[Freesurfer] rotation applied by mri_convert

Hi everyone, I have a question related to mri_convert (I use FreeSurfer version 5.1). I noticed that when I convert some images without specifying anything about the orientation (mri_convert MY_DICOMS 001.mgz), in a high proportion of the case, mri_convert will identify an orientation matrix w

Re: [Freesurfer] error in analyze command failed: mri_concat

Hi Doug, I run the mri_concat command with 9 subjects in the command line. for the LH thickness and volume. A segmentation fault is the problem. What do i have to do in this case? Many thanks, Stan freesurfer-Linux-centos5_x86_64-dev-20110315 SUBJECTS_DIR /data1/proje

Re: [Freesurfer] reconall without graphics card or GPU?

Yes, that should be fine Bruce On Nov 16, 2012, at 1:40 AM, Linda Zhang wrote: > Dear all, > > At our university, we have the option of using a high performance computing > facility to run "computing intensive" analysis, but it doesn't have a 3D > graphics card or GPU. Is it advisable to r

[Freesurfer] Defining a region of interest

Dear experts: I used the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization?highlight=%28ROI%29 to defining a region of interest, but when I make a series of left clicks on the surface， then click the "Make Closed Fill Boundary" icon in the tools window. howevre, the

Re: [Freesurfer] Defining a region of interest

sorry, not sure I understand. After you click "make closed fill boundary" what happens? Before you click do you see the points hilighted on the surface? On Fri, 16 Nov 2012, xiangbo_2010 wrote: Dear experts:    I used the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualizati

[Freesurfer] Defining a region of interest

psylab-desktop:/media/freesurfer1/CT> tksurfer fsaverage rh inflated -annot aparc.annot -fthresh 2 -overlay lh.COMTthree.glmdir/COMTthree/sig.mgh setting fthresh to 2. subject is fsaverage hemiis rh surface is inflated surfer: current subjects dir: /media/freesurfer1/CT surfer: not in "scr

Re: [Freesurfer] re white matter mask

Hi Catherine you need to put extensions on the image files you post so that we know what format they are in. cheers Bruce On Fri, 16 Nov 2012, Catherine Bois wrote: Hi, I have a question re the screenshot attached in the present email... Several slices of the white matter mask of this scan

Re: [Freesurfer] re white matter mask

the holes that are interior and don't have any surface adjacent to them are fine. The others you may need to edit the wm.mgz, but it's impossible for us to tell from just this image. Make sure you look at the data in multiple orientations to see whether those voxels should have been labeled wm o

Re: [Freesurfer] fieldsign-sess problem in retinotopy

Hi Doug, It seems the previous fieldsign-sess problem is due to that I stored data on one server while freesurfer is on the other server. But when I put the data and freesurfer on the same server and run the retinotopy analysis again, it reported fail msg for "selxavg3-ses" : -- ntptot = 80, nX

[Freesurfer] contrast matrix

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: