[Freesurfer] unable to set everything to version 7

External Email - Use Caution Dear List, I installed version 7 into a directory named 'freesurfer' where there are already Verion 6 and Version 7(beta) is installed. My OS is 'Ubuntu_FS_600_700b1_TutorialData' "/usr/local/freesurfer/6.0.0-1" "/usr/local/freesurfer/7.0.0-0.1b1" So I

Re: [Freesurfer] vol2subfield single time course from multiple regions

External Email - Use Caution Please, could you check the command line. I suspect that an error is there. Thanks. Stefano mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o Left-Ventroposterior.mgz > Il 30 aprile 2020 alle 18.51 "Douglas N. Greve" ha >

Re: [Freesurfer] unable to set everything to version 7

External Email - Use Caution Hello Safi, I would make a directory named /usr/local/freesurfer/7.0.0-1 and put the freesurfer 7 release under that directory. Then set FREESURFER_HOME to one of /usr/local/freesurfer/6.0.0-1/usr/local/freesurfer/7.0.0-0.1b1/usr/local/freesurfer/7.0.0

Re: [Freesurfer] vol2subfield single time course from multiple regions

Hi Stefano can you elaborate? Why do you suspect there is an error? cheers Bruce On Mon, 11 May 2020, std...@virgilio.it wrote: External Email - Use Caution Please, could you check the command line. I suspect that an error is there. Thanks. Stefano mri_binarize --i Thalami

Re: [Freesurfer] Downloading Matlab runtime - ubuntu

External Email - Use Caution Thank you Tim! Also I was wondering, how should I specify the version (i.e. R2012b) of matlab in the code - "cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +

[Freesurfer] Information regarding FreeSurferColorLUT.txt

External Email - Use Caution Dear Freesurfer, *Q.1*: The colors of FreeSurferColorLUT.txt corresponds to which mgz file? I wanted to extract Substancia-Nigra but with reference to a conversion, held in 2019, https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63560.html,

Re: [Freesurfer] mris_fix_topology command does not finish

no, I wouldn't think so. YOu can try mris_topo_fixer instead if you want, but really you need to diagnose what the cause of your problem is On Sun, 10 May 2020, Billah, Tashrif wrote: Hi Bruce, Thanks for your prompt reply. I shall look at them as you noted. In the meantime, putting in some m

Re: [Freesurfer] mris_fix_topology command does not finish

Hi Bruce, Thanks for your prompt reply. I shall look at them as you noted. In the meantime, putting in some more logs from the perpetuating defect correction by mris_fix_topology: 13381 modVnum: vno:23308 has 6673 immediate neighbours mrisurf_topology.cpp:370 13382 vno:23308 now has 6673 immedi

Re: [Freesurfer] mris_fix_topology command does not finish

what does the aseg look like? Why isn't the cerebllum being removed? Dura is harder (unless you have a T2 or FLAIR) On Sun, 10 May 2020, Billah, Tashrif wrote: Running the commands separately, I see the following log for some of the defects. Is the weblink my cue? CORRECTING DEFECT 0 (vertice

Re: [Freesurfer] mris_fix_topology command does not finish

Running the commands separately, I see the following log for some of the defects. Is the weblink my cue? CORRECTING DEFECT 0 (vertices=4912, convex hull=886, v0=0) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may c

Re: [Freesurfer] mris_fix_topology command does not finish

Hi Tashrif it is most likely not a bug in mris_fix_topology, but rather a defect that is too large to accurately correct. The topology correction complexity is quadratic in the side of the largest defects, so small ones are fast and big ones are super slow. In most cases the really big ones ar

[Freesurfer] mris_fix_topology command does not finish

Hi there, The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2` does not finish for some of our data: #@# Fix Topology lh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub

Re: [Freesurfer] Downloading Matlab runtime - ubuntu

External Email - Use Caution You do not have write permission to $FREESURFER_HOME, which is /usr/local/freesurfer/ in your case, it seems. There are 2 options: 1) run the command again but put 'sudo ' in front. This should give you permission to write to that location. 2) insta