[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] problemi with mri_glmfit-sim

HI all, I have another problem with mri_glmfit-sim. It looks for something that is not available in my FS (see below the error message) How can I solve this problem? thank you! Angela mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces cmdline mri_glmfit --y /Users/

Re: [Freesurfer] Cortical gray matter surface area

Hi Will, I use the following commands to get surface area from the pial surface: In the subject label dir: mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial mris_anatomical_stats

Re: [Freesurfer] longitudinal base problem - bad surfaces

Hi Cedric, the base image looks bad. The reason could be a mis-registration. More likely though you have two time points that come from different subjects? Best, Martin On 09/02/2014 04:09 AM, Koolschijn, Cédric wrote: Dear experts, I'm performing a longitudinal analysis, and have done so

[Freesurfer] Job offer: 1 PhD and 1 PostDoc in Neuroimaging of Epilepsy - Tübingen, Germany

We currently have two open job opportunities at the University of Tübingen, Germany. Both in the field of neuroimaging in epilepsy. 1) PostDoc to work on post-processing of functional and structural MRI / network analysis (graph-theory, classification algorithms, EEG-fMRI) 2) PhD-Student to wor

[Freesurfer] Nframes greater than 1...

Hi: I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Con

Re: [Freesurfer] Nframes greater than 1...

Hi Gonzalo what is in the two frames? Bruce On Tue, 2 Sep 2014, Gonzalo Rojas Costa wrote: Hi: I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical I

[Freesurfer] Group cortical thickness QDEC help

Hello, I am having some troubles using QDEC to analyze the thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after).

[Freesurfer] watershed surface to volume rendering repost

Freesurfer, Sorry for the repost, but I did not get any further details: We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, i

Re: [Freesurfer] watershed surface to volume rendering repost

Hi Matthew, yes, you can use mris_fill to fill the interior of a topologically correct, closed surface. You'll need to run some boolean operations on them to get the volumes you want, but it should be pretty easy I think. cheers Bruce On Tue, 2 Sep 2014, Sherwood, Matt wrote: Freesurfer,