gz --s MNI152_T1_2mm \ --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z \ --o ${ROI_DIR}${roi}_FSvol.nii.gz --nearest Since the MNI space ROIs also overlaid in FS space, I also tried skipping this first step and going straight to the next step, which was to use mri_vol2label to create the label file. For example, like this: mri_vol2label --i ${ROI_DIR}${roi}_FSvol.nii.gz --id 1 --l ${ROI_DIR}${roi}_FSvol.label Then I used mri_label2label to move the label to each subject's space, like so: mri_label2label --srcsubject fsaverage \ --srclabel ${ROI_DIR}${roi}.label --trgsubject ${subfolder} \ --trglabel ${SUBJECTS_DIR}/rois/${sub}_${roi}_FSvol.label --regmethod volume I also tried moving the label output of this final step (in subject space) back to a volume, though this doesn't seem necessary, as I could extract the data from the label file: mri_label2vol --label ${SUBJECTS_DIR}/rois/${sub}_${roi}_mni.label \ --o ${SUBJECTS_DIR}/rois/${sub}_${roi}_FSvol.mgh --identity --temp ${SUBJECTS_DIR}/${subfolder}/mri/T1.mgz I have attached a screenshot of the label file for the cerebellar ROI (in yellow) in subject space, overlaid on the subject's T1 from: /subject_directory/mri/T1.mgz (I apologize that it's not the best view, as I'm working from home and it's very slow using the GUI to change the view). I also apologize in advance if I've left out critical info to answer this question - please let me know. I appreciate any advice you might have! This seems like it should be a pretty common, straightforward process, yet I have not been able to find anything that works. Thank you, Tammi RA Kral, PhD Center for Healthy Minds University of Wisconsin-Madison she/her

1 0

Re: [Freesurfer] Password VM FStutorial
by fsbuild 24 Apr '20

24 Apr '20

External Email - Use Caution I will send it to your email shortly. - R. On Apr 24, 2020, at 07:43, Etienne Abassi <etienne.abassi(a)isc.cnrs.fr> wrote:       External Email - Use Caution        Dear all,I tried to install the virtual image of Freesurfer you provided on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_winIt worked well, but I can't find the password for the "Developer" account, and so I can't log into the VM. Could you please provide the password ?I thank you in advance for you time.Best,Etienne-- Etienne Abassi, PhD StudentInstitut  des Sciences Cognitives Marc Jeannerod - CNRS UMR 522967, Boulevard Pinel - 69675 BRON (Lyon), France_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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