Dear Doug,

Thank you for your reply!


This label on this specific case is basically the sum of the labels from 
Heschl's Gyrus, Heschl's Sulcus and Planum temporale.

The labels from Heschl's Gyrus, Heschl's Sulcus and Planum temporale are 
firstly produced inside 'Recon-all'.

The aggregation of these 3 labels is produced  by the following command line:

mri_mergelabels -i 
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/​lh.G_temp_sup-G_T_transv.label -i  
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh.G_temp_sup-Plan_tempo.label -i 
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/​lh.S_temporal_transverse.label -o 
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label

The volume calculated by 'mris_anatomical_stats' ​of the aggregated label is 
equal to the sum of the volumes from these 3 labels produced during "Recon-all'.


But the issue is these values differ from the one obtained using "mri_binarize" 
and "mri_segstats" based on the '.curv' file of the portion of surface 
(Heschl's Gyrus + Heschl's Sulcus + Planum temporale).


Best regards,

Josue


________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve 
<gr...@nmr.mgh.harvard.edu>
Sent: Friday, October 14, 2016 7:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes


How did you create the label ?

On 10/14/16 12:43 PM, Josue Luiz Dalboni Da Rocha wrote:

Dear Doug,


From the curvature file of the ROI (selected portion of surface), we extract 
the volume using this 2 command lines:

mri_binarize --i $D_load/lh_masked_all.curv --max -.0000001 --o 
$D_load/lh_masked_all_bin.mgh
mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i 
$SUBJECTS_DIR/$subj/surf/lh.volume --accumulate --sum 
$D_load/lh_masked_all_bin.txt

From the label file of the same ROI, we extract the volume using the following 
command line:
mris_anatomical_stats -l 
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label -f 
$outD/lh_masked_all_Volume $subj lh


As the '.curv' file and the '.label' file represent the same ROI, we were 
expecting to get the same volume (total gray matter volume of the selected 
portion of surface). But the results using the first method are always about 3 
time higher than using the second method.

We would like to understand what is going on, because for some selected 
portions of ROI we just have the '.curv' file to extract the volume from.

Thank you very much for your help!

​Best regards,
Josue

________________________________

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>
Sent: Friday, October 14, 2016 5:54 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Quantifying volumes


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
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> 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>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
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> http://www.partners.org/complianceline . If the e-mail was sent to you in
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