[Freesurfer] Segmentation fault: 11

External Email - Use Caution Hello Team, I just installed freesurfer and freeview using the methods mentioned in https://secure-web.cisco.com/1oeEk1V3fGDlcuYEIm1RFYCYdQcU2m3TJysRGz7NAzZIOMDfxJiOPbas0gR6C45O_k9X6OvLE4pS75bwDoZy4yIzpxK5rduxKwxnHn7m8NEYSw4zXC5joOtwNk5Ms6X54nQoAn7rrCj

[Freesurfer] mkdir: /Applications/freesurfer/7.3.2/subjects/sub01: Permission denied

External Email - Use Caution Hello Team, Thanks for the help before I successfully opened freeview. now i am trying to run recon-all for a nifti file. After setting the path export FREESURFER_HOME=/Applications/freesurfer/7.3.2 export SUBJECTS_DIR=$FREESURFER_HOME/subjects sour

[Freesurfer] Running recon-all in parallel

External Email - Use Caution Hello team, As freesurfer takes lot of time for processing one subject, I was searching on how to run recon-all for multiple subjects in parallel and I found the following in Andy's brain book doc https://secure-web.cisco.com/1MEMXaE4I_nNiI-Rew0Vd8aEQ

Re: [Freesurfer] Running recon-all in parallel

> sudo apt install tcsh > ``` > > -Paul > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of priya padma < > pr...@phenomx.ai> > *Sent:* Wednesday, October 12, 2022 3:16 AM &g

[Freesurfer] mghread : cannot open the file

External Email - Use Caution Hello Team, I am trying to find the volume of WM, GM, CSF separately and I came across this command namely "mri_compute_volume_fractions" Looking through all the email archives I gave the following line as the command after setting the paths $ mri_co

Re: [Freesurfer] mghread : cannot open the file

> > mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129 > /mri/norm.mgz > > -Paul > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of priya padma <

[Freesurfer] Skullstripping

External Email - Use Caution Hello Team, I am trying to do only Skull stripping for my image and get the output. is there any command of freesurfer, when it executes only the first step- skull stripping. My objective is to get whole brain segmentation where only the brain tissues

Re: [Freesurfer] mghread : cannot open the file

External Email - Use Caution Hello Team, Is there any solution for the above mentioned issue? I am still struck in the same place. Thank you On Fri, Oct 14, 2022 at 10:20 AM priya padma wrote: > Hi Paul, > > Thank you for your email. I tried how t

[Freesurfer] conversion of .stats to .csv

External Email - Use Caution Dear Team, I would like to convert the .stats files that are being generated in the stats folder as an output from recon-all to csv file or excel file. Is there any way to convert .stats to .csv or .excel format? any help on this would be much apprecia

[Freesurfer] change in mask size

External Email - Use Caution Dear Team, I tried using freesurfer for skull stripping and I got results all of size 256X256X256 but the original data size is different, it's 512X512X537. Is there any way to bring back the original size in freesurfer? Any help would be appreciated.

[Freesurfer] Original image and the mask file dimension mismatch

External Email - Use Caution Hello Team, I have a nifti file of dimension (256, 256, 156) but once I run the freesurfer recon-all the subregions mask "*aparc.DKTatlas+aseg.mgz*" has a dimension of (256,256,256) due to this I am unable to view the segmentation overlaid on the origin

[Freesurfer] CSF mask generation

External Email - Use Caution Dear Team, I have tried creating binary CSF mask from # CSF: # - 4: Left-Lateral-Ventricle # - 14: 3rd-Ventricle # - 43: Right-Lateral-Ventricle but I would like to know whether is it possible for us to get outer CSF similar to fastsurfer. An