by the label that I have specified
Thanks.
Jeni Chen
Douglas N.
Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
Wed, 14 Mar 2018 15:32:51
-0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20180314>
Is t
Both average hemispheres look very bad, they don't even look like a brain.
The two monkey surfaces look reasonable, except for some topological defect
that I think could be fixed with some manual editing. Is there anything I
could try?
Thanks a lot
Francesca
2018-03-14 23:41 GMT+01:00 Douglas N.
Hi,
I have some functional data for the same localizer (dimensions 80x80x38x246)
that was acquired in the same subject on two separate days. I would like day
1's raw data to be spatially aligned to the anatomical taken on day 2, but
still have the low resolution dimensions of functional space.
I don't know what is going on there except that the average surfaces are
probably wrong in some way. It looks like it made it all the way through
except for that step, so all of the output should be there. How does it
look?
On 03/13/2018 05:27 PM, Francesca Strappini wrote:
> Dear Experts,
>
You should be able to use --regheader ANTSaverage (assuming ANTSaverage
is the name you gave it when running recon-all)
On 03/12/2018 01:32 PM, Charlotte Grosse Wiesmann wrote:
> Hi Doug,
>
> I was trying to map my volume mask from my study-specific average subject
> template space to the
I'm not sure what you are doing as I have never used fieldtrip. I would
suggest contacting the fieldtrip developers. If you can isolate the
problem to something that FS is doing (eg, an error in recon-all), then
please repost with the recon-all.log file.
On 03/11/2018 04:19 PM, Maria Carla
Is this a volume or surface-based analysis? How did you try to visualize it?
On 03/10/2018 12:56 AM, Chen Jen-I. wrote:
> Hello,
>
> I want to do a FDR correction using mri_fdr within a ROI mask (in .label
> format). I see the option of passing the sig.mgh volume through a mask, and I
> read
No, sorry. You can do it easily enough in matlab, eg
seg = MRIread('seg.mgz');
input = MRIread('input.mgz');
ind = find(seg.vol == SegNo);
segmode = mode(input.vol(ind));
[h x] = hist(input.vol(ind),100);
On 03/13/2018 07:58 PM, Yash Patel wrote:
> Any updates or ideas in extracting
I don't know what you mean. did you create the cohensd.mgh file? You can
get the mean value of it in each cluster with
mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --o
sum.dat
The mean will be in the mean column
On 03/14/2018 01:46 PM, Hannah Claussenius-Kalman wrote:
>
Hi Sudeshna
according to our local neuranatomical expert:
it is probably ventral claustrum (ventral claustrum stretches in to
the temporal lobe ,especially at the anteriorly (slightly anterior to
amygdala).
so this region is not cortex and you shouldn't worry about the surfaces
there.
We used the gamma.mgh and rstd.mgh files to derive an effect size file that
we called cohensd.mgh. How can I access these files to report effect size
(Cohen's *d*) for significant clusters?
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Hi Laura,
the .gcs file is a probabilistic atlas with lots of information such as
neighborhood clique potentials. You are probably better off applying it to
fsaverage and computing the centroids of parcels in that space.
cheers
Bruce
On Wed, 14 Mar 2018, Laura Juan Galmes
wrote:
Hi
Hi all,
I have a question about how to get a .nii or .mgz file out of a .gcs. What I
actually want to do is get the coordinates of the centroids of the regions of
my atlas ( which is lausanne2008), or even the coordinates of all the voxels in
each region so I could compute the mean myself.
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