[Freesurfer] Hippocampal/Amygdala subfield segmentation error - Freesurfer devel-20180612

External Email - Use Caution Dear experts, I am running the hippocampal/amygdala segmentation on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR] This has worked successfully for roughly 1000 participants

Re: [Freesurfer] recon-all -make all error

Hi Vasudev you don't need the whole path for the -s switch, just the subject ID (in this case it looks like HC13) cheers Bruce On Mon, 8 Oct 2018, Dev vasu wrote: External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on

[Freesurfer] recon-all -make all error

External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s

Re: [Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject

Hi Vasudev there is a patch to recon-all that fixes the -make all functionality, that should start wherever you left off. Andrew: can you post the location of the makefile patches? thanks Bruce On Sun, 7 Oct 2018, Dev vasu wrote: External Email - Use Caution Dear

Re: [Freesurfer] masking cortical thickness

External Email - Use Caution Dear Douglos, I did not understand how to use mri_label2label with the mask option(there is srcmask options not mask alone !). I extract my labels and as you explained I wanted to create i.e. binary mask of rh.fusiform.label with mri_label2label :

Re: [Freesurfer] nu_correct disk i/o issues

External Email - Use Caution Michael, I can't thank you enough. Knowing that it writes to /tmp made all the difference. In my case I mounted an external directory on /tmp instead of the sessiondir approach, but it now runs fine. Jasper On Fri, 5 Oct 2018 at 23:47, Michael Krause

[Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject

External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev ___