[Freesurfer] Error in running make_average_subject

2018-02-19 Thread M Janani
Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/tala

[Freesurfer] Segmenting the Corpus Callosum

2018-02-19 Thread Benjamin Yeske
Hello Freesurfer Experts, I was looking through your website to see if I could find any info/papers that explained what landmarks you use for segmenting the corpus callosum, but I couldn't find anything on the topic. Could you please point me to a paper or resource that explains how freesurfer cap

Re: [Freesurfer] Segmenting the Corpus Callosum

2018-02-19 Thread Bruce Fischl
Hi Ben we find the CC as the region where there is the largest left/right WM connection. We then orient it to be vertical and find principle directions, and divvy it up into however many segments you want (I think the default is 5 but this can be changed). We then grow it out laterally as far a

Re: [Freesurfer] Read 13, expected 64, could not read .nii.gz as type 24

2018-02-19 Thread Ben Smith
Thanks for your help on this! It was a corruption problem, just as you said- didn't seem to be a disk space problem, but I deleted the file, re-ran, and things went fine. Cheers Ben ___ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.i

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

2018-02-19 Thread Bruce Fischl
Hi Shim Hee we need to know what commands you ran, the full screen output from them, and what version of FS you are using (at least!) cheers Bruce On Mon, 19 Feb 2018, Shim Hee Youn wrote: Hi Freesurfer team, I am currently using ADNI dataset to run Freesurfer  Recon all for MPRAGE, SPGR

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

2018-02-19 Thread Shim Hee Youn
Hi Bruce, Thanks for your email. I am using Freesurfer version 6 and the command I used to run is this: qsub -m n -o o -e e -V recon-all -subjid ${Z}_${Image}_fs -i ${step1LocalDir}/$T1 -FLAIR ${step1LocalDir}/${FLAIR} -FLAIRpial -all Best Regards, Shim Hee Youn Research Assistant Multimodal N