Thanks, that's useful for getting the ROI volumes and a list of all that's
been found for a particular data set.
I would still like to have a way to identify a listed region as gray matter
or not so that I can parse the file for only GM regions that have been
returned, particularly as different nu
FDR does not have blobs either, but I think I get what you mean:). You
should run mri_surfcluster specifying the FDR-determined voxel-wise
threshold as the --thmin, the sig.mgh as the --in, --subject fsaverage
--hemi the-hemi-you-use, and --ocn ocn.mgh
Then
mri_segstats --i y.mgh --seg ocn.mgh
I'm sorry, I might not have used the right word. Let's say 'blob' instead
of cluster. It's something like the plot attached. Each circle/square is a
subject. I would like to export that so I can make the plot myself.
Best,
Mihaela
On Mon, Nov 7, 2016 at 4:38 PM, Douglas N Greve
wrote:
> What do
What do you mean a "plot"? I had assumed you wanted to average over
clusters, but FDR does not produce clusters
On 11/07/2016 04:26 PM, Mihaela Stefan wrote:
> That seems to be for Monte Carlo simulation. What if I use FDR or if I
> want to look at a plot from an uncorrected map?
>
> Thanks!
>
I did not see binary values. The values were 255 in the mnc volume. The
caveat here is that I can only read it in using FS, so if there is
something burried in the FS code that causes the values to change from 1
to 255, I might not see it. Is there a minc viewer you can use to
resolve this?
O
That seems to be for Monte Carlo simulation. What if I use FDR or if I want
to look at a plot from an uncorrected map?
Thanks!
Mihaela
On Mon, Nov 7, 2016 at 3:16 PM, Douglas N Greve
wrote:
> Run mri_glmfit-sim using the Qdec output folder as the --glmdir and
> setting the thresholds and signs
It looks like the input has values of 255 and 0, not 1 and 0. How do you
verify that the values are 0 and 1?
On 11/07/2016 03:43 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> I have uploaded the label_aalf.mnc and testsurfaceoverlay.mgz
>
> Here is an example of the mri_vol2surf that I use
>
> *
I don't know that we have a complete list in one place of just the
aparc+aseg ROIs, but you can get one by running
mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat
then look in the sum.dat file
On 11/03/2016 04:32 PM, P Taylor wrote:
> Is there an available list of GM regions wit
On 11/07/2016 03:24 PM, Daniel Alejandro Reyna Torres wrote:
>
> Hello,
>
>
> my name is Daniel Reyna, I am currently working with Freesurfer to
> analyse the cortical segmentations and parecellations that the program
> outputs. I have analysed some MRI but I am not sure whether I have
> achie
Thank you!
Elisabetta
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Monday, November 7, 2016 3:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical white matter
no, it does not.
On 11/07/2016 02:44
Hello,
my name is Daniel Reyna, I am currently working with Freesurfer to analyse the
cortical segmentations and parecellations that the program outputs. I have
analysed some MRI but I am not sure whether I have achieve best results or
probably there is something I should improve.
One questi
Use the --surf subject hemi option. Run it with --help to get an example
On 11/07/2016 11:32 AM, Sophie Wohltjen wrote:
> Hi,
>
> I am trying to create cortical surface labels from several brain
> masks. All are .mgz files, separated by hemisphere, and aligned to
> fsaverage.
>
> Here is the co
Run mri_glmfit-sim using the Qdec output folder as the --glmdir and
setting the thresholds and signs as you had them in qdec. The output
will then be in a file called something like cache.th20.pos.y.ocn.dat.
the cluster summary table will be in cache.th20.pos.sig.cluster.summary
On 11/07/2016
no, it does not.
On 11/07/2016 02:44 PM, Del Re, Elisabetta wrote:
>
> Dear FreeSurfer team,
>
> does the cortical white matter volume include the cerebellum?
>
> Thank you,
>
> regards,
>
> Elisabetta
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> F
Dear FreeSurfer team,
does the cortical white matter volume include the cerebellum?
Thank you,
regards,
Elisabetta
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The infor
Hi All,
During the experiment, a wedge was presented clockwise, starting from the low
vertical meridian, and a ring was presented from center to peripheral. The
analysis done successfully with fs5.3 generated values of polar angle and
eccentricity for each voxel. For example, the voxel A has
Hello Freesurfers,
I am doing a group analysis using Qdec. I have a few significant clusters
and I would like to plot one of them. Qdec does that if I click on 'Find
Clusters and Goto Max' but I don't see options for the design of the plot.
How can I export the thickness values from my cluster to
in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Ciao Daniele,
This is weird. Would you mind verifying that file T1resampled.mgz actually
exists in the temporary directory of the subject? You can do that by CDing to
$SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command:
find . -name “T1resampled.mgz”
Cheers,
/Eugenio
Juan Eugenio Iglesias
ER
Dear experts,
I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for
hippocampal subfield features extraction (always on Ubuntu 14.01 environment).
After several trial I realized that before pipeline ends I've got the following
error:
/opt/FreeSurfer-6-Beta/bin//mri_
Hi,
I am trying to create cortical surface labels from several brain masks. All
are .mgz files, separated by hemisphere, and aligned to fsaverage.
Here is the command I entered to create the labels:
mri_cor2label --i .mgz --l .label --id 1
When I run this command, I successfully create the labe
Thank you very much Bruce. Last questions. When I replace FS generated
brainmask.mgz with mine, does the original also remain in the mri folder(
that's having 2 brainmask.mgz) or is the original permanently replaced with
my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)? Second
Dear FreeSurfer Developers,
We have been trying out, for the past few months, the freesurfer dev releases,
and in particular this one:
freesurfer-X86_64-unknown-linux-gnu-dev5-20150924
My question is, does the above version classify as a nightly version of
FreeSurfer 5, or as an early beta
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