[Freesurfer] hippocampal subfields analysis took 10 min

Dear Eugenio, I had to run the hippocampal subfield segmentation analysis in Freesurfer v6 manually by running segmentSF_T1.sh program. When I call it through recon-all, it only processed the left hemisphere but not the right. The issue is that running segmentSF only took 10 min per hemisphere. I

Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg

Hi Kari I think that's not a real error. They are both surface overlays, just with the nvertices dimension in different slots. You could load one of them into matlab and use reshape to make it the same dimensions as the other, then write it out cheers Bruce On Fri, 20 May 2016, Kari Parsons

[Freesurfer] Lab coordinator position at the University of Michigan

Please see the ad below concerning a research position available in the new M(SD) lab at the University of Michigan directed by Dr. Adriene Beltz in the department of Psychology. Interested candidates should apply at http://umjobs.org/job_detail/125962/lab_coordinator and can reach Dr. Beltz at abe

[Freesurfer] LME MATLAB, X matrix error

Dear FreeSurfer Team, I processed in MATLAB for Linear Mixed Effects Models Analysis with this X matrix: X matrix is 'Subjects N X 11', 11 columns are as follow, 1. Intercept (all '1') 2. time (from baseline time point) 3. time2 4. Patients group = 1, Control = 0 5. 4.X time 6. 4.X time2 7. Pati

[Freesurfer] Group Analysis: Two Groups and Two Covariates.

Dear FreeSurfer Team, I processed the Group analysis by FreeSurfer 5.3.0 Our data has two groups (Patient, Control) and two covariate values (age, extra value) mtx, contrast is 1 -1 0 0 0 0 The mris_preproc, and mri_surf2surf command were completed without error. mris_preproc --fsgd **G2V2.fsgd

Re: [Freesurfer] LME MATLAB, X matrix error

Hi Han, Try to find a local statistician to help you with your analysis. About your matrix: rows need to be number of all time points from all subject. Time 2 should probably not be there. Also columns 7-9 need to be dropped (they are just the negative of the rows before). Best Martin On May 21,

Re: [Freesurfer] LME MATLAB, X matrix error

Dear Martin Reuter, Thank you for your reply. Our patients have several time points, but controls have only 1 time points, so when I coded the patients group =1, controls groups = 0 , the 2. time and 3. time2 column were same as 5. 4.X time 6. 4.X time2 column. and 8. 7. X time and 9. 8. X time

[Freesurfer] DTI error

Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Grad