Hi Bram, there is not a way to do it with a single command. You could
use the aparc+aseg, merge the two hemi labels into one, then run
mri_segstats. If you want to stick with pure surface-based analysis,
then you'd have to run mri_segstats twice, then just compute a weighted
mean of the two wa
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Hello FreeSurfer Team,
I've made a New Year's resolution to stop bothering Andrew Hoopes and
instead send my questions to the FreeSurfer Mailing List.
I would like to calculate a single average waveform for two surface labels
on contralateral hemisphe
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The WM was cropped out by applying a grey-matter mask in SPM, and I am trying
to extract non-zero voxels with mri_segstats.
Best,
Renxi
> On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D.
> wrote:
>
> I don't understand why WM was cropped out.
what is your command line?
On 11/29/2020 2:55 PM, RENXI LI wrote:
> External Email - Use Caution
>
> The WM was cropped out by applying a grey-matter mask in SPM, and I am trying
> to extract non-zero voxels with mri_segstats.
>
> Best,
> Renxi
>
>> On Nov 29, 2020, at 11:23 AM, Greve, D
I don't understand why WM was cropped out. What command were you trying
to use?
On 11/18/2020 2:39 AM, RENXI LI wrote:
> External Email - Use Caution
>
> Hi Freesurfer experts:
>
> I am trying to extract the mean-time series from the functional image using
> mri_segstats. However, the c
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Hi Freesurfer experts:
I am trying to extract the mean-time series from the functional image using
mri_segstats. However, the cerebral white matter signals were cropped out in my
functional images, and the regions that I am trying to extract signal f
Thanks Doug,
That is what I needed to know!
Brad
On Jun 26, 2014, at 11:13 AM, Douglas N Greve wrote:
>
> It is helpful to have a command line, but I think I can figure it out
> from what you have written. The first row is everything outside your
> seg. The second is everything inside your
It is helpful to have a command line, but I think I can figure it out
from what you have written. The first row is everything outside your
seg. The second is everything inside your seg.
doug
On 06/25/2014 05:54 PM, Martins, Brad wrote:
> Hi everyone,
>
> I’m new to Freesurfer and I have a que
Hi everyone,
I’m new to Freesurfer and I have a question about the output of mri_segstats. I
have created an ROI in which I am measuring cortical thickness. When I run
mri_segstats I get a table with 2 rows of segmentation values. What are the 2
rows? The SegId of the two rows are 0 and 1 but I
>
> On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your help. I had two questions that came up from doing
>> some preliminary analysis with the mri_segstats:
>>
>> 1) When running the mri_segstats command with --seg
>> aparc+aseg_nocortex.mgz (which is
On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your help. I had two questions that came up from doing
> some preliminary analysis with the mri_segstats:
>
> 1) When running the mri_segstats command with --seg
> aparc+aseg_nocortex.mgz (which is the resul
Hi Doug,
Thanks again for your help. I had two questions that came up from doing
some preliminary analysis with the mri_segstats:
1) When running the mri_segstats command with --seg
aparc+aseg_nocortex.mgz (which is the result of the matlab code you
provided below) and with --seg wmparc.mgz, even
That is great,
Thanks a lot, Doug!
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I m
You can just do it in matlab, somethhing like
a = MRIread('aparc+aseg.mgz');
ind = find(a.vol > 999);
a.vol(ind) = 0;
MRIwrite(a,'nocortex.mgz')
On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> I'm sorry, what I meant to ask in the previous question is whether there
>
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume in
the --s
If you want the volume of cortex, you should definitely not use
aseg.mgz. aparc+aseg is better, but the best is to use the surface-based
measure found in aseg.stats
doug
On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your reply. One last question: Th
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or is
On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks for the quick reply! In addition:
>
> 1) The average intensity measure in the above example does not include the
> intensity of the skull, just everything inside, right?
It includes all the structures that are segmented i
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not include the
intensity of the skull, just everything inside, right?
2) Just to be clear on the purpose of including the segmentations in the
command line: The segmentations only specify
On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS community,
>
> I had some questions regarding the mri_segstats command:
>
> 1) In the excludeid flag, are the ids the ones shown in the
> FreeSurferColorLUT.txt?
Yes
> 2) In case I would like to measure the mean intensity of the orig f
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
2) In case I would like to measure the mean intensity of the orig file as
outlined in the second example in
https://surfer.nmr.mgh.harvard.
Hi ,
I would like to use mri_segstats with an aprac parcellation to get the
mean/stddev of the norm.mgz intensities by parcel. I have tried the
following usage:
mri_segstats --annot con_2304 lh aparc --ctab-default --nonempty
--excludeid 0 --sum con_2304.norm.aseg.sum --in
$SUBJECTS_DIR/con
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