[Freesurfer] Error running recon from command line

Hello, I installed FreeSurfer according to instructions on the website. To overlay FSL data, I used the following instructions from the FMRIB website. avwswapdim TEST x -z y TEST_reorient slices TEST_reorient bet TEST_reorient TEST_brain -f 0.4 mri_convert /home/bbernal/freesurfer/subjects/TEST/m

[Freesurfer] Tksurfer Error

Hello, I am facing a problem in running tkmedit or tksurfer. So I looked up the posts and found a thread which explained using tkmedit.static instead of tkmedit. I did that and I could run tkmedit. However, I can't find the tksurfer.static file in that same directory. Please let me know how I coul

[Freesurfer] Error: Nu Correct

Hi all, I am trying to use FreeSurfer to overlay FSL data. On running the command $ recon-all -stage1 -subjid TEST I get the following error, Nu Intensity Correction Tue Mar 1 14:54:08 EST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=1.00, TE=0.00, TI=0

[Freesurfer] (no subject)

Hi all, My earlier error was due to perl not properly configured. Thank you all for the help. However, on running recon-all -stage1 -subjid TEST, I am now getting the error message mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transfor