[Freesurfer] Buried sulci problem and freesurfer

I recently came across Chloe Hutton¹s buried (or closed sulci) problem discussed here Hutton, C., De Vita, E., Ashburner, J., Deichmann, R., Turner, R. (2008). Voxel-based cortical thickness measurements in MRI. NeuroImage, 40(4), 1701-1710. doi:10.1016/j.neuroimage.2008.01.027 How well does

[Freesurfer] Number of Voxels different between wmparc.mgz and wmparc.stats

Hello, After segmenting using recon-all –all, I want to look at how much voxels there is in each segmented structure. I did the following procedure : I opened the wmparc.mgz volume with 3DSlicer as a label volume and computed the LabelStatistics. For the label 1005 (ctx-lh-cuneus), the

Re: [Freesurfer] MRS mask

Hi Lena, this is not a problem for surface-based approaches unless a grid is used in some underlying algorithm (e.g. level sets) cheers Bruce On Fri, 12 Feb 2010, Lena Palaniyappan wrote: Hi Bruce and team I have a ROI mask in analyze (img_hdr) format obtained from MR spectroscopic group

[Freesurfer] talairach

Hello freesurfer team, I am trying to run tkregister2 and I come up with this error message : No glx extension! register: ### tkoInitWindow(name) failed Any idea on what this could be from? Previously this command had worked. Thanks, Tina Jeon ___

Re: [Freesurfer] Number of Voxels different between wmparc.mgz and wmparc.stats

Hi Christopher, the values in wmparc.stats are computed with partial volume correction. Sita. On Wed, 12 May 2010, Christopher Coello wrote: Hello, After segmenting using recon-all –all, I want to look at how much voxels there is in each segmented structure. I did the following

[Freesurfer] talairach to native space

Hello freesurfers, I am trying to align my T1W image in native space to the surface files (?h.pial, ?h.white, ?h.inflated, ?h.base) but it seems that they do no align perfectly. I thought the labeling information is in native space? However this does not seem to be the case because in the

[Freesurfer] Methods for white matter hypointensities measure

Hello guys, I am curious as to how white matter hypointensities (on T1 mprage) are measured automatically for the aseg.stats file in FS? A group at UCSF is interested in using this measure for a study and would like to have a nice explanation or citation to describe how it is generated. I

[Freesurfer] problems with tksurfer

Hi all! I have some problems to visualize surfaces by tksurfer. When I try to load a surface with the command tksurfer my_subj_name lh inflated I receive the following error: ERROR: could not read header info from T1 or orig in homes//my_subj_name/mri The SUBJECTS_DIR is the correct one and in

Re: [Freesurfer] Methods for white matter hypointensities measure

Hi Victor we treat it as any other label - it's manually labeled in the training subjects and propagated into the aseg. Koen Van Leemput (ccd) has some tools for segmenting them from multi-spectral data that probably works better though (they aren't that well defined only on a T1). cheers

Re: [Freesurfer] problems with tksurfer

Hi Maria, what version are you using? If the data is local to MGH and you point me at it I'll take a look Bruce On Wed, 12 May 2010 iac...@nmr.mgh.harvard.edu wrote: Hi all! I have some problems to visualize surfaces by tksurfer. When I try to load a surface with the command tksurfer

Re: [Freesurfer] Methods for white matter hypointensities measure

Thank you for the prompt answer, as always Bruce!! I would be very interested in the techniques for multispectral measurement of hyperintensities, as we have a pretty sizeable database of T1 images with corresponding T2 flairs for which we are very interested in accurate measures of white

Re: [Freesurfer] Methods for white matter hypointensities measure

sure. Let me know how it goes Bruce On Wed, 12 May 2010, Laluz, Victor wrote: Thank you for the prompt answer, as always Bruce!! I would be very interested in the techniques for multispectral measurement of hyperintensities, as we have a pretty sizeable database of T1 images with