[Freesurfer] Recon-all Run Time

Hi Freesurfers, I've recently downloaded free surfer onto a new computer. It's working correctly, but the running time for the recon-all -all command is 30-50 hours. This is in contrast to when I've used free surfer on previous computers where the run time was 6-12 hours. I'm wondering why this wo

Re: [Freesurfer] Cannot open FreeSurfer application zipped file

Hi Lee, I guess it worked. It looks like several hundreds of files were unzipped., however, in the end, there was still the following message: gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now At this

[Freesurfer] Cannot open FreeSurfer application zipped file

Dear experts, I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes:“gzip: freesurfer-L

[Freesurfer] How can I use mri_vol2surf to map the white matter volume cortical surface in order to generate a white matter map that is similar to the gray matter volume map produced by mris_preproc?

DearFreeSurferexperts, HowcanIusemri_vol2surftomapthewhitemattervolumecorticalsurfaceinordertogenerateawhitemattermapthatissimilartothegraymattervolumemapproducedbymris_preproc? ShouldIusebinarymaskcreatedinMatlabtoremovelabelsthatarenotwhitematter? Best regards KnutJørgenBjuland NTNU __

[Freesurfer] visualization of a "spherical" cut

Dear List, I have a visualization problem which is not directly relevant to freesurfer but which may be easily solvable with the freesurfer tools. I have also posted this question to the ImageJ discussion list. I would like to visualize "spherical" cuts through an MR. An axial cut is the interse