[Freesurfer] subcortical masks

Hi, I'd like to create binary masks in the nifti-format from each of the subcortical segmentations in freesurfer, separately (one for hippocampus, one for thalamus, and so forth..). Is there any way to do this automatically from the command line? Thanks, Martin Ystad Ph.D. cand

[Freesurfer] Version re-run

2 my manual edits will be saved by default. However, is there any need to re-run the autorecon1-steps for my subjects? Also: when do you plan to release the next version of FreeSurfer? Many thanks, Martin Ystad ___ Freesurfer mailing list Frees

[Freesurfer] create volumes from surfaces

le frontal lobe, so that only the voxels intersected by the surface belonging to the specific label I choose appear white, and everything else is black. How do I get this output from FreeSurfer? Thanks, Martin Ystad PhD-candidate, University of Bergen, Norway __

Re: [Freesurfer] create volumes from surfaces

ze aparc+aseg.mgz to > give a mask of an area (use --match), then take the intersection of the > mask with the surface-in-volume. > > doug > > Martin Ystad wrote: > >> Hi, >> I'm working on a fractal dimension analysis of the pial- and >> white-m

Re: [Freesurfer] create volumes from surfaces

there any way to do this with FreeSurfer? Thanks, Martin Douglas N Greve wrote: > The 2nd step only creates a mask of the entire surface. You need a > step 3 in which you multiply them together: > > > 3. mris_calc -o product.mgz lobe.mgz mul lobe_surface.mgz > > Martin Ystad w

[Freesurfer] Problems with FSGD file

Hi, I'd like to try out some simple regression analysis on some of my data. I've completed the tutorial until the mri_glmfit step where I get the error message: ERROR: gdfRead: gruppefil.txt is not formated properly I really can't see what's wrong with my file, I've even copy-pasted one of the

[Freesurfer] Resuming recon-all

-calabel, would there be a command that re-runs -calabel and the rest of the autorecon2 stream? Thanks, Martin Ystad University of Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] Version problems

% of the 3.0.1-volumes. What is the reason for this? How much of the processing stream do I have to re-run? Thanks, Martin Ystad Medical Student University of Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Subcortical segmentation

Hi, I noticed that routinely checking the subcortical segmentation (aseg.mgz) is not part of the Recommended Reconstruction Work Flow. Is this because the subcortical segmentation is highly accurate, or because manual intervention in the aseg is not recommended anyway? Thanks, Martin Ystad PhD

Re: [Freesurfer] Subcortical segmentation

ted? > > On May 13, 2010, at 7:58 AM, Martin Ystad wrote: > > >> Hi, I noticed that routinely checking the subcortical segmentation >> (aseg.mgz) is not part of the Recommended Reconstruction Work Flow. Is >> this because the subcortical segmentation is highly accurate

[Freesurfer] Intensity problems

re of? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Intensity problems

d If it hasn't worked, let me know, maybe there's another problem. good luck, Jenni On Fri, 28 Oct 2005, Martin Ystad wrote: Hi, I'm currently running the latest developmental release for RedHat 9, but I seem to have some problems concerning the intesity-normalization. Unfortuna

[Freesurfer] Normalization problem

volume looks ok? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Normalization problem

e the first normalization done without control points, and the wm.mgz -volume is also bad. So are the surfaces. How do I make freesurfer produce the same good results as I got during the first normalization? Do I need to specify the use of control points again, even though the brain.mgz volume l

[Freesurfer] Control-points

t the subcortical segmentation won't work properly? Will this munificent use of control-points constitute a source of error for the cortical segmentation, or are the protocols relatively robust? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies ve

[Freesurfer] dev-version/new version question.

its to the brainmask- or wm-volume? Thanks, Martin Ystad University of Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Autorecon1

edited, so I'd like to keep these changes) Another question; if I run the -autorecon2-wm flag, will I save a lot of computing time if I manually remove the Optic Nerve before doing so? Thanks, Martin Ystad University of Bergen, N

[Freesurfer] Talairach question

nmask volume, and others made from the nu volume? Should I make new transforms for all subjects, even though some of the original ones are fine? Thanks, Martin Ystad University of Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar