Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

Pass code request
by Lorenzo Civilla 11 Nov '22

11 Nov '22

External Email - Use Caution Dear Freesurfer team, thank you for the great software you're developing, it is extremely nice! I am writing to ask you for a pass code to open the 7z archive I downloaded from the following page: https://secure-web.cisco.com/1a_Lk7dJKn84XrIID0fEz1mmFgsz5S6WNCBj4IDEm0i7Kd… I would like to use Freesurfer for research purposes in Neurosurgery, in particular in neurovascular. My best regards, Lorenzo Civilla, MSc -------------------- Senior Scientist at Medical University of Vienna lorenzo.civilla(a)meduniwien.ac.at

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Segmentation of hippocampus(left), grey and white matter regions.
by PRASAD D 10 Nov '22

10 Nov '22

External Email - Use Caution Hello everyone. I’m new to FREESURFER I would like to segment the sMRI images. I have extracted(skull stripped) the brain region from the sMRI image using BET. but i'm interested in hippocampus(left), grey and white matter regions. Can you please guide me how to segment those specific regions automatically. Thanks in advance. -- *Yours sincerely* *D.PRASAD* *Full Time Research Scholar(QIP)* *Dept. of ECE, PTU.*

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[Freesetfer] Requesting Password for VM soft
by Андрей Калиниченко 10 Nov '22

10 Nov '22

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Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error
by fsbuild 10 Nov '22

10 Nov '22

External Email - Use Caution On MacOS I would try running the fs_install_mcr script with, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b That script should setup the environment to find the libmwm* libraries it installs in the freesurfer tree under $FREESURFER_HOME/MCRv84/bin/glnxa64. But If your shell environment (e.g., via $HOME/.cshrc or $HOME/.bashrc) somehow sets LD_LIBRARY_PATH to point to a different matlab installation, then you may not pick up the matlab distribution from the freesurfer tree. - R.

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volumes/surfaces FS6.0 vs FS7.2/3.2
by Alexopoulos, Dimitrios 09 Nov '22

09 Nov '22

External Email - Use Caution We have processed a large pediatric cohort (9-10 y.o. subjects) acquired with 1 mm isotopic voxels using FS 6.0. We are now beginning to rescan the same cohort at 15-16 y.o. using the exact same imaging protocol and scanner (3T, Prizma). If we process with FS 7.2/7.3.2, can we analyze the surface/volume measures/outputs with the earlier FS.6.0. structural outputs? We'd like to look at volume changes and cortical expansion analysis between the 2 timepoints. Is this reasonable or should we run the new cohort using 6.0 as well? Or rerun the earlier cohort at 7.2/7.3.2. Any suggestions as to the best approach. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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FS-FAST preprocessing of rs-fMRI data and extracting timeseries from Yeo's Networks
by stdp82＠virgilio.it 09 Nov '22

09 Nov '22

External Email - Use Caution I aim at FS-FAST preprocessing of rs-fMRI data and extracting timeseries from Yeo's Networks. 1 - I won’t perform a seed based analysis. 2 - I want to exclude the five sets of nuisance variables in mkanalysis-sess. Please could you check whether the command lines listed below are corrected for this aim? mkanalysis-sess -analysis fc.noseed.surf.lh -surface fsaverage lh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten -force mkanalysis-sess -analysis fc.noseed.surf.rh -surface fsaverage rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten -force selxavg3-sess -s subj_folder_name -a fc.noseed.surf.lh -overwrite -no-con-ok selxavg3-sess -s subj_folder_name -a fc.noseed.surf.rh -overwrite -no-con-ok 3 - I want to extract the timecourse, subject-by-subject, from each spitted Yeo's component. The feature of produced "fc.noseed.surf" files are: type: nii dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 I have tried to use mri_segstats --slabel ${1} lh subj/label/Xcomponent --i ${1}/rest/fc.noseed.surf.lh/meanfunc.nii.gz --sum /Xcomponent.sum.txt --avgwf Xcomponent.wav.txt But an error of dimension mismatch between input volume and seg occurs. input 163842 1 1 seg 116809 1 1 The input should be in fsaverage. Which is the correct average of set? And what do I do to run correctly at this step? Thanks Stefano

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Preproc-sess crashed - 3dvolreg.afni error
by Gillian Grennan 09 Nov '22

09 Nov '22

External Email - Use Caution Hello FreeSurfer Developers, I downloaded Freesurfer v7.3.2 <https://secure-web.cisco.com/1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPI…> onto my local drive and am attempting to run preprocessing through FSFAST. I wasn't able to get access to the .tar.gz Darwin file but downloaded Xquartz, Freesurfer, FSL, and Matlab individually and was able to source Freesurfer using the following commands: export FREESURFER_HOME=/Applications/freesurfer/7.3.2 export PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt export SUBJECTS_DIR=$PROJECT_DIR/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh However, when I run preproc-sess in my analysis folder I get the following error: command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run error message: ++ Initializing alignment base Choleski factorization failure in startup_lsqfit mri_startup_lsqfit: bad call to startup_lsqfit! ++ Starting final pass on 44 sub-bricks: 0 Fatal Signal 11 (SIGSEGV) received mri_3dalign_one 3dvolreg main Bottom of Debug Stack ** AFNI version = AFNI_2011_12_21_1014 Compile date = May 22 2013 ** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]] ** Program Abort ** ** If you report this crash to the AFNI message board, ** please copy the error messages EXACTLY, and give ** the command line you used to run the program, and ** any other information needed to repeat the problem. ** You may later be asked to upload data to help debug. ERROR: 3dvolreg.afni Invalid null command. I'm confused on what more I need to install? Is there a way I can get an updated link to the tar file with the relevant software packages needed to run FSFAST? Best, Gillian Grennan

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average lobar cortical thickness
by James Brown 09 Nov '22

09 Nov '22

External Email - Use Caution Dear Freesurfer experts, I would like to know if this procedure is correct. I have cortical thickness data from aparc+aseg for every ROI in DTK atlas (i.e. output of recon-all). I need average cortical thickness in frontal, parietal, temporal, cingulate and occipital lobes. Is it correct to average thickness measurement of every sub lobe roi (e.g. average thickness in frontal lobe = average of: - Superior Frontal - Rostral and Caudal Middle Frontal - Pars Opercularis, Pars Triangularis, and Pars Orbitalis - Lateral and Medial Orbitofrontal - Precentral - Paracentral - Frontal Pole and so on for other lobes... Do we need to correct for the number of vertices in every region when we measure the lobar average thickness? Alternatively, do I need to run these commands to generate lobes then measure thickness in every lobe? # mri_annotation2label --subject subject --hemi lh --lobesStrict lobes # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \ # --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \ # --annot lobes --base-offset 200 [--base-offset must be last arg] Thank you James

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cortical thickness in frontal lobe
by James Brown 09 Nov '22

09 Nov '22

External Email - Use Caution Dear Freesurfer experts, We are new to Freesurfer. We appreciate your help & apologize if the question is simple. We need cortical thickness in lobes instead of parcellates. Is it correct to take the average of the parcelates from the aparc+aseg.stats file under subjid/stats folder. For example, cortical thickness of frontal lobe = sum of frontal parcellates divided by number of parcallates . Do we need to do any correction such as weighing the surface area measurements ? Thank you James

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Question about a skullstripping error
by dimitra kokkinou 09 Nov '22

09 Nov '22

External Email - Use Caution Dear freesurfer experts, I am analysing some MP2RAGE images on freesurfer and found an error I am unable to correct. After the recon-all finished successfully, I looked at the T1 and brainmask images on freeview and I noticed a skullstripping error on the brainmask volume. On one side of the brain there was also skull (and other non brain parts), and on the other half there was a lot of missing cortex. I tried to change the watershed threshold but this didn't work, I also tried to put control points but most of them were ignored since they were outside of the estimated pial surface. What would be the best way to correct this problem? Regards, DK

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Freesurfer November 2022