Re: [Freesurfer] recommende pc and cuda

On 05/04/11 16:55, Richard G. Edgar wrote: > > On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote: >> Richard G. Edgar wrote: >>> On the standard test case we use here, a full recon-all run takes 8 >>> hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using >>> the Tesla C2050. >>>

Re: [Freesurfer] preproc-sess path structure

You should check that anatomical analysis and make sure that it is correct. Once that is done, make sure that the subjectname in the subjectname file is correct, then preproc-sess should run. doug Michelle Umali wrote: > Hi Doug, > > I've run recon-all -all. I ended up inputing an .mgz file co

Re: [Freesurfer] Interpreting results from Qdec

yes, something like ?h.volume.fwhm10.fsaverage.mgh doug Gallen, Courtney (NIH/NIDA) [F] wrote: > Hi Doug > > Thanks for helping me with this! > > First time around I did everything as is outlined in 'Define a Region of > Interest' here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecG

Re: [Freesurfer] preproc-sess path structure

Hi Doug, I've run recon-all -all. I ended up inputing an .mgz file converted from a .nii file that was converted from a .dicom. Was needed info lost somewhere along the way? Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does one need -anat?)successfully, because it genera

[Freesurfer] 2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy

*2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC, http://www.unitn.it/en/cimec), University of Trento, there will soon be an opening for a two-year postdoctoral fe

Re: [Freesurfer] Interpreting results from Qdec

Hi Doug Thanks for helping me with this! First time around I did everything as is outlined in 'Define a Region of Interest' here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. I'll try your suggestion now. The input data would be something like ?h.volume.fwhm10.fsave

Re: [Freesurfer] Mapping segmentations to SPM Functional Space

There's nothing explicit, but it's not hard to do. You need to analyze your SPM data in the native functional space. Then register the functional to the anatomical using bbregister. Then map the segmentations into the functional space with mri_label2vol. doug On 4/5/11 3:04 PM, Palzes, Vanessa

[Freesurfer] Mapping segmentations to SPM Functional Space

I am wondering if there is a similar function as aseg2feat (which maps the automatic segmentations from Freesurfer to FSL FEAT functional space) for the use in SPM functional analysis. This tool poses to be very useful in creating ROI masks, however, we are using SPM for functional analysis rather

Re: [Freesurfer] preproc-sess path structure

Hi Michelle, the SUBJECTS_DIR is an environment variable that you have to set prior to running the anatomical analysis (disregarding the functional analysis for a moment). Before running the functional analysis, you must run recon-all on the anatomical data, eg recon-all -all -subject LD08-a

Re: [Freesurfer] Convert annotations longitudinally

Thanks, Doug-- that's what I was looking for! Andrew On Tue, 2011-04-05 at 11:51 -0400, Douglas Greve wrote: > Try using mri_surf2surf with the --sval-annot flag. > > doug > > On 4/5/11 11:20 AM, Andrew Dumas wrote: > > Hi FreeSurfer experts, > > > > Is there a way to move annotations from the

[Freesurfer] preproc-sess path structure

Hi Doug, Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program is? I had done this: setenv SUBJECTS_DIR /home/fsl/structural So this SUBJECTS_DIR is not located where FreeSurfer is. Is the following the exact correct path: FreeSurfer/$SUBJECTS_DIR/LD08/subjectname where LD08 is

Re: [Freesurfer] Convert annotations longitudinally

Hi Andrew, not sure if I understand. The surfaces in the longitudinal directories across time (within subject) are in registration, so you should be able to use the same annotation for all time points. Martin On Tue, 2011-04-05 at 11:20 -0400, Andrew Dumas wrote: > Hi FreeSurfer experts, > >

Re: [Freesurfer] recommende pc and cuda

On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote: > Richard G. Edgar wrote: > > On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote: > > > > > Will a Tesla C2050 or another good CPU be able to reduce the running > > > time from 20-24 hr to less time like for instance 8hr or below that >

Re: [Freesurfer] Convert annotations longitudinally

Try using mri_surf2surf with the --sval-annot flag. doug On 4/5/11 11:20 AM, Andrew Dumas wrote: > Hi FreeSurfer experts, > > Is there a way to move annotations from the same subject at one > timepoint to another? I've tried doing this using a discrete-valued > surface and using seg2annot, but, w

Re: [Freesurfer] recommende pc and cuda

Richard G. Edgar wrote: On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote: Will a Tesla C2050 or another good CPU be able to reduce the running time from 20-24 hr to less time like for instance 8hr or below that time. On the standard test case we use here, a full recon-all run ta

[Freesurfer] Convert annotations longitudinally

Hi FreeSurfer experts, Is there a way to move annotations from the same subject at one timepoint to another? I've tried doing this using a discrete-valued surface and using seg2annot, but, when I convert surfaces there are vertices between regions whose values are averages of bordering vertices. T

Re: [Freesurfer] preproc-sess

Make sure that your subjectname file has the name of the FreeSurfer subject folder as found in $SUBJECTS_DIR (it looks like it is empty). You don't need the retinotopy data in the $SUBJECTS_DIR. doug Michelle Umali wrote: > Dear Freesurfers, > I am still struggling with the retinotopy analysis.

Re: [Freesurfer] different vertexes and faces on pial and inflated surface of the same hemisphere

Hi Forrest, You can probably try running recon-all -make all -s and see if that fixes the problem. Sita. On Sun, 3 Apr 2011, Forrest Sheng Bao wrote: > hi all, > > I encountered a strange problem today. I used > > recon-all -all > > to get surfaces of a subject. I have no problem with his

Re: [Freesurfer] recommende pc and cuda

On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote: > Will a Tesla C2050 or another good CPU be able to reduce the running > time from 20-24 hr to less time like for instance 8hr or below that > time. On the standard test case we use here, a full recon-all run takes 8 hours on a 3.2 GHz Neha

[Freesurfer] edit volume remotely

Dear all, We are trying to edit a new wm volume remotely. We want to substitute the mouse click with an external command. Since we are not familiar with tcl/tk we don't know where this action (mouse click to edit volume) happens within the script tkmedit.tcl. Could you please help us: How coul

Re: [Freesurfer] recommende pc and cuda

Will a Tesla C2050 or another good CPU be able to reduce the running time from 20-24 hr to less time like for instance 8hr or below that time. Knut J > From: rg...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Date: Mon, 4 Apr 2011 09:23:07 -0400 > Subject: Re: [Freesurfer] recomme

[Freesurfer] N3 for improving cerebellum segmentation

Dear list, I have a question regarding intensity non-uniformity correction using N3 (as in Boyes et al, 2008). Does anyone have experience of using it for improving cerebellum segmentation, specifically distinguishing between white and grey matter in cerebellum? If yes, what are the best values fo