Not from a group analysis, but you can get it from running
asegstats2table. See our tutorial on ROIs
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
On 2/2/2021 11:44 AM, Sara Lyn wrote:
External Email - Use Caution
If that's the correct way to do it then yes
External Email - Use Caution
If that's the correct way to do it then yes since I don't know about this.
If not, is the volume of white matter obtained from freesurfers glmfit
group analyses?
On Tue, Feb 2, 2021 at 11:39 AM Douglas N. Greve
wrote:
> sorry, still don't
sorry, still don't understand. do you want to get the volume of WM from DTI?
On 2/2/2021 11:19 AM, Sara Lyn wrote:
External Email - Use Caution
Hi Dr Greve,
Instead of using DTI to get at the FA/MD etc measures is there a way
to get at the volume of the white matter?
Best,
Sara
External Email - Use Caution
Hi Dr Greve,
Instead of using DTI to get at the FA/MD etc measures is there a way to get
at the volume of the white matter?
Best,
Sara
On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve
wrote:
> Not sure what you mean
>
> On 2/1/2021 12:32 PM, Sara
Not sure what you mean
On 2/1/2021 12:32 PM, Sara Lyn wrote:
External Email - Use Caution
Hi,
Is there a way to get at the white matter volume from a group analysis?
Sara
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External Email - Use Caution
Hi,
Is there a way to get at the white matter volume from a group analysis?
Sara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is cerebral white matter, so it excludes brainstem and cerebellar white
On 2/21/19 11:14 AM, Mehndiratta, Ambica wrote:
> Hello,
>
> I am trying to extract the white matter volume based off the
> aseg.stats. I noticed the text includes "total cortical white matter
> volume" and I was
Hello,
I am trying to extract the white matter volume based off the aseg.stats. I
noticed the text includes "total cortical white matter volume" and I was
wondering if that is the same as overall white matter volume in the brain?
Thank you,
Ambica Mehndiratta
Clinical Research Coordinator
You will need to create an annotation with your label in it. This might
be tricky to do depending on what you want. The easy way is to run
mris_label2annot with only your label, then run mri_aparc2aseg to
generate something like the wmparc.mgz (look in the recon-all.log file
for the command
Hi Josue
how would you define the borders of the white matter of the gyrus? I guess
you could use the wmparc stuff and just count voxels based on a distance
constraint
cheers
Bruce
On Tue, 9
May 2017, Josue Luiz Dalboni Da Rocha wrote:
Dear Freesurfer team,
I am working with
Dear Freesurfer team,
I am working with calculated volumes of a gyrus (a costumized label).
I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in
label format).
According to the freesurfer tutorial (as I understood), one of the stats
outputted from
not that I know of. I think you'll have to do it by hand (sorry)
On 3/21/17 11:02 AM, Ahearn, T wrote:
Hello
I need separate grey and white volumes for the frontal and temporal
lobes. I have values for grey volume from
mri_annotation2label --subject 01 --hemi lh --lobesStrict
Hello
I need separate grey and white volumes for the frontal and temporal lobes. I
have values for grey volume from
mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation
mris_anatomical_statson the lh.lobar_annotation.annot file to generate a
text file.
I've also
The values in wmparc.stats will have partial volume correction. The
onesfrom fslstats will not.
On 9/12/15 3:44 PM, John Anderson wrote:
Hi Bruce,
Kindly I want to inquire about the _difference between_ white matter
volume generated by freesurfer ( specifically the white matter
Hi John
I'm actually not sure how fslstats works. I'll cc MJ so he can answer that
part of it. When we measure volume (e.g. in the stats files) we do partial
volume correction as opposed to counting voxels, which we have found to be
more accurate and repeatable.
cheers
Bruce
On Sat, 12 Sep
Hi Bruce,
Kindly I want to inquire about the difference between white matter volume generated by freesurfer ( specifically the white matter parcellations volume mentioned in wmparc.stats) and the vwhite matter volume generated by other tools like fslstats.
For example:
If I use a binarized
On 11/06/2014 12:53 AM, Alshikho, Mohamad J. wrote:
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the
statistics at the end of there running and we can check the results
in aseg.stats (the
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume
On 11/06/2014 12:53 AM, Alshikho, Mohamad J. wrote:
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the
statistics at the end
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the statistics at
the end of there running and we can check the results in aseg.stats (the
output of recon-all) and fa.stats (the output of dt-recon for FA).
Hi Bruce,
I wanted to calculate the right and left hemispheric white matter volume using
a mask.
Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of
mris_volmmask after binarize them) and the right and left hemispheric white
matter masks from aseg.mgz atlas (the output
The aseg is not surface-based and will not be as accurate
doug
On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
Hi Bruce,
I wanted to calculate the right and left hemispheric white matter
volume using a mask.
Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the
outputs of
, October 31, 2014 10:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume
The aseg is not surface-based and will not be as accurate
doug
On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
Hi Bruce,
I wanted to calculate the right and left hemispheric white
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 10:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume
The aseg is not surface-based and will not be as accurate
...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 11:04 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume
I would suggest using the value in aseg.stats. Is that not possible?
On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote:
Thanks Doug!
So do you suggest
: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 11:35 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White matter volume
Hi Mohamad
this is probably due to the partial
...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 11:35 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White matter volume
Hi Mohamad
this is probably due to the partial-volume correction that we typically
compute when
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 11:35 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White matter volume
Hi Mohamad
this is probably due to the partial-volume correction that we typically
Hi Gonzalo, the segmentation that you are seeing is paired with the
insula parcellation.
doug
On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote:
Hi Doug:
The command is:
mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/lobulitos.mgz --annot
don't know what's going on. Can you upload the subject to our file drop?
doug
On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote:
Hi Doug:
The command is:
mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax
Hi Douglas:
The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I
re-processed using freesurfer 5.2.0...
Sincerely,
Gonzalo Rojas Costa
On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
don't know what's going on. Can you upload the subject
colored region (red arrow)... Which
neuroanatomical area is ?...
Sincerely,
Gonzalo Rojas Costa
Message: 15
Date: Mon, 27 May 2013 22:41:41 -0400
From: Douglas Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] white matter volume per lobe...
To: freesurfer@nmr.mgh.harvard.edu
region (red arrow)... Which
neuroanatomical area is ?...
Sincerely,
Gonzalo Rojas Costa
Message: 15
Date: Mon, 27 May 2013 22:41:41 -0400
From: Douglas Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] white matter volume per lobe...
To: freesurfer@nmr.mgh.harvard.edu
Message
gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] white matter volume per lobe...
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you will need to run mri_annotation2label and specify the output
Hi Doug:
The command is:
mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200
and the terminal output is:
mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
--volmask --o
gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] white matter volume per lobe...
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you will need to run mri_annotation2label and specify the output
that you told me... But, why I get the gray
colored region (red arrow) ?...
Sincerely,
Gonzalo Rojas Costa
Message: 15
Date: Mon, 27 May 2013 22:41:41 -0400
From: Douglas Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] white matter volume per lobe...
To: freesurfer
] white matter volume per lobe...
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you will need to run mri_annotation2label and specify the output to be
an annotation file instead of a segmentation
Hi:
I used the following commands to get the cortical volume per each lobe:
mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict
lobulos --seg lobulos --stat lobulos
mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict
lobulos --seg lobulos --stat lobulos
you will need to run mri_annotation2label and specify the output to be
an annotation file instead of a segmentation. Then you will have to run
mri_aparc2aseg, specifying your lobes annotation as well as --labelwm
(look in the recon-all.log file for an example of how wmparc.mgz is
created).
...
-Ursprüngliche Mitteilung-
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: dolphinede dolphin...@aol.com; freesurfer
freesurfer@nmr.mgh.harvard.edu
Verschickt: Di, 25 Okt 2011 5:05 pm
Betreff: Re: [Freesurfer] white matter volume in a ROI
Yes, I see what you mean. mri_aparc2aseg
Verschickt: Mo, 31 Okt 2011 3:20 pm
Betreff: Re: [Freesurfer] white matter volume in a ROI
Use mri_segstats. You can look in the recon-all.log file in
subject/scripts. Find the call to mri_segstats used to generate the
wmparc stats, copy it and make the customizations you need.
doug
dolphin
-beginner...
Best regards
Daniel
-Ursprüngliche Mitteilung-
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: dolphinede dolphin...@aol.com; freesurfer
freesurfer@nmr.mgh.harvard.edu
Verschickt: Mo, 24 Okt 2011 10:04 pm
Betreff: Re: [Freesurfer] white matter volume in a ROI
Dear FreeSurfer experts,
i have created a ROI in qdec , where i have found a significant correlation
between lgi and age.
I mapped this ROI to all subjects.
I am interested to compare in this ROI the pial-surface area, the grey matter
volume and if possible the white matter volume for this
For GM area and volume, you can use mris_anatomical_stats. See the
recent thread on how. For the WM volume, how would you define the WM
volume that corresponds to you label? We have a routine that parcellates
WM based on closest proximity to a cortical label.
doug
dolphin...@aol.com wrote:
@nmr.mgh.harvard.edu
Verschickt: Mo, 24 Okt 2011 4:48 pm
Betreff: Re: [Freesurfer] white matter volume in a ROI
For GM area and volume, you can use mris_anatomical_stats. See the
recent thread on how. For the WM volume, how would you define the WM
volume that corresponds to you label? We have
Dear Freesufer experts,I would like to do the group comparison of white matter volume in various white matter regions base on white matter parcellation. I have no idea about how to do that. Is it the same as cortical thickness comparison in qdec ? could any one give some guide about how to do that
You can use the data in the wmparc.stats file. You can load that as a
spreadsheet into any stats program (eg, SPSS).
doug
t...@ms36.hinet.net wrote:
Dear Freesufer experts,
I would like to do the group comparison of white matter volume in
various white matter regions base on white matter
Dear all,
I have 4 ROIs created from a whole brain group comparison. I want to examine
the differences in white matter volume immediately beneath these rois.
Wmparc contains whitematter segmented in accordance with the inbuilt
annotations is it possible to extract wmparc info for GM rois?
Dear Freesurfers,
Is it acceptable to use the program mris_wm_volume from version 4.0.5
(Cent OS, x86_64) to calculate total white matter volume from data
processed with version 3.0.5? Would I need to subtract any subcortical
volumes such as ventricles, basal ganglia, etc, from the output of
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