sometimes the -hires flag does not work very well. For the subjects where it does complete, do the surfaces look ok? You can also use recon-all.v6.hires with the -conf2hires option (available in fs6 on our network).
On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:
Hi Bruce
Thank you very much for your reply.
Here is my command:
recon-all -all -s ${subj} -i ./${subj}/anat/016/mT1v2.nii -expert ./scripts/expertopts/expert.opts -hires -mail zn025 -parallel
I also attached my .log file.
Thanks
MOna
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu Sent: Thursday, February 21, 2019 2:23:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all -hires
Hi MOna
what was your full command line? And can you send us the recon-all.log file?
cheers Bruce On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts
I was running recon-all command with hires flag for our high resolution fMRI data, but it has been in a constant status since yesterday.
I copied the last few lines that are currently in my terminal. I had the same issue with another subject before, and I had to terminate the recon-all and run it without -hires.
Could you please let me know how I can solve this issue?
Thanks
Mona
#@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
cp ../surf/rh.orig.nofix ../surf/rh.orig
cp ../surf/rh.inflated.nofix ../surf/rh.inflated
#@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
mris_fix_topology -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology. lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
#@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
mris_fix_topology -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology. rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
Waiting for PID 8994 of (8994 8997) to complete...
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