Re: [Freesurfer] recon-all bug
External Email - Use Caution Hello Kody, One thing you could try to get more information printed about what is going on is to edit the very first line in the recon-all script to be: #! /bin/tcsh -xf … instead of #! /bin/tcsh -f Adding the x option will echo each line in the script as it’s run with the variable values expanded, and seeing that output could help with debugging. - R. On Apr 1, 2021, at 20:29, zalewk zal...@uw.edu wrote:External Email - Use CautionHi Freesurfer team,My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all..I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine. Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem.It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient.Best,Kody Zalewski___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all bug
External Email - Use Caution Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine. Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, Kody Zalewski ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] retaining label ids
External Email - Use Caution Hello Experts, I did like to extract wm whilst retaining the label ids. I tried mri_extract_labels but it didn't work. Any help would be appreciated. Many thanks, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] quantification of volume of perivascular spaces
External Email - Use Caution Dear experts, elaborating on the topics: As I read the samseg paper, I see that the flag --lesion wouldn't probably work well, since the imposed shape model, tuned for MS lesions, is not appropriate for perivascular spaces which have different shape. Is here a way for user to redefine the shape prior for samseg to tune it for perivascular spaces segmentation? Thank you in advance for any help, Antonin Dear experts,We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you think, that --lesion flag in samseg would work estimation of perivascular spaces? Or other setting of samseg will be better option? Or, would you rather recommend other tools? Any idea/comment will be greatly appreciated. Regards, Antonin Skoch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Left-Right labeled brain MRI
External Email - Use Caution Oh wow you're brilliant as always, Anastasia! Thank you :) Yendiki, Anastasia Wed, 31 Mar 2021 14:30:26 -0700 How about an aseg volume? The left and right are labeled with different numbers From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Arman Avesta Sent: Wednesday, March 31, 2021 5:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Left-Right labeled brain MRIExternal Email - Use Caution Hi, Thank you again for responding to my previous questions! I'm writing a python class to show MR images, and I need to have one brain MRI volume (e.g. nifti or mgz) in which left and right are labeled in some way. FSL website used to provide a test MRI volume that was labeled: [Inline image] Unfortunately I can't find this volume on the internet anymore! So I need help :) Thank you, Arman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
