Re: [Freesurfer] surfreg cannot allocate memory

External Email - Use Caution WOW I cannot. Freeview showed “failed to load MRI .../mri/brain.mgz”. I had permission to read and write though... Haoran > On Dec 20, 2018, at 3:50 PM, Hoopes, Andrew wrote: > > Hi Haoran, are you able to load the subject’s mri/brain.mgz in freevi

Re: [Freesurfer] surfreg cannot allocate memory

Hi Haoran, are you able to load the subject’s mri/brain.mgz in freeview without getting this error? Andrew From: on behalf of Haoran Xu Reply-To: FS Help Date: Thursday, December 20, 2018 at 2:33 PM To: FS Help Subject: Re: [Freesurfer] surfreg cannot allocate memory External Emai

[Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

External Email - Use Caution Hello Freesurfer Community, I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask. Using mri_surf2surf to register scans t

Re: [Freesurfer] surfreg cannot allocate memory

External Email - Use Caution Thank you Andrew! The log is copied here below. Haoran $ surfreg --s subj001 --t fsaverage_sym --lh --xhemi Thu Dec 20 13:01:31 EST 2018 setenv SUBJECTS_DIR /home/haoran/FP/data/NBMLdata/anatomicals/ cd /home/haoran/FP/data/NBMLdata/anatomicals/subj00

Re: [Freesurfer] mris preproc for folding index

External Email - Use Caution Thank you so much Dr. Fischl, that information is very helpful. On Thu, Dec 20, 2018 at 12:18 PM Bruce Fischl wrote: > Hi Martin > > you can use whichever surface you want - they are just different > biological questions. The files we write out by de

Re: [Freesurfer] mris preproc for folding index

Hi Martin you can use whichever surface you want - they are just different biological questions. The files we write out by default relate to the white surface, but you can certainly generate the equivalent for the pial using mris_curvature. In general the curvature is 1/r, where r is the rad

Re: [Freesurfer] surfreg cannot allocate memory

Hi Haoran, that error is the hallmark of a corrupted volume file. Do you mind sending the log, or at least the end of it? It’d be helpful to see when this error is actually occurring. thanks Andrew From: on behalf of Haoran Xu Reply-To: FS Help Date: Thursday, December 20, 2018 at 1:05 PM

Re: [Freesurfer] mris preproc for folding index

External Email - Use Caution Thank you so much every one for helping me in this regard. I have some follow up questions: I am interested in associating mean curvature (H) with some behavioral measure. After extracting subject-wise mean curvature estimates, I found a significant po

Re: [Freesurfer] surfreg cannot allocate memory

External Email - Use Caution Thanks for the suggestion! But it seems the max memory size was unlimited already. Any more thoughts about this? Best, Haroan $ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority

Re: [Freesurfer] Finding the surface vertex for a voxel in the cortex

Hi Tim yes, you can use min Euclidean distance as a metric but it may not be terribly stable, since the center of a voxel might be close to equidistant from two banks of a sulcus. Particularly in cases where there is a thickness asymmetry, like the central sulcus. You might need to do someth

Re: [Freesurfer] using custom surface template

sounds good. Bruce On Thu, 20 Dec 2018, Jason Tourville wrote: External Email - Use Caution Thanks Bruce. I was considering playing around with doing it both ways...seeing if the parcellation based on our template makes a difference, but sounds like it would be small. If I

[Freesurfer] Finding the surface vertex for a voxel in the cortex

External Email - Use Caution Dear FreeSurfer experts, given a voxel in the cortex of the fsaverage subject, I would like to find the vertex on the surface that corresponds to the voxel (e.g., if volume data would be projected to the surface). I found the documentation at http:

[Freesurfer] x y dimension mismatch dt_recon

External Email - Use Caution Dear community: I have an issue that I have seen in the past still don´t know how to fix. Bval shows rows of 16 values and bvecs 17 values in one row only the rest 2 show 16 as apparently should be. What can I do? Sincerely, Andrade. __

[Freesurfer] subject IDs for qdec

External Email - Use Caution Please, what format should the subject IDs have for qdec. At the moment my subjects IDs are alphanumeric (e.g. h00013), and although the SUBJECTS_DIR is set correctly, the files are not being found. I have changed the first to numeric only (024), but

Re: [Freesurfer] using custom surface template

External Email - Use Caution Thanks Bruce. I was considering playing around with doing it both ways...seeing if the parcellation based on our template makes a difference, but sounds like it would be small. If I do and find any appreciable difference, will let you know. Always appr

Re: [Freesurfer] FreeSurfer: trouble processing subjects

Hi Andrade, I'm adding the FreeSurfer support list so other can benefit. To answer your question, you would use the first dicom from the diffusion scan... but since you don't have the dicoms that won't work. You can combine all of the DTI nifty files into one multi-frame diffusion 4d volume us

Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444)

Hi Jeongson it certainly looks like something went badly wrong. 2mm may be too thick - we typically recommend <=1.5mm for any voxel direction. Can you send us the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid? cheers Bruce On Thu, 20 De