Re: [Freesurfer] Total GM and WM volumes

Dear Christian, Thanks for your suggestion. I followed the instructions to derive the GM and WM volumes. Here are the (rounded-off) results for one example: mris_volume lh.pial: 532767 mris_volume rh.pial: 536127 mris_wm_volume lh: 251139 mris_wm_volume rh: 254730 Accordingly: gm lh = 532767 -

[Freesurfer] subcortical structure coordinates

Hi I used FreeSurfer to automatically segment subcortical structures, and I would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this

Re: [Freesurfer] subcortical structure coordinates

Hi Aya, you should be able to convert our segmentations to Nifti, which I assume Brainvoyager can read. You can load any of our volumes into matlab with either MRIread.m or load_mgh.m and go from there. cheers Bruce On Wed, 27 Oct 2010, Aya Ben Yakov wrote: > Hi > > I used FreeSurfer to auto

Re: [Freesurfer] subcortical structure coordinates

I'm also interested in these segmentations for analysis in Matlab. In particular, which volumes should be loaded to get the coordinates of the segmentations? I assume the segmentation volumes are just indices (all voxel belonging to the same segment are assigned the same unique index), correct ?

Re: [Freesurfer] subcortical structure coordinates

yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt cheers Bruce On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote: I'm also interested in the

Re: [Freesurfer] Make functional ROI's from clusters

Alice, You might find this tutorial helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual and mri_volcluster or mri_surfcluster Allison -- On Tue, 26 Oct 2010, Alice Albrecht wrote: > Hi Everyone, > > I'm new to freesurfer so I apologize if my question ha

Re: [Freesurfer] subcortical structure coordinates

Hi I'm sorry for all these questions, but I'm very new to freesurfer, and I still don't really understand how things work. Is it necessary to convert to nifti? if I understand correctly, mri.vol should hold the needed information. In what space is this information (assuming some processing was don

Re: [Freesurfer] Longitudinal processing

Dear Martin and Douglas, I had the same question as Sandra and searching the mailing list I found your answers. However, it is not still clear for me which data I need to use for the mris_calc (reply from Martin) or mris_preproc (reply from Douglas), i.e. ( & ) or (.long. & .long.). Could you plea

Re: [Freesurfer] subcortical structure coordinates

Hi Aya, you can convert the aseg back to the original voxel space with mri_convert. I think the cmdline would be: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz -rl = reslice like -rt = resample type cheers Bruce On Wed, 27 Oct 2010, Aya Ben Yakov wrote: Hi I'm sorry f

Re: [Freesurfer] Total GM and WM volumes

Dear Bruce/Allison, Could you please try to give response to my question which wm and gm volumes I shoud use, see my today's submission below. Ed On 27 Oct 2010, at 14:41, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Christian, Thanks for your suggestion. I followed the instructions to

Re: [Freesurfer] Total GM and WM volumes

Ed, I would use the values in the aseg.stats. I'm not sure why there is this difference (Doug might be able to elaborate on how the values in aseg.stats are calculated) but for v5.0, we went over how all the stats were being calculated and make sure the values in the aseg.stats were the most ac

Re: [Freesurfer] Total GM and WM volumes

Hi Allison, Thanks. It is still confusing: for the gm the aseg.stats lists cortical as well as subcortical and the total volumes (being the sum of both). But for wm only cortical volumes are present. Is there no subcortical wm volume present or defined? Ed On 27 Oct 2010, at 15:58, Allison Stev

Re: [Freesurfer] Longitudinal processing

Hi always use the data from tp.long.base , they are less variable and more accurate than the cross sectional results. (that is why you tun the long stream at all). Best Martin On 27.10.2010, at 09:13, sima chalavi wrote: > Dear Martin and Douglas, > I had the same question as Sandra and searc

Re: [Freesurfer] Total GM and WM volumes

Nope - the subcortical structures are all gm. Allison -- On Wed, 27 Oct 2010, Ed Gronenschild wrote: > Hi Allison, > > Thanks. > It is still confusing: for the gm the aseg.stats lists cortical as > well as subcortical and the total volumes (being the sum of both). > But for wm only cortical vol

Re: [Freesurfer] Retinotopic mapping of only polar data]

Hi Douglas, Thanks a lot, I made dummy data for the eccen and that worked. Last problem: when I try to overlay the data on an inflated brain, the registration is off (patches are frontal and in parts I didn't scan, while they for sure should be posterior and within my actually scanned scans).