[Freesurfer] longitudinal base problem - bad surfaces

Dear experts, I'm performing a longitudinal analysis, and have done so before, but I encounter an error after running -base for one subject which I haven't seen before. The cross surfaces of both timepoints look OK, but the base surface is seems to be shrunken for unknown reasons. I reran all

Re: [Freesurfer] hypothalamus?

ow similar procedures to map to native space. Though I must note that this ROI is not perfect. All depends on your research question of course, how detailed do you want your ROI to be. Best of luck, Cédric P.C.M.P. Koolschijn (Cé

Re: [Freesurfer] QDEC double trouble: 1. VerifySubjects 2. MatrixMultiply: m1 is null!

where you show one line of the file, it looks like Subj# is >the first column and SubjID is the second. > >Nick > > > >On Thu, 2013-09-19 at 14:07 +, Koolschijn, Cédric wrote: >> Dear FS, >> >> >> I' ve run into some strange things in QDEC whic

[Freesurfer] Missing pial surface right hemisphere for multiple subjects

pbox.com/s/so5jfd7wuo19ax6/recon-all.o128591 Do you have any idea what might be causing this? And of course, how to fix this? Many thanks! Cheers, Cédric P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain

Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long). Best, Martin On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote: Hi Martin, Thanks for your fa

Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

arable. Cheers, Martin On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote: Hi FreeSurfers, I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there. Out of curiosity I c

[Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

e for the longitudinal data or is something else going wrong, or is this normal? Many thanks! Cheers, Cédric P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E p.c.m.p.kool

[Freesurfer] optseq2 malloc memory / matrix rank-deficient

anges each time. In addition, the process consumes my RAM (8GB) like it's nothing. The strange thing is, I do get usable output. Any ideas what might be causing this? Many thanks! Cédric ---- P.C.M.P. Koolschijn (Cédric), PhD

Re: [Freesurfer] How to calcutate Brain volume?

corticla volume (mm3) of that created DLPFC. Any helps'll be greatly appreciated. ________ From: Anupa AV mailto:av.an...@yahoo.com>> To: "Koolschijn, Cédric" mailto:p.c.m.p.koolsch...@uva.nl>>; Freesurfer mailto:freesurfer@nmr.mgh.harvard.edu

[Freesurfer] dimension mismatch: Cortical Thickness of a Volume-defined ROI

Hi Doug and other FS-experts, I succesfully applied the registration step of the Cortical Thickness of a Volume-defined ROI wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness However, I'm having troubles at the end. 3) Map the ROI-mask to the fsaverage surface, to create an

[Freesurfer] Register marsbar nii to freesurfer fs average

"Export ROI to image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as DLPFC.nii If I view the ROI on marsbar it looks good. Did I miss some prior step, or is something else wrong? Thanks in advance! Best wishes, Cédric -----------