[Freesurfer] mri_glmfit & .nii.gz & FSF_OUTPUT_FORMAT

Hi, all. I have come across a problem when using mri_glmfit. We know that the output format is controlled by the $FSF_OUTPUT_FORMAT. I have checked that in my environment, $FSF_OUTPUT_FORMAT is nii.gz. But the output fils are all in mgh format. How can I get output files in nii.gz? Thanks! Xian

[Freesurfer] problem about cortical area values

Dear teacher, I haven't found the page describes the workflow to extract freesurfer cortical area values for a region-of-interest (ROI) defined by myself (used another software), I only saw how to calculate cortical thickness values, please help me~ Thank you very much! Student: He Qin_

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

Hi ,  Thank you so much for the answer Bruce and Michael.  I tried the command given by Michael and it works.  I didn't already find a way for calculating the RMS distance between matched vertices and Hausdorff.  As soon as I do that,  I will compare the results and  I'll give you a feedback. Ch

[Freesurfer] setting thresholds in qdec

Hello, Is it no longer possible to set the Min, Mid, and Max thresholds directly on the Qdec display tab? The only way I seem to be able to change them is via the sliders in the histogram at the bottom, which I don't recall previously being the case. This is Qdec 1.4 (FS 5.2) on a RHEL 5.9 system

Re: [Freesurfer] mri_glmfit & .nii.gz & FSF_OUTPUT_FORMAT

Hi Xiang-zhen, mri_glmfit does not read the FSF_OUTPUT_FORMAT. Instead, control the output format with --nii.gz doug On 04/12/2013 07:58 AM, Xiangzhen Kong wrote: > Hi, all. > I have come across a problem when using mri_glmfit. > We know that the output format is controlled by the $FSF_OUTPUT_FOR

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

HiLucille, you can use mris_diff with the --xyz-rms optionto compute the RMS difference. Don't know about Hausdorff doug On 04/12/2013 09:39 AM, Lucille Deroche wrote: > Hi , > > Thank you so much for the answer Bruce and Michael. > I tried the command given by Michael and it works. > I didn't al

Re: [Freesurfer] problem about cortical area values

Hi He Qin, What format is your ROI in? A label file on the surface? doug On 04/12/2013 09:20 AM, 仙豆 wrote: > Dear teacher, > > I haven't found the page describes the workflow to extract freesurfer > cortical area values for a region-of-interest (ROI) defined by myself > (used another software)

Re: [Freesurfer] setting thresholds in qdec

I just transferred all the data to a different system running CentOS 5.5 and I'm able to set the display thresholds in qdec on that system. It also uses a different FS version (5.1) but I think it is an OS issue, and not a FS version issue, since I have the same problem on the original RHEL 5.9 s

[Freesurfer] announcement for MGH email list (fwd)

FYI -- Forwarded message -- Date: Fri, 12 Apr 2013 00:27:38 +0200 From: Jorge Jovicich To: Bruce Fischl Subject: announcement for MGH email list Ciao Bruce, would you mind forwarding for me the postdoc position announcement below? Thanks, Jorge -

[Freesurfer] mkbrainmask error with libmeshclass.so

Hello all, when running preproc-sess, I got this error message: ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain Try running mkbrainmask-sess with -per-run I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . -fsd bold

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

I don't think there is one between surfaces - you would need to compute it yourself. Pretty easy in matlab, although probably very slow On Fri, 12 Apr 2013, Douglas N Greve wrote: HiLucille, you can use mris_diff with the --xyz-rms optionto compute the RMS difference. Don't know about Hausdorf

Re: [Freesurfer] mkbrainmask error with libmeshclass.so

Hi Corinna, if you just run bet2 at the command line, do you get the same error? doug On 04/12/2013 03:56 PM, Corinna Bauer wrote: > Hello all, when running preproc-sess, I got this error message: > ERROR: could not determine file for > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/

[Freesurfer] unit of corpus callosum segmentation

Hi all, I have a quick question related to the corpus callosum segmentation: I read in previous posts that the reference explaining more about the CC subdivision in 5 segments was the one by Rosas et al, Neuroimage 2010. But in this publication, you show thickness of the corpus callosum as the

Re: [Freesurfer] unit of corpus callosum segmentation

Hi Marie, 400 or 900 what? Not mm. How are you calculating thickness? I think in Diana's paper it was the radius of the inscribed circle on the medial axis, wasn't it? Bruce On Apr 12, 2013, at 10:44 PM, Marie Schaer wrote: > > Hi all, > > I have a quick question related to the corpus callos

Re: [Freesurfer] unit of corpus callosum segmentation

Hi Bruce, Thanks for your response. My question was indeed: what is the unit of the CC_* output in the aseg.stats? E.g. in the attached file, the last 5 rows depict CC segmentation measurements (between ~400+ and 900+), and I was wondering what was the unit of these measurements. The other val