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 -
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
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
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 ?
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
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
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
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
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
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
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
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
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
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
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).
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