Re: [Freesurfer] Run Recon-all Parallel on Linux

Hi Frank do you mean completing a single recon faster? The easiest way to do that is to use the -openmp flag, and set to the number of threads/cores you want to use. Alternatively if you have enough RAM you can just run multiple recon-alls at the same time (which will give you a bigger effe

Re: [Freesurfer] mis-registration question

Dear Freesurfer experts I have a follow up question about mis-registration and I appreciate if you could please reply. I am having trouble fixing the registration for one of my subjects in highres scan. The tkregister-sess values looked bad (around 0.8). So I checked the registration with tkreg

Re: [Freesurfer] (no subject)

OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote: External Email - Use Caution My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcot

Re: [Freesurfer] mis-registration question

Can you send me your project folder and SUBJECTS_DIR? On 1/3/2020 9:53 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts I have a follow up question about mis-registration and I appreciate if you could please reply. I am having trouble fixing the registration for one of my subjects in high

Re: [Freesurfer] Retinotopy, design ill-conditioned

Can you send your paradigm files? Can you also send the terminal output? One more thing, can you send the X.mat file from the output folder? On 1/2/2020 3:19 AM, Marco Ninghetto wrote: External Email - Use Caution Hello experts, I'm performing retinotopy analysis but when running the co

Re: [Freesurfer] hardware upgrade affect Freesurfer?

I don't think that will make a difference On 12/20/2019 3:17 PM, Dincer, Aylin wrote: External Email - Use Caution Hi FreeSurfer Experts, Would upgrading computer hardware affect FreeSurfer output? We are using FreeSurfer version 5.3-HCP and we are considering upgrading our server. It

[Freesurfer] Amygdala Segmentation T1.v20 Command

Dear Freesurfer experts, Happy new year! I encountered an issue with the quantifyHAsubregions.sh command as I tried to extract amygdala subnuclei values from a previously segmented dataset. I tried both commands below, specifying the version (v20) and not: quantifyHAsubregions.sh amygNuc T1 All

Re: [Freesurfer] (no subject)

External Email - Use Caution Thank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here? Best, Boris MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR

Re: [Freesurfer] Surface file format differences

Hey Josh, Thanks for bringing this to our attention. This newline, which was always ignored by our surface reading utils, was inadvertently removed after a large refactor of the codebase (moving to c++). This is an innocuous change except for the fact that it, of course, breaks external surface

Re: [Freesurfer] Surface file format differences

External Email - Use Caution Andrew, That was very helpful. Thank you! J. On Fri, Jan 3, 2020 at 5:02 PM Hoopes, Andrew wrote: > Hey Josh, > > Thanks for bringing this to our attention. This newline, which was always > ignored by our surface reading utils, was inadvertently re

[Freesurfer] Getting issue in running bt_recon

External Email - Use Caution Hi, Please suggest something for the following error. Cannot allocate memory unsupported matlab format 839537524 (unknown) Best, Sudhakar Mishra Research Scholar Website *सर्वद्वारेषु देहेऽस्मिन्प्र

Re: [Freesurfer] Run Recon-all Parallel on Linux

External Email - Use Caution Dear Bruce, No, I want to run recon-all on 4-8 subjects at the same time. I could find detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs 4 recon-all -s {.} -i {} -all -qcache", after installing Xcode and Homebrew.) But I couldn't