Re: [Freesurfer] white matter volume

[Douglas N. Greve]

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 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 
mailto:dgr...@mgh.harvard.edu>> wrote:


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

On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

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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Re: [Freesurfer] white matter volume

[Sara Lyn]

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 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
>
> 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 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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Re: [Freesurfer] white matter volume

[Douglas N. Greve]

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

On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


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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Re: [Freesurfer] white matter volume

[Sara Lyn]

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 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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Re: [Freesurfer] white matter volume

[Douglas N. Greve]

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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[Freesurfer] white matter volume

[Sara Lyn]

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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Re: [Freesurfer] White matter volume from aseg

[Greve, Douglas N.,Ph.D.]

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 wondering if that is the same as overall white 
> matter volume in the brain?
>
> Thank you,
>
> Ambica Mehndiratta
> Clinical Research Coordinator
> Massachusetts General Hospital
> 149 13th Street, Charlestown MA 02129
> amehndirat...@mgh.harvard.edu
> (617)-724-8823
>
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[Freesurfer] White matter volume from aseg

[Mehndiratta, Ambica]

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
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
amehndirat...@mgh.harvard.edu
(617)-724-8823
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Re: [Freesurfer] White matter volume of a costumized Gyrus

[Douglas Greve]

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 line that generated wmparc.mgz but specify your annot 
with --annot). View the label to make sure it is what you want, then run 
mri_segstats.



On 5/9/17 7:23 AM, Josue Luiz Dalboni Da Rocha wrote:


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 mris_anatomical_stats is the volume of the gray 
matter surrounding the white/gray matter border (a surface) specified 
by the inputted label.


We are actually interested in the white matter volume (instead of gray 
matter volume) inside this ROI (a gyrus in our case) specified by the 
label.


I didn't find yet a command in freesurfer from where I can extract the 
white matter volume of a gyrus from a costumized label.


Could someone advise me?


Best regards,

Josue



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Re: [Freesurfer] White matter volume of a costumized Gyrus

[Bruce Fischl]

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 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 mris_anatomical_stats is the volume of the gray matter
surrounding the white/gray matter border (a surface) specified by the
inputted label.

We are actually interested in the white matter volume (instead of gray
matter volume) inside this ROI (a gyrus in our case) specified by the label.

I didn't find yet a command in freesurfer from where I can extract the white
matter volume of a gyrus from a costumized label.

Could someone advise me?


Best regards,

Josue


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[Freesurfer] White matter volume of a costumized Gyrus

[Josue Luiz Dalboni Da Rocha]

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 mris_anatomical_stats is the volume of the gray matter 
surrounding the white/gray matter border (a surface) specified by the inputted 
label.

We are actually interested in the white matter volume (instead of gray matter 
volume) inside this ROI (a gyrus in our case) specified by the label.

I didn't find yet a command in freesurfer from where I can extract the white 
matter volume of a gyrus from a costumized label.

Could someone advise me?


Best regards,

Josue
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Re: [Freesurfer] White matter volume in each lobe

[Douglas Greve]

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 lobar_annotation

mris_anatomical_statson the  lh.lobar_annotation.annot file to 
generate a text file.


I’ve also run similar to the following and now have a text file 
wmparc.a2009.stats.


mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown

--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg 
aparc.a2009s+aseg.mgz


mri_segstats --seg mri/wmparc.a2009s.mgz --sum

stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0

--brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz

--in-intensity-name norm --in-intensity-units MR --subject subject

--surf-wm-vol

--ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv

Is there a standard list of labels in this file that are used to 
create the frontal and temporal lobes?


Thanks



The University of Aberdeen is a charity registered in Scotland, No 
SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, 
Àir. SC013683.



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[Freesurfer] White matter volume in each lobe

[Ahearn, T]

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 run similar to the following and now have a text file 
wmparc.a2009.stats.

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz

  mri_segstats --seg mri/wmparc.a2009s.mgz --sum
stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0
--brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --subject subject
--surf-wm-vol
--ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv


Is there a standard list of labels in this file that are used to create the 
frontal and temporal lobes?


Thanks




The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. 
SC013683.
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Re: [Freesurfer] White matter volume

[Douglas Greve]

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 
parcellations volume mentioned in wmparc.stats) and the vwhite matter 
volume generated by other tools like fslstats.

For example:
If I use a binarized mask from wmparc.mgz for the precentral gyrus in 
the command : fslstats -i MPRAGE.nii.gz ( reoriented and skull 
stripped) -k  -V

Then
What is the differecne between this volume generated by "fslstats" and 
the precenral gyrus volume mentioned in wmparc.stats. Which one is 
more accurate?

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 4and the white matter volume generated by other 
methods like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 
03755

Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419


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Re: [Freesurfer] White matter volume

[Bruce Fischl]

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 2015, John Anderson wrote:


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 mask from wmparc.mgz for the precentral gyrus in the
command : fslstats -i MPRAGE.nii.gz ( reoriented and skull stripped) -k
 -V 
Then
What is the differecne between this volume generated by "fslstats" and the
precenral gyrus volume mentioned in wmparc.stats. Which one is more
accurate?
 
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 4and the white matter volume generated by other methods
like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

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[Freesurfer] White matter volume

[John Anderson]

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 mask from wmparc.mgz for the precentral gyrus in the command : fslstats -i MPRAGE.nii.gz ( reoriented and skull stripped) -k  -V 

Then

What is the differecne between this volume generated by "fslstats" and the precenral gyrus volume mentioned in wmparc.stats. Which one is more accurate?

 

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 4and the white matter volume generated by other methods like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] White matter volume

[Douglas N Greve]

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 output of recon-all) and fa.stats (the output of 
 dt-recon for FA).

 In those files we have the white matter volume for many different 
 parts of the brain like the right and left cerebral white matter.

 If we check the volumes in those files we can see that we have 
 differences between the numbers and I can explain that by the 
 following: in aseg.stats the white matter volume is derived from the 
 T1 segmentation in the structural space and in fa.stats the white 
 matter volume is derived from the FA map in diffusion space and the 
 difference between the volumes is the difference between the accuracy 
 of the images in different spaces.

Almost. The value in aseg.stats is derived from the surfaces which is 
even more accurate than the 1mm space values (though they are pretty close).

 Now:

 1. If we want to study the relationship between the FA and the right 
 hemispheric white matter volume for example, we should not care about 
 the volumes in fa.stasts  because it is not accurate?!

I would use the value from the aseg.stats file. I would not say that the 
value from fa.stats is not accurate, it is just not as accurate as the 
surface-based measure.

 in this case what is the optimal and correct method in freeSurfer to 
 do such like this comparison, is it by moving the FA map to the 
 structural space by registering the FA map to T1  or by using the 
 volumes in aseg.stats and the metrics values from fa.stats? or we can 
 use the fa values and the volumes from fa.stats?

Use the value from the aseg.stats

 2.What is the exact usage for the volumes mentioned in FA.stats

They may or may not be used for anything. They are just values that are 
recorded by the program.

 3. What is the meaning and the exact usage of min-max intensity range 
 (intensity of what) in aseg.stats and fa.stats

The min is the minimum value of the intensity (norm.mgz or fa.nii) in 
the ROI, max is the maximum. Again, they may or may not be used for 
anything. They are just values that are recorded by the program.

doug


 So Sorry for this long email but as always I am looking forward to 
 learn from you

 Thanks


 Mohamad




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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Doug and Bruce.
Many thousands of thanks

Mohamad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, November 06, 2014 12:12 PM
To: freesurfer@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 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).

 In those files we have the white matter volume for many different
 parts of the brain like the right and left cerebral white matter.

 If we check the volumes in those files we can see that we have
 differences between the numbers and I can explain that by the
 following: in aseg.stats the white matter volume is derived from the
 T1 segmentation in the structural space and in fa.stats the white
 matter volume is derived from the FA map in diffusion space and the
 difference between the volumes is the difference between the accuracy
 of the images in different spaces.

Almost. The value in aseg.stats is derived from the surfaces which is
even more accurate than the 1mm space values (though they are pretty close).

 Now:

 1. If we want to study the relationship between the FA and the right
 hemispheric white matter volume for example, we should not care about
 the volumes in fa.stasts  because it is not accurate?!

I would use the value from the aseg.stats file. I would not say that the
value from fa.stats is not accurate, it is just not as accurate as the
surface-based measure.

 in this case what is the optimal and correct method in freeSurfer to
 do such like this comparison, is it by moving the FA map to the
 structural space by registering the FA map to T1  or by using the
 volumes in aseg.stats and the metrics values from fa.stats? or we can
 use the fa values and the volumes from fa.stats?

Use the value from the aseg.stats

 2.What is the exact usage for the volumes mentioned in FA.stats

They may or may not be used for anything. They are just values that are
recorded by the program.

 3. What is the meaning and the exact usage of min-max intensity range
 (intensity of what) in aseg.stats and fa.stats

The min is the minimum value of the intensity (norm.mgz or fa.nii) in
the ROI, max is the maximum. Again, they may or may not be used for
anything. They are just values that are recorded by the program.

doug


 So Sorry for this long email but as always I am looking forward to
 learn from you

 Thanks


 Mohamad




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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] White matter volume

[Alshikho, Mohamad J.]

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).
In those files we have the white matter volume for many different parts of the 
brain like the right and left cerebral white matter.
If we check the volumes in those files we can see that we have differences 
between the numbers and I can explain that by the following: in aseg.stats the 
white matter volume is derived from the T1 segmentation in the structural space 
and in fa.stats the white matter volume is derived from the FA map in diffusion 
space and the difference between the volumes is the difference between the 
accuracy of the images in different spaces.
Now:
1. If we want to study the relationship between the FA and the right 
hemispheric white matter volume for example, we should not care about the 
volumes in fa.stasts  because it is not accurate?! in this case what is the 
optimal and correct method in freeSurfer to do such like this comparison, is it 
by moving the FA map to the structural space by registering the FA map to T1  
or by using the volumes in aseg.stats and the metrics values from fa.stats? or 
we can use the fa values and the volumes from fa.stats?
2.What is the exact usage for the volumes mentioned in FA.stats
3. What is the meaning and the exact usage of min-max intensity range 
(intensity of what) in aseg.stats and fa.stats

So Sorry for this long email but as always I am looking forward to learn from 
you
Thanks

Mohamad

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[Freesurfer] White matter volume

[Alshikho, Mohamad J.]

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 of mri_binarize command line)?
I am asking this question because those masks gave me different estimation for 
the volume?

Thanks!
Mohamad
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] White matter volume

[Douglas N Greve]

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 mris_volmmask after binarize them) and the right and left 
 hemispheric white matter masks from aseg.mgz atlas (the output of 
 mri_binarize command line)?
 I am asking this question because those masks gave me different 
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Thanks Doug! 
So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of 
mris_volmask?

From: freesurfer-boun...@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
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 mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] White matter volume

[Douglas N Greve]

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 to use lh.dwhite.mgz , rh.dwhite.mgz the output of 
 mris_volmask?
 
 From: freesurfer-boun...@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
 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 mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] White matter volume

[Bruce Fischl]

Hi Mohamad

this is probably due to the partial-volume correction that we typically 
compute when we estimate volumes in the stats files.

cheers
Bruce
On Fri, 31 Oct 2014, 
Alshikho, Mohamad J. wrote:

 Thanks Doug,
 In order to improve my understanding for the analysis that I am working on 
 and in the process of my learning I am tring to calculate the volume in many 
 different ways. Actually It is very easy, simple  and possible to use the 
 numbers mentioned in aseg.stats but what if we got different results when we 
 use different methods?
 I caclated the right and left hemispheric white matter volume in FSL using a 
 mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , 
 rh.dwhite.mgz then I binarized those masks and I registered them to my T1 
 then I used the command line fslstats T1 -k my mask -V  What surprised me 
 is that the volume was totally different from the one mentioned in aseg.stats 
 (attached)

 I highly appreciate any advice.
 looking forward to learn from you
 Mohamad
 
 From: freesurfer-boun...@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 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 to use lh.dwhite.mgz , rh.dwhite.mgz the output of 
 mris_volmask?
 
 From: freesurfer-boun...@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
 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 mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Hi Bruce,
Actually I am totally confused and this is the reason for my question!
What is the best  and trusted approach in this case? 
I want to  study the relationship between the FA and the right and left 
hemispheric white matter. I generated the DTI metrics and volume using FSL. I 
am sure that the calculated white matter volume in FSL is not correct because 
it is closer to what I am thinking about. 
in this case can I use and is it valid if I use the volume from the output of 
Freesurfer  and the metrics from FSL in my analsysis?

Thanks


From: 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-volume correction that we typically
compute when we estimate volumes in the stats files.

cheers
Bruce
On Fri, 31 Oct 2014,
Alshikho, Mohamad J. wrote:

 Thanks Doug,
 In order to improve my understanding for the analysis that I am working on 
 and in the process of my learning I am tring to calculate the volume in many 
 different ways. Actually It is very easy, simple  and possible to use the 
 numbers mentioned in aseg.stats but what if we got different results when we 
 use different methods?
 I caclated the right and left hemispheric white matter volume in FSL using a 
 mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , 
 rh.dwhite.mgz then I binarized those masks and I registered them to my T1 
 then I used the command line fslstats T1 -k my mask -V  What surprised me 
 is that the volume was totally different from the one mentioned in aseg.stats 
 (attached)

 I highly appreciate any advice.
 looking forward to learn from you
 Mohamad
 
 From: freesurfer-boun...@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 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 to use lh.dwhite.mgz , rh.dwhite.mgz the output of 
 mris_volmask?
 
 From: freesurfer-boun...@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
 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 mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] White matter volume

[Bruce Fischl]

yes. Partial volume correction helps both accuracy and repeatability. You 
can certainly use our (partial-volume) corrected WM volumes and the FA 
from FSL if you want

cheers
Bruce
On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote:

 Hi Bruce,
 Actually I am totally confused and this is the reason for my question!
 What is the best  and trusted approach in this case?
 I want to  study the relationship between the FA and the right and left 
 hemispheric white matter. I generated the DTI metrics and volume using FSL. I 
 am sure that the calculated white matter volume in FSL is not correct because 
 it is closer to what I am thinking about.
 in this case can I use and is it valid if I use the volume from the output of 
 Freesurfer  and the metrics from FSL in my analsysis?

 Thanks

 
 From: 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-volume correction that we typically
 compute when we estimate volumes in the stats files.

 cheers
 Bruce
 On Fri, 31 Oct 2014,
 Alshikho, Mohamad J. wrote:

 Thanks Doug,
 In order to improve my understanding for the analysis that I am working on 
 and in the process of my learning I am tring to calculate the volume in many 
 different ways. Actually It is very easy, simple  and possible to use the 
 numbers mentioned in aseg.stats but what if we got different results when we 
 use different methods?
 I caclated the right and left hemispheric white matter volume in FSL using a 
 mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , 
 rh.dwhite.mgz then I binarized those masks and I registered them to my T1 
 then I used the command line fslstats T1 -k my mask -V  What surprised 
 me is that the volume was totally different from the one mentioned in 
 aseg.stats (attached)

 I highly appreciate any advice.
 looking forward to learn from you
 Mohamad
 
 From: freesurfer-boun...@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 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 to use lh.dwhite.mgz , rh.dwhite.mgz the output of 
 mris_volmask?
 
 From: freesurfer-boun...@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
 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 mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 ___
 Freesurfer

Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Thanks a lot!!


From: 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 11:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White matter volume

yes. Partial volume correction helps both accuracy and repeatability. You
can certainly use our (partial-volume) corrected WM volumes and the FA
from FSL if you want

cheers
Bruce
On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote:

 Hi Bruce,
 Actually I am totally confused and this is the reason for my question!
 What is the best  and trusted approach in this case?
 I want to  study the relationship between the FA and the right and left 
 hemispheric white matter. I generated the DTI metrics and volume using FSL. I 
 am sure that the calculated white matter volume in FSL is not correct because 
 it is closer to what I am thinking about.
 in this case can I use and is it valid if I use the volume from the output of 
 Freesurfer  and the metrics from FSL in my analsysis?

 Thanks

 
 From: 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-volume correction that we typically
 compute when we estimate volumes in the stats files.

 cheers
 Bruce
 On Fri, 31 Oct 2014,
 Alshikho, Mohamad J. wrote:

 Thanks Doug,
 In order to improve my understanding for the analysis that I am working on 
 and in the process of my learning I am tring to calculate the volume in many 
 different ways. Actually It is very easy, simple  and possible to use the 
 numbers mentioned in aseg.stats but what if we got different results when we 
 use different methods?
 I caclated the right and left hemispheric white matter volume in FSL using a 
 mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , 
 rh.dwhite.mgz then I binarized those masks and I registered them to my T1 
 then I used the command line fslstats T1 -k my mask -V  What surprised 
 me is that the volume was totally different from the one mentioned in 
 aseg.stats (attached)

 I highly appreciate any advice.
 looking forward to learn from you
 Mohamad
 
 From: freesurfer-boun...@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 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 to use lh.dwhite.mgz , rh.dwhite.mgz the output of 
 mris_volmask?
 
 From: freesurfer-boun...@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
 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 mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 ___
 Freesurfer mailing list
 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
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop

Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

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 lobulos --wmparc-dmax 200

 and the terminal output is:

 mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
 --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200

 SUBJECTS_DIR /usr/local/freesurfer/subjects
 subject OAS1_0001_MR1
 outvol mri/lobulitos_2.mgz
 useribbon 0
 baseoffset 0
 labeling wm
 labeling hypo-intensities as wm
 dmaxctx 200.00
 RipUnknown 1

 Reading lh white surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white

 Reading lh pial surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial

 Loading lh annotations from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
 reading colortable from annotation file...
 colortable with 8 entries read (originally none)

 Reading rh white surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white

 Reading rh pial surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial

 Loading rh annotations from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
 reading colortable from annotation file...
 colortable with 8 entries read (originally none)
 Have color table for lh white annotation
 Have color table for rh white annotation
 Loading ribbon segmentation from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
 Loading filled from 
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
 Ripping vertices labeled as unkown
 Ripped 7659 vertices from left hemi
 Ripped 7544 vertices from right hemi

 Building hash of lh white

 Building hash of lh pial

 Building hash of rh white

 Building hash of rh pial

 Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
 ASeg Vox2RAS: ---
 -1.000   0.000   0.000   128.000;
   0.000   0.000   1.000  -128.000;
   0.000  -1.000   0.000   128.000;
   0.000   0.000   0.000   1.000;
 -

 Labeling Slice
0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  
 19
   20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  
 39
   40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  
 59
   60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  
 79
   80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  
 99
 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 
 119
 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 
 139
 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 
 159
 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 
 179
 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 
 199
 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 
 219
 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 
 239
 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931
 Used brute-force search on 139 voxels
 Fixing Parahip LH WM
Found 0 clusters
 Fixing Parahip RH WM
Found 0 clusters
 Writing output aseg to mri/lobulitos_2.mgz

Sincerely,


 Gonzalo Rojas Costa


 On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:
 can you send me your full command line as well as the terminal output?

 On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:
 Hi Doug:

 But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
 200 option... I put that big value to test it, but I got the image
 that I sent you...

 Sincerely,


 Gonzalo Rojas Costa
 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl



-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

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 200

 and the terminal output is:

 mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
 --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200

 SUBJECTS_DIR /usr/local/freesurfer/subjects
 subject OAS1_0001_MR1
 outvol mri/lobulitos_2.mgz
 useribbon 0
 baseoffset 0
 labeling wm
 labeling hypo-intensities as wm
 dmaxctx 200.00
 RipUnknown 1

 Reading lh white surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white

 Reading lh pial surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial

 Loading lh annotations from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
 reading colortable from annotation file...
 colortable with 8 entries read (originally none)

 Reading rh white surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white

 Reading rh pial surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial

 Loading rh annotations from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
 reading colortable from annotation file...
 colortable with 8 entries read (originally none)
 Have color table for lh white annotation
 Have color table for rh white annotation
 Loading ribbon segmentation from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
 Loading filled from 
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
 Ripping vertices labeled as unkown
 Ripped 7659 vertices from left hemi
 Ripped 7544 vertices from right hemi

 Building hash of lh white

 Building hash of lh pial

 Building hash of rh white

 Building hash of rh pial

 Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
 ASeg Vox2RAS: ---
 -1.000   0.000   0.000   128.000;
   0.000   0.000   1.000  -128.000;
   0.000  -1.000   0.000   128.000;
   0.000   0.000   0.000   1.000;
 -

 Labeling Slice
0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  
 19
   20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  
 39
   40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  
 59
   60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  
 79
   80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  
 99
 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 
 119
 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 
 139
 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 
 159
 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 
 179
 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 
 199
 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 
 219
 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 
 239
 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931
 Used brute-force search on 139 voxels
 Fixing Parahip LH WM
Found 0 clusters
 Fixing Parahip RH WM
Found 0 clusters
 Writing output aseg to mri/lobulitos_2.mgz

Sincerely,


 Gonzalo Rojas Costa


 On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:
 can you send me your full command line as well as the terminal output?

 On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:
 Hi Doug:

 But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
 200 option... I put that big value to test it, but I got the image
 that I sent you...

 Sincerely,


 Gonzalo Rojas Costa
 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl



-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 at
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but does not contain patient information, please 

Re: [Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

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 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 200

 and the terminal output is:

 mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
 --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200

 SUBJECTS_DIR /usr/local/freesurfer/subjects
 subject OAS1_0001_MR1
 outvol mri/lobulitos_2.mgz
 useribbon 0
 baseoffset 0
 labeling wm
 labeling hypo-intensities as wm
 dmaxctx 200.00
 RipUnknown 1

 Reading lh white surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white

 Reading lh pial surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial

 Loading lh annotations from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
 reading colortable from annotation file...
 colortable with 8 entries read (originally none)

 Reading rh white surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white

 Reading rh pial surface
   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial

 Loading rh annotations from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
 reading colortable from annotation file...
 colortable with 8 entries read (originally none)
 Have color table for lh white annotation
 Have color table for rh white annotation
 Loading ribbon segmentation from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
 Loading filled from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
 Ripping vertices labeled as unkown
 Ripped 7659 vertices from left hemi
 Ripped 7544 vertices from right hemi

 Building hash of lh white

 Building hash of lh pial

 Building hash of rh white

 Building hash of rh pial

 Loading aseg from
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
 ASeg Vox2RAS: ---
 -1.000   0.000   0.000   128.000;
   0.000   0.000   1.000  -128.000;
   0.000  -1.000   0.000   128.000;
   0.000   0.000   0.000   1.000;
 -

 Labeling Slice
0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
 18  19
   20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37
 38  39
   40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57
 58  59
   60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77
 78  79
   80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97
 98  99
 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
 118 119
 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137
 138 139
 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157
 158 159
 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177
 178 179
 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197
 198 199
 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217
 218 219
 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237
 238 239
 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx =
 688931
 Used brute-force search on 139 voxels
 Fixing Parahip LH WM
Found 0 clusters
 Fixing Parahip RH WM
Found 0 clusters
 Writing output aseg to mri/lobulitos_2.mgz

Sincerely,


 Gonzalo Rojas Costa


 On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:

 can you send me your full command line as well as the terminal output?

 On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:

 Hi Doug:

 But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
 200 option... I put that big value to test it, but I got the image
 that I sent you...

 Sincerely,


 Gonzalo Rojas Costa

 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl



 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 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 at
 http://www.partners.org/complianceline . If 

Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

It is probably the region that is more than 5mm away from cortex. In the 
wmparc it should be labeled as wm-lh-unknown

doug

On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote:
 Hi Doug:

I used the instructions that you told me to get the white matter per
 each lobule... But, I got the grey 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
 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. 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). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug
 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

Hi Doug:

  But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
200 option... I put that big value to test it, but I got the image
that I sent you...

  Sincerely,


Gonzalo Rojas Costa

On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:

 It is probably the region that is more than 5mm away from cortex. In the
 wmparc it should be labeled as wm-lh-unknown

 doug


 On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote:

 Hi Doug:

I used the instructions that you told me to get the white matter per
 each lobule... But, I got the grey 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
 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. 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). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug

 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 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 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

can you send me your full command line as well as the terminal output?
On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:
 Hi Doug:

But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
 200 option... I put that big value to test it, but I got the image
 that I sent you...

Sincerely,


 Gonzalo Rojas Costa

 On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:
 It is probably the region that is more than 5mm away from cortex. In the
 wmparc it should be labeled as wm-lh-unknown

 doug


 On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote:
 Hi Doug:

 I used the instructions that you told me to get the white matter per
 each lobule... But, I got the grey 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
 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. 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). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug
 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 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 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

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 mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200

SUBJECTS_DIR /usr/local/freesurfer/subjects
subject OAS1_0001_MR1
outvol mri/lobulitos_2.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 200.00
RipUnknown 1

Reading lh white surface
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white

Reading lh pial surface
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial

Loading lh annotations from
/usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
reading colortable from annotation file...
colortable with 8 entries read (originally none)

Reading rh white surface
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white

Reading rh pial surface
 /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial

Loading rh annotations from
/usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
reading colortable from annotation file...
colortable with 8 entries read (originally none)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from
/usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
Loading filled from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 7659 vertices from left hemi
Ripped 7544 vertices from right hemi

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
ASeg Vox2RAS: ---
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931
Used brute-force search on 139 voxels
Fixing Parahip LH WM
  Found 0 clusters
Fixing Parahip RH WM
  Found 0 clusters
Writing output aseg to mri/lobulitos_2.mgz

  Sincerely,


Gonzalo Rojas Costa


On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 can you send me your full command line as well as the terminal output?

 On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:

 Hi Doug:

But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
 200 option... I put that big value to test it, but I got the image
 that I sent you...

Sincerely,


 Gonzalo Rojas Costa

--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

what is is labled?
On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:
 Hi Doug:

I use the instructions 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@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. 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). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug
 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

Hi Doug:

  It is labeled as wm-rh-fusiform and wm-lh-fusiform

  Sincerely,



Gonzalo Rojas Costa

On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 what is is labled?

 On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:

 Hi Doug:

I use the instructions 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@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. 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). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug

 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 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 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

You will need to create a new color table. It is currently referencing 
FreeSurferColorLUT.txt. If you load the segmentation as both a 
segmentation and the aux volume, you can see the number associated with 
the color. You will need to create a table similar to FreeSurferColorLUT.txt
doug




On 05/28/2013 01:51 PM, Gonzalo Rojas Costa wrote:
 Hi Doug:

It is labeled as wm-rh-fusiform and wm-lh-fusiform

Sincerely,



 Gonzalo Rojas Costa

 On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:
 what is is labled?

 On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:
 Hi Doug:

 I use the instructions 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@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. 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). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug
 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 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 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

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
mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh
mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh

  Which commands (sintaxis) must I use to compute the white matter
volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats
commans with different options, but I couldn't get the volume that I
need...

  Sincerely,


--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] white matter volume per lobe...

[Douglas Greve]

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). Then run mri_segstats (you can also get an example from the 
recon-all.log file).
doug


On 5/27/13 5:53 PM, Gonzalo Rojas Costa wrote:
 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
 mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 
 rh
 mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 
 lh

Which commands (sintaxis) must I use to compute the white matter
 volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats
 commans with different options, but I couldn't get the volume that I
 need...

Sincerely,


 --
 Gonzalo Rojas Costa
 Laboratory for Advanced Medical Image Processing
 Department of Radiology
 Clínica las Condes
 Lo Fontecilla 441, Las Condes, Santiago, Chile.
 Tel: 56-2-2105170
 Cel: 56-9-97771785
 www.clc.cl

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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Freesurfer@nmr.mgh.harvard.edu
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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 at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

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...@aol.com wrote:
 Hi Doug,

 to get the white matter volume of my ROI-label, i have done the 
 following steps:

 1. mris_label2annot
 (mris_label2annot --s ZPN20 --h lh --ctab 
  /Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a 
  myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh)


 2. mri_aparc2aseg, with my real ROI label and  a dumy label for the 
 other hemisphere.

 mri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown 
 --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/

 How do i get from the wmparc.mgz the white matter volume for my ROI 
 label/myaparc ?
 Should i use mris_wm_volume?

 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: Di, 25 Okt 2011 5:05 pm
 Betreff: Re: [Freesurfer] white matter volume in a ROI


 Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both 
 hemis. The easiest way around it is just to create a dummy label for the 
 right hemisphere.
 doug

 dolphin...@aol.com mailto:dolphin...@aol.com wrote:
  Hi Doug,
 
  thanks a lot your advice.
 
  I created an annnotation of my ROI-label as called 
  lh.cluster1.labe.label with the command line:
 
  /mris_label2annot --s ZPN20 --h lh --ctab 
  //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a 
  myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh
 
  This works fine. After that i have used your commmand in this way:
 
  m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown 
  --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/
 
  and i get the following error, which is cause that i have no 
  lh.cluster1.labe.label in the right hemisphere:
 
  /Loading lh annotations from 
  /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot
  reading colortable from annotation file...
  colortable with 36 entries read (originally 
  //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab)
 
  Reading rh white surface
   /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white
 
  Reading rh pial surface
   /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial
 
  Loading rh annotations from 
  /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
  could not read annot file 
  /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
  No such file or directory
  ERROR: MRISreadAnnotation() failed 
  /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/
 
  The question i have is if all these steps are right and/if i have to 
  do some more steps to get white matter volume of my annotation and 
  where i can find it?
 
  Excuse my numerous questions but I am just a freesurfer-beginner...
 
  Best regards
 
  Daniel
 
 
 
 
 
 
 
 
 
  -Ursprüngliche Mitteilung-
  Von: Douglas N Greve gr...@nmr.mgh.harvard.edu 
  mailto:gr...@nmr.mgh.harvard.edu
  An: dolphinede dolphin...@aol.com mailto:dolphin...@aol.com; freesurfer 
  freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
  Verschickt: Mo, 24 Okt 2011 10:04 pm
  Betreff: Re: [Freesurfer] white matter volume in a ROI
 
  It will be more involved than that. You will need to create an 
  annotation that contains your label (maybe in addition to other labels), 
  then uses mri_aparc2aseg with the --labelwm option, something like
 
  mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown 
  --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot
 
  doug
 
  dolphin...@aol.com mailto:dolphin...@aol.com mailto:dolphin...@aol.com 
  mailto:dolphin...@aol.com? wrote:
   Hi Doug,
  
   thanks a lot for your answer.
  
   So i understand you right that i can get exact knowledge about the 
   thickness, grey matter volume and pial surface area in my ROI, but in 
   case of the ROI white matter volume, i have to look to which 
   cortical label my ROI counts and then I use the wmparc.files for this 
   label?
  
   Best regards
  
   Daniel Klein
  
  
  

  
  
  
  
  
   -Ursprüngliche Mitteilung-
   Von: Douglas N Greve gr...@nmr.mgh.harvard.edu 
   mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
   mailto:gr...@nmr.mgh.harvard.edu?
   An: dolphinede dolphin...@aol.com mailto:dolphin...@aol.com 
   mailto:dolphin...@aol.com mailto:dolphin...@aol.com?
   Cc: freesurfer freesurfer@nmr.mgh.harvard.edu 
   mailto:freesurfer@nmr.mgh.harvard.edu 
   mailto:freesurfer@nmr.mgh.harvard.edu 
   mailto:freesurfer@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

Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

Your ROI must be listed in the color table, so you'll need to create a 
custom color table. For this you will need the ID eventually assigned to 
your ROI. To find this out, load the wmparc your created in tkmedit as 
both a segmentation and as the aux volume. When you click on your ROI, 
the tkmedit control window should show the name of your ROI. The aux 
field will show a value. This is the value you need.
doug

dolphin...@aol.com wrote:
 Hi Doug,

 thanks a lot for your reply.

 I have run the following command to get wm volume stats of my ROI:


 mri_segstats --seg 
 /Users/dolphinede/Desktop/Probanden/ARS23/mri/wmparc.mgz --sum 
 /Users/dolphinede/Desktop/Probanden/ARS23/stats/wmparc.stats --pv 
 /Users/dolphinede/Desktop/Probanden/ARS23/mri/norm.mgz --excludeid 0 
 --brain-vol-from-seg --brainmask 
 /Users/dolphinede/Desktop/Probanden/ARS23/mri/brainmask.mgz --in 
 /Users/dolphinede/Desktop/Probanden/ARS23/mri/norm.mgz 
 --in-intensity-name norm --in-intensity-units MR --etiv --subject 
 ARS23 --surf-wm-vol --ctab 
 /Applications/freesurfer//FreeSurferColorLUT.txt

 But I think it is not right cause my ROI, my annotation is not listed 
 there in the wmparc.stats. I thought that with my annotation i did 
 modify my wmparc.mgz and this yields to a new wmparc.stats.


 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, 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...@aol.com mailto:dolphin...@aol.com wrote:
  Hi Doug,
 
  to get the white matter volume of my ROI-label, i have done the 
  following steps:
 
  1. mris_label2annot
  (mris_label2annot --s ZPN20 --h lh --ctab 
   /Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a 
   myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh)
 
 
  2. mri_aparc2aseg, with my real ROI label and  a dumy label for the 
  other hemisphere.
 
  mri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown 
  --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/
 
  How do i get from the wmparc.mgz the white matter volume for my ROI 
  label/myaparc ?
  Should i use mris_wm_volume?
 
  Best regards
 
  Daniel...
 
 
 
   
 
  -Ursprüngliche Mitteilung-
  Von: Douglas N Greve gr...@nmr.mgh.harvard.edu 
  mailto:gr...@nmr.mgh.harvard.edu
  An: dolphinede dolphin...@aol.com mailto:dolphin...@aol.com; freesurfer 
  freesurfer@nmr.mgh.harvard.edu mailto: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 is hard coded to accept both 
  hemis. The easiest way around it is just to create a dummy label for the 
  right hemisphere.
  doug
 
  dolphin...@aol.com mailto:dolphin...@aol.com mailto:dolphin...@aol.com 
  mailto:dolphin...@aol.com? wrote:
   Hi Doug,
  
   thanks a lot your advice.
  
   I created an annnotation of my ROI-label as called 
   lh.cluster1.labe.label with the command line:
  
   /mris_label2annot --s ZPN20 --h lh --ctab 
   //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a 
   myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh
  
   This works fine. After that i have used your commmand in this way:
  
   m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown 
   --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/
  
   and i get the following error, which is cause that i have no 
   lh.cluster1.labe.label in the right hemisphere:
  
   /Loading lh annotations from 
   /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot
   reading colortable from annotation file...
   colortable with 36 entries read (originally 
   //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab)
  
   Reading rh white surface
/Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white
  
   Reading rh pial surface
/Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial
  
   Loading rh annotations from 
   /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
   could not read annot file 
   /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
   No such file or directory
   ERROR: MRISreadAnnotation() failed 
   /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/
  
   The question i have is if all these steps are right and/if i have to 
   do some more steps to get white matter volume of my annotation and 
   where i can find it?
  
   Excuse my numerous questions but I am just a freesurfer-beginner...
  
   Best regards
  
   Daniel
  
  
  
  
  
  
  
  
  
   -Ursprüngliche Mitteilung-
   Von

Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both 
hemis. The easiest way around it is just to create a dummy label for the 
right hemisphere.
doug

dolphin...@aol.com wrote:
 Hi Doug,

 thanks a lot your advice.

 I created an annnotation of my ROI-label as called 
 lh.cluster1.labe.label with the command line:

 /mris_label2annot --s ZPN20 --h lh --ctab 
 //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a 
 myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh

 This works fine. After that i have used your commmand in this way:

 m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown 
 --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/

 and i get the following error, which is cause that i have no 
 lh.cluster1.labe.label in the right hemisphere:

 /Loading lh annotations from 
 /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot
 reading colortable from annotation file...
 colortable with 36 entries read (originally 
 //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab)

 Reading rh white surface
  /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white

 Reading rh pial surface
  /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial

 Loading rh annotations from 
 /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
 could not read annot file 
 /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
 No such file or directory
 ERROR: MRISreadAnnotation() failed 
 /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/

 The question i have is if all these steps are right and/if i have to 
 do some more steps to get white matter volume of my annotation and 
 where i can find it?

 Excuse my numerous questions but I am just a freesurfer-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

 It will be more involved than that. You will need to create an 
 annotation that contains your label (maybe in addition to other labels), 
 then uses mri_aparc2aseg with the --labelwm option, something like

 mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown 
 --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot

 doug

 dolphin...@aol.com mailto:dolphin...@aol.com wrote:
  Hi Doug,
 
  thanks a lot for your answer.
 
  So i understand you right that i can get exact knowledge about the 
  thickness, grey matter volume and pial surface area in my ROI, but in 
  case of the ROI white matter volume, i have to look to which 
  cortical label my ROI counts and then I use the wmparc.files for this 
  label?
 
  Best regards
 
  Daniel Klein
 
 
 
   
 
 
 
 
 
  -Ursprüngliche Mitteilung-
  Von: Douglas N Greve gr...@nmr.mgh.harvard.edu 
  mailto:gr...@nmr.mgh.harvard.edu
  An: dolphinede dolphin...@aol.com mailto:dolphin...@aol.com
  Cc: freesurfer freesurfer@nmr.mgh.harvard.edu 
  mailto:freesurfer@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 a routine that parcellates 
  WM based on closest proximity to a cortical label.
  doug
 
  dolphin...@aol.com mailto:dolphin...@aol.com wrote:
   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 
   specific region and i am not sure how to do this?
  
   Best regards
  
   Daniel Klein
   
  
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   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 mailto:gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358 
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
  http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 
 
 
  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 
 at
  http://www.partners.org/complianceline . If the e-mail was sent to you

[Freesurfer] white matter volume in a ROI

[dolphinede]

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 specific region and i 
am not sure how to do this?

Best regards 

Daniel Klein
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Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

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:
 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 
 specific region and i am not sure how to do this?

 Best regards

 Daniel Klein
 

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Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

It will be more involved than that. You will need to create an 
annotation that contains your label (maybe in addition to other labels), 
then uses mri_aparc2aseg with the --labelwm option, something like

mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown 
--volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot

doug

dolphin...@aol.com wrote:
 Hi Doug,

 thanks a lot for your answer.

 So i understand you right that i can get exact knowledge about the 
 thickness, grey matter volume and pial surface area in my ROI, but in 
 case of the ROI white matter volume, i have to look to which 
 cortical label my ROI counts and then I use the wmparc.files for this 
 label?

 Best regards

 Daniel Klein



  





 -Ursprüngliche Mitteilung-
 Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
 An: dolphinede dolphin...@aol.com
 Cc: freesurfer freesurfer@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 a routine that parcellates 
 WM based on closest proximity to a cortical label.
 doug

 dolphin...@aol.com wrote:
  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 
  specific region and i am not sure how to do this?
 
  Best regards
 
  Daniel Klein
  
 
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 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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 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 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] white matter volume and qdec

[tulu]

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 ? thank in advancebestJLH--- 本郵件來自HiNet WebMail ---___
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Re: [Freesurfer] white matter volume and qdec

[Douglas N Greve]

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 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 ? thank in advance
 best
 JLH


 --- 本郵件來自HiNet WebMail ---
 

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] White matter volume corresponding to a surface ROI

[Lena Palaniyappan]

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?

Cheers
Lena
___
Lena Palaniyappan 
PhD Student  Honorary StR | Division of Psychiatry ( University of
Nottingham) 
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH


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[Freesurfer] white matter volume - version 3.0.5 vs 4.0.5

[Paul Greenberg]

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 
mris_wm_volume (version 4.0.5) in order to get the most accurate 
measurement of total white matter volume?


Thanks!
Paul

--

Paul Greenberg, Ph.D.
Radiology Department, University of California, San Diego
VA San Diego Healthcare System (116A-13)
3350 La Jolla Village Drive
San Diego, CA  92161
Phone: (858) 552-8585 ext. 2903
Fax:  (858) 642-3836
[EMAIL PROTECTED] 


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