[Freesurfer] recon-all on group

Can we apply recon-all on a group of subjects simultaneously? My system has good enough processing power to preprocess 40 subjects at a time, but I have to open 40 terminal windows for doing it now. I need an efficient way to do it. Any suggestions? Best Regards, Muhammad Naveed Iqbal Qure

Re: [Freesurfer] converting .nii to .mgz

Hi Bruce, Thanks for getting back to me so quickly! I just tried that and got the following error: reading from ct.anat.nii... niiRead(): error opening file /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii I'm wondering if the nifti file is possibly corrupted. Is there a way to check

Re: [Freesurfer] converting .nii to .mgz

Hi Mia If all you want to do is convert try mri_convert ct.anat.nii ct.anat.mgz Cheers Bruce > On Jan 19, 2015, at 10:33 PM, Borzello, Mia wrote: > > Hi Freesurfers, > > I'm looking at Freesurfer files from are from years ago trying to look at the > ct.anat file. Unfortunately, i have the

[Freesurfer] using merge_stats_tables to merge broadman areas for multiple subjects.

Hi, Following earlier device from this list, I was able to run the merge_stats_tables command for a single subject as so: merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats --all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume But when I tried to pass a series of su

[Freesurfer] converting .nii to .mgz

Hi Freesurfers, I'm looking at Freesurfer files from are from years ago trying to look at the ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so I'm wondering if there is a way to create it. In trying to find an answer online, I found this: https://mail.nmr.mgh.harvar

Re: [Freesurfer] regarding license.txt file

The freesurfer installation does NOT contain a license file. You must create it, first by creating a file called license.txt in your FREESURFER_HOME directory, then copy/paste the contents specified in the email you recieved into the license.txt file. -Zeke > Hi, > > I downloaded the latest vers

[Freesurfer] regarding license.txt file

Hi, I downloaded the latest version of the freesurfer and tried to install it. After running the installation, I registered my information in https://surfer.nmr.mgh.harvard.edu/registration.html I received an email after few minutes with an information that I have to replace a text inside the

Re: [Freesurfer] Creating a .gca file

Hi Pradeep pbsubmit is a wrapper script for submitting a job to a PBS cluster. If you don't have a cluster you should just run the commands that it runs. cheers Bruce On Mon, 19 Jan 2015, pradeep mahato wrote: > Hello experts, > I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I

[Freesurfer] using -cw256 as default is good?

Dear experts, We are processing a dataset that gives us this error quite often: ERROR! FOV=300.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Is it ok if I use -cw256 by default to all my scans even for those with FOV=256 that do not need

[Freesurfer] Confirm Siemens 3T Trio sequence parameters please

Could someone please confirm that the following parameters will result in optimized data for grey matter volumetry with Freesurfer. If there are changes that would be better I would really appreciate that as well. Siemens MPRAGE (Magnetization Prepared RApid Gradient Echo) 9 minutes and 50 seconds

[Freesurfer] Creating a .gca file

Hello experts, I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to create a atlas using previous registered subjects. It does not complete the mri_ca_normalize phase and stops there. It shows pbsubmit: Command not found as error. Please correct me. Also attaching the rebuil