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
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
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
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
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
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
