Hi Doug

Thank you very much for your reply.

Actually the recon finished today without any error. It just took so long to be done for only one subject (almost two days!)!

I checked the registration and It looks ok.

I will try -conf2hires for my other subject that -hires didn't work on it.

Thanks

Mona

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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <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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