Re: [Freesurfer] recon-all Flirt Error

Anil, flirt is an FSL utility that is included in the freesurfer distribution in the $FREESURFER_HOME/fsl directory (in bin). Normally, freesurfer will setup a path to it. Make sure it is in your path. Nick On Mon, 2007-11-26 at 16:26 -0600, Anil Roy wrote: > Hello All, > > I wanted to test t

RE: [Freesurfer] recon-all Flirt Error

The FSL library or the path to FSL is missing. regards, Pedro Paulo Oliveira Jr. -- mens. original -- Assunto:[Freesurfer] recon-all Flirt Error De: "Anil Roy" <[EMAIL PROTECTED]> Data: 26/11/2007 22:38 Hello All, I wanted to test the Freesurfer installation by running re

Re: [Freesurfer] recon-all Flirt Error

Looks like you don't have FSL installed or it is not in your path. Anil Roy wrote: Hello All, I wanted to test the Freesurfer installation by running recon-all but I received an error saying flirt no found. Can someone point me to the cause of this problem, is it a missing library or some ot

[Freesurfer] recon-all Flirt Error

Hello All, I wanted to test the Freesurfer installation by running recon-all but I received an error saying flirt no found. Can someone point me to the cause of this problem, is it a missing library or some other issue? I have posted the output from running recon-all on bert below. Thanks, Anil

Re: [Freesurfer] About Gaussian Random Field Theory on fsaverage

It depends on how you measure the FWHM that you are going to plug into GRF. How are you computing it? If you are using our tools, then you would use neither. Rather, you'd use the average surface area for the group. This is stored in the average surface. You can determine it with mris_info jo

Re: [Freesurfer] Make_average_subject

Sorry, what's the error in there? Alexander Fornito wrote: Sorry, I ran the --debug flag after running the first command. It is not the cause of the error. Here is the output after testavg has been deleted. make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann0

Re: [Freesurfer] loading data to matlab?

Yes, that should work. Make sure to specify --noreshape and to use mgh format as the output. Then in matlab you can run f = MRIread('yourfile.mgh'); The pixel data will be in f.vol doug Bruce Fischl wrote: Hi Maryam, not sure if Doug is still reading email, but he would be the one to ask.

Re: [Freesurfer] Error with mc-sess

Can you run any of the other matlab-based fsfast commands? I've never tried it on a power pc, so maybe the matlab version is slightly different (looks like it does not know when to quit). You can try running it outside of mc-sess with: cd /Users/lreddy/Desktop/Leila-Data/FSFAST_Tutorial/Sessio

Re: [Freesurfer] DODS or DOSS?

Hi, sorry for the delay. In theory, DODS is better than DOSS because you have an extra parameter you can use to fit the data and it will not bias you to find a false positive. On the other hand, it does cost you DOF, so if you have a small number of subjects, it can increase the false negative

Re: [Freesurfer] Error with mc-sess

Are you still having this problem? What platform are you running on? Leila Reddy wrote: Hi, I recently installed freesurfer, AFNI etc but am having problems with mc-sess. The script runs and gets to the stage in each run where it calls up matlab, enters the MRIwrite command but then gives the

Re: [Freesurfer] flat map issue

try this: mris_flatten -distances 20 20 lh.occip.patch.3d lh.occip.flat.patch.flat On Mon, 26 Nov 2007, romain valabregue wrote: Hello, I define a patch of the occipital lob flat_patch and run the comand mris_flatten lh.occip.patch.3d lh.occip.flat.patch.3d why do I end up with a 'closed'

[Freesurfer] flat map issue

Hello, I define a patch of the occipital lob and run the comand  mris_flatten  lh.occip.patch.3d lh.occip.flat.patch.3d why do I end up with a 'closed' flattened surface  points around the cutting line stay close and not far away like in classical view like this one : What's wrong