Re: [Freesurfer] Talairach_afd error (Bruce Fischl)

wow, we haven't seen that happen. Does the recon-all.log from the parallel machine have any clues as to why it is empy? On Mon, 26 Oct 2015, Anna I. Garcia Diaz wrote: Hi Bruce, Thanks for the reply. The talairach.xfm file generated by the palarellizing machine is empty; it looks as follows:

Re: [Freesurfer] error finding Matlab

Hi Jason do you have matlab installed? If so, you need to setup your environment so that it is in your path. This doesn't really have anything to do with FreeSurfer - you need to be able to type "matlab" from the command line and have it find the binary cheers Bruce On Wed, 28 Oct 2015,

Re: [Freesurfer] error finding Matlab

Hi Bruce, Thanks so much for your response. I can only start Matlab from the terminal when I use the following command within the Matlab applications folder: ./matlab Am I to understand that the matlab command must be globally accessible? If so, how might I achieve that? Thanks so much, Jason

Re: [Freesurfer] error finding Matlab

Hi Jason you need to talk to a local sysadmin, but basically you need to add the path to matlab to your path environment variable. The syntax for this depends on the shell you are using, but for example in csh/tcsh it would be something like (in your .cshrc file in your home directory) set

Re: [Freesurfer] Minc-tools - cannot find required library hdf5 - Ubuntu 12.04

To give yourself the greatest likelihood of success building freesurfer, please follow the directions in this page specifically noting section 3: http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page If you wish to use your own customized version of the minc tools, I

Re: [Freesurfer] comparison of 4 groups: mri_glmfit or Qdec?

Dear Doug,   thanks for reply.   But isn't it statistically the same: compare e.g. the thickness of morbid group 1 with the controll group via Qdec respectively compare both groups via contrasts (e.g. 1 0 0 -1) in mri_glmfit? For me the only advantage of mri_glmfit is to controll for more

[Freesurfer] Understanding the brainstem AtlasMesh file structure format

Hello, Is the AtlasMesh under the following pathway a standard mesh structure? If so, what is it? Better yet, is there a way for those meshes in the AtlasMesh to be converted to a standard stl file or some other standard mesh file format? To be clear, I know the .gz is a compressed file; I'm

Re: [Freesurfer] how to display individual Desikan parcels?

Break up the annot into separate labels then recombine the ones you want into a new annotation. Use mri_annotation2label for the first step then mris_label2annot for the second. On 10/27/2015 02:35 PM, Mihaela Stefan wrote: > Hello Freesurfers, > > I would like to be able to display just a few

Re: [Freesurfer] how to display individual Desikan parcels?

Thanks! Mihaela On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve wrote: > Break up the annot into separate labels then recombine the ones you want > into a new annotation. Use mri_annotation2label for the first step then > mris_label2annot for the second. > > > On

Re: [Freesurfer] Funcroi-Table-Sess Error

Thanks!! > On Oct 27, 2015, at 1:18 PM, Douglas Greve wrote: > > > > On 10/27/15 1:09 PM, Morenikeji Adebayo wrote: >> Hi Doug, >> >> Thanks for the help! So, you’re saying that: >> >> By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using >>

[Freesurfer] How to realign a surface in matlab to a realigned parent volume

Dear All, I ran recon-all and generated a brain.mgz and say, lh.pial. I converted brain.mgz to brain.nii, imported the latter to matlab/spm and realigned it to rbrain.nii, generating a transform matrix M=rbrain.reorient.mat. if MM is the header for rbrain.nii, the header O for the original

[Freesurfer] reproducing sig.mgh

Hello Freesurfer Experts, I am trying to reproduce the values in sig.mgh using matlab, just to confirm that I know what is going on. My numbers do not match exactly, and I am hoping someone can explain my error, or point me in the right direction. With Qdec, I built a model with one discrete

Re: [Freesurfer] remove label from aseg

I think this one thread might have disappeared (if not, I apologize for my impatience). Heidi On 10/27/15, 5:16 PM, "Jacobs H (NP)" wrote: >I just checked again in freeview and indeed they have the same index (e.g. >CA1 has value 206 for left and also for