please send command lines
On 10/14/16 6:36 AM, Damien MARIE wrote:
Hi,
Just adding a word about the e-mail of ma colleague Josue. What he
meant is that he extracted volumes for exactly the same ROI (a merging
of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum
temporale) using 1- a .curv file of this ROI, mri_binarize and
mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats.
We get a different volume output (ratio of difference between the 2
methods = approx. 2.5, similar to mean thickness I would say…), so we
would like to understand what is happening exactly.
Using the method 1, it’s actually a surface measurement we get no?
Would that be possible to convert a .cuvr file to a .label file ?
Thank you and best,
Damien
Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700
Dear Doug,
Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded
ROI" using
your recommended command lines (mri_binarize and mri_segstats ), but
unfortunately the results are much smaller (around 3 times) than when we
extract total gray matter volumes from a respective ".label file
encoded ROI"
using mris_anatomical_stats .
Example:
Volumes from a ".curv file encoded ROI" using your recommended command
lines
(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI"
(mris_anatomical_stats):
Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491
Are the volumes extracted from a ".curv file encoded ROI" (using
mri_binarize
and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?
Thank you very much,
Josue Dalboni
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu>>
on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu>>
Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Quantifying volumes
I would binarize the curv file with
mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o
lh.yourcurvfilebin.mgh
Then compute the volume with
mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum
On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information inside an
> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
<http://nmr.mgh.harvard.edu>
> <freesurfer-boun...@nmr.mgh.harvard.edu
<http://nmr.mgh.harvard.edu>> on behalf of Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu>>
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
> On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
>> Dear Douglas,
>>
>>
>> I have a segmented gyrus curvature file (.curv or .w) and I would like
>> to calculate the volume (and other statistics) of this gyrus.
>>
>>
>> I currently only know mris_anatomical_stats to perform that, but
>> requiring a '.label' file.
>>
>>
>> Can I extract statistics directly from the ".curv" file?
>>
>>
>> Or can I convert directly from .curv to .label in order to extract
>> these statistics?
>>
>>
>> As another option, is it feasible to convert the '.curv' file to nifti
>> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to
>> label (mri_cor2label)?
>>
>>
>> What does the output nifti file from 'mri_surf2vol' contain? Does it
>> contain the complete volume behind the surface? Or does it only
>> contain the surface over the 3D space?
>>
>>
>> Thank you very much in advance for your help!
>>
>>
>> Best regards,
>>
>> Josue
>>
>>
>>
>> _______________________________________________
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu>
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> Fax: 617-726-7422
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