[Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Glen Lee]

Dear freesurfer users

I'm wondering if there is any way of figuring out the surface size within a
mask image (mask.mgh)
which is generated after running a group-level GLM analysis (2nd RFX) using
mri_glmfit.

As I'm thinking, this may be:
  number of vertex by dimension of one vertex (1mm).

But I could be wrong and let me know if anyone knows the solution.

-Glen

fyi) the group analysis was performed in freesurfer sym space.
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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Douglas N Greve]

Hi Glen, you can use

mri_segstats --seg mask.mgh --id 1 --i 
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat

doug


On 06/10/2013 03:17 PM, Glen Lee wrote:
> Dear freesurfer users
>
> I'm wondering if there is any way of figuring out the surface size 
> within a mask image (mask.mgh)
> which is generated after running a group-level GLM analysis (2nd RFX) 
> using mri_glmfit.
>
> As I'm thinking, this may be:
>   number of vertex by dimension of one vertex (1mm).
>
> But I could be wrong and let me know if anyone knows the solution.
>
> -Glen
>
> fyi) the group analysis was performed in freesurfer sym space.
>
>
>
> ___
> 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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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Glen Lee]

Thanks Doug!

I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
ERROR: Option --o unknown

I don't see --o option when I looked up mri_segstats --help either. FYI,
I'm using v5.1.
Any idea?



On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve
wrote:

>
> Hi Glen, you can use
>
> mri_segstats --seg mask.mgh --id 1 --i
> $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat
>
> doug
>
>
> On 06/10/2013 03:17 PM, Glen Lee wrote:
> > Dear freesurfer users
> >
> > I'm wondering if there is any way of figuring out the surface size
> > within a mask image (mask.mgh)
> > which is generated after running a group-level GLM analysis (2nd RFX)
> > using mri_glmfit.
> >
> > As I'm thinking, this may be:
> >   number of vertex by dimension of one vertex (1mm).
> >
> > But I could be wrong and let me know if anyone knows the solution.
> >
> > -Glen
> >
> > fyi) the group analysis was performed in freesurfer sym space.
> >
> >
> >
> > ___
> > 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
>
>
> 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.
>
>
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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Douglas Greve]

It's --sum for this, not --o
doug

On 6/10/13 4:44 PM, Glen Lee wrote:

Thanks Doug!

I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i 
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat

ERROR: Option --o unknown

I don't see --o option when I looked up mri_segstats --help either. 
FYI, I'm using v5.1.

Any idea?



On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



Hi Glen, you can use

mri_segstats --seg mask.mgh --id 1 --i
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat

doug


On 06/10/2013 03:17 PM, Glen Lee wrote:
> Dear freesurfer users
>
> I'm wondering if there is any way of figuring out the surface size
> within a mask image (mask.mgh)
> which is generated after running a group-level GLM analysis (2nd
RFX)
> using mri_glmfit.
>
> As I'm thinking, this may be:
>   number of vertex by dimension of one vertex (1mm).
>
> But I could be wrong and let me know if anyone knows the solution.
>
> -Glen
>
> fyi) the group analysis was performed in freesurfer sym space.
>
>
>
> ___
> 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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The information in this e-mail is intended only for the person to
whom it is
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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.




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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Glen Lee]

thanks Doug.
it worked and I got the following result on which I have clarifying
questions:

--
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0 1   81837  81837


1) I'm assuming that voxel here refers to vertex since I'm submitting the
surface data.

2) what does 'found 1 segmentations mean'?

3) the dimension is 81837mm^2, correct?




On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve
wrote:

>  It's --sum for this, not --o
> doug
>
>
> On 6/10/13 4:44 PM, Glen Lee wrote:
>
>  Thanks Doug!
>
>  I just tried, but I got an error:
> mri_segstats --seg mask.mgh --id 1 --i
> /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
>   ERROR: Option --o unknown
>
>  I don't see --o option when I looked up mri_segstats --help either. FYI,
> I'm using v5.1.
> Any idea?
>
>
>
> On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Hi Glen, you can use
>>
>> mri_segstats --seg mask.mgh --id 1 --i
>> $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat
>>
>> doug
>>
>>
>> On 06/10/2013 03:17 PM, Glen Lee wrote:
>> > Dear freesurfer users
>> >
>> > I'm wondering if there is any way of figuring out the surface size
>> > within a mask image (mask.mgh)
>> > which is generated after running a group-level GLM analysis (2nd RFX)
>> > using mri_glmfit.
>> >
>> > As I'm thinking, this may be:
>> >   number of vertex by dimension of one vertex (1mm).
>> >
>> > But I could be wrong and let me know if anyone knows the solution.
>> >
>> > -Glen
>> >
>> > fyi) the group analysis was performed in freesurfer sym space.
>> >
>> >
>> >
>>  > ___
>> > 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
>>
>>
>> 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.
>>
>>
>
>
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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Douglas Greve]

what is your full command line?

On 6/11/13 10:04 AM, Glen Lee wrote:

thanks Doug.
it worked and I got the following result on which I have clarifying 
questions:


--
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0 1   81837  81837


1) I'm assuming that voxel here refers to vertex since I'm submitting 
the surface data.


2) what does 'found 1 segmentations mean'?

3) the dimension is 81837mm^2, correct?




On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


It's --sum for this, not --o
doug


On 6/10/13 4:44 PM, Glen Lee wrote:

Thanks Doug!

I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
ERROR: Option --o unknown

I don't see --o option when I looked up mri_segstats --help
either. FYI, I'm using v5.1.
Any idea?



On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Hi Glen, you can use

mri_segstats --seg mask.mgh --id 1 --i
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat

doug


On 06/10/2013 03:17 PM, Glen Lee wrote:
> Dear freesurfer users
>
> I'm wondering if there is any way of figuring out the
surface size
> within a mask image (mask.mgh)
> which is generated after running a group-level GLM analysis
(2nd RFX)
> using mri_glmfit.
>
> As I'm thinking, this may be:
>   number of vertex by dimension of one vertex (1mm).
>
> But I could be wrong and let me know if anyone knows the
solution.
>
> -Glen
>
> fyi) the group analysis was performed in freesurfer sym space.
>
>
>
> ___
> 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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person to whom it is
addressed. If you believe this e-mail was sent to you in
error and the e-mail
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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Glen Lee]

mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat


On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve
wrote:

>  what is your full command line?
>
>
> On 6/11/13 10:04 AM, Glen Lee wrote:
>
> thanks Doug.
> it worked and I got the following result on which I have clarifying
> questions:
>
>  --
>  Voxel Volume is 1 mm^3
> Generating list of segmentation ids
> Found   1 segmentations
> Computing statistics for each segmentation
>   0 1   81837  81837
>  
>
>  1) I'm assuming that voxel here refers to vertex since I'm submitting
> the surface data.
>
>  2) what does 'found 1 segmentations mean'?
>
>  3) the dimension is 81837mm^2, correct?
>
>
>
>
>  On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>  It's --sum for this, not --o
>> doug
>>
>>
>> On 6/10/13 4:44 PM, Glen Lee wrote:
>>
>>  Thanks Doug!
>>
>>  I just tried, but I got an error:
>> mri_segstats --seg mask.mgh --id 1 --i
>> /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
>>   ERROR: Option --o unknown
>>
>>  I don't see --o option when I looked up mri_segstats --help either.
>> FYI, I'm using v5.1.
>> Any idea?
>>
>>
>>
>> On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Glen, you can use
>>>
>>> mri_segstats --seg mask.mgh --id 1 --i
>>> $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat
>>>
>>> doug
>>>
>>>
>>> On 06/10/2013 03:17 PM, Glen Lee wrote:
>>> > Dear freesurfer users
>>> >
>>> > I'm wondering if there is any way of figuring out the surface size
>>> > within a mask image (mask.mgh)
>>> > which is generated after running a group-level GLM analysis (2nd RFX)
>>> > using mri_glmfit.
>>> >
>>> > As I'm thinking, this may be:
>>> >   number of vertex by dimension of one vertex (1mm).
>>> >
>>> > But I could be wrong and let me know if anyone knows the solution.
>>> >
>>> > -Glen
>>> >
>>> > fyi) the group analysis was performed in freesurfer sym space.
>>> >
>>> >
>>> >
>>>  > ___
>>> > 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
>>>
>>>
>>> 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.
>>>
>>>
>>
>>
>
>
___
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Glen Lee]

Hi Doug --
I copied and pasted the summary file below.
It looks like mask.mgh was treated as volumetric image.
Also I'm not sure how to interpret TableCol.



# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
# cmdline mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat
# sysname  Linux
# hostname rage.uphs.upenn.edu
# machine  x86_64
# user gel
# anatomy_type volume
#
# SegVolFile mask.mgh
# SegVolFileTimeStamp  2013/06/05 14:50:24
# InVolFile  /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area
# InVolFileTimeStamp  2013/05/22 16:49:43
# InVolFrame 0
# Only reporting non-empty segmentations
# VoxelVolume_mm3 1
# TableCol  1 ColHeader Index
# TableCol  1 FieldName Index
# TableCol  1 Units NA
# TableCol  2 ColHeader SegId
# TableCol  2 FieldName Segmentation Id
# TableCol  2 Units NA
# TableCol  3 ColHeader NVoxels
# TableCol  3 FieldName Number of Voxels
# TableCol  3 Units unitless
# TableCol  4 ColHeader Volume_mm3
# TableCol  4 FieldName Volume
# TableCol  4 Units mm^3
# TableCol  5 ColHeader Mean
# TableCol  5 FieldName Intensity Mean
# TableCol  5 Units unknown
# TableCol  6 ColHeader StdDev
# TableCol  6 FieldName Itensity StdDev
# TableCol  6 Units unknown
# TableCol  7 ColHeader Min
# TableCol  7 FieldName Intensity Min
# TableCol  7 Units unknown
# TableCol  8 ColHeader Max
# TableCol  8 FieldName Intensity Max
# TableCol  8 Units unknown
# TableCol  9 ColHeader Range
# TableCol  9 FieldName Intensity Range
# TableCol  9 Units unknown
# NRows 1
# NTableCols 9
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
  1   1 8183781837.0  Seg0001 0.3836 0. 0.1297
1.1861 1.0563


On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve  wrote:

> Did you look in the summary file? If you have questions about that, can
> you send it?
> doug
>
>
> On 06/11/2013 11:34 AM, Glen Lee wrote:
>
>> mri_segstats --seg mask.mgh --id 1 --i 
>> /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area
>> --sum sum.dat
>>
>>
>> On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> what is your full command line?
>>
>>
>> On 6/11/13 10:04 AM, Glen Lee wrote:
>>
>>> thanks Doug.
>>> it worked and I got the following result on which I have
>>> clarifying questions:
>>>
>>> --
>>> Voxel Volume is 1 mm^3
>>> Generating list of segmentation ids
>>> Found   1 segmentations
>>> Computing statistics for each segmentation
>>>   0 1 81837 81837 
>>>
>>> 
>>>
>>> 1) I'm assuming that voxel here refers to vertex since I'm
>>> submitting the surface data.
>>>
>>> 2) what does 'found 1 segmentations mean'?
>>>
>>> 3) the dimension is 81837mm^2, correct?
>>>
>>>
>>>
>>>
>>> On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve
>>> >> >
>>> wrote:
>>>
>>> It's --sum for this, not --o
>>> doug
>>>
>>>
>>> On 6/10/13 4:44 PM, Glen Lee wrote:
>>>
 Thanks Doug!

 I just tried, but I got an error:
 mri_segstats --seg mask.mgh --id 1 --i
 /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --o sum.dat
 ERROR: Option --o unknown

 I don't see --o option when I looked up mri_segstats --help
 either. FYI, I'm using v5.1.
 Any idea?



 On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve
 >>> >
 wrote:


 Hi Glen, you can use

 mri_segstats --seg mask.mgh --id 1 --i
 $SUBJECTS_DIR/fsaverage_sym/**surf/lh.area --o sum.dat

 doug


 On 06/10/2013 03:17 PM, Glen Lee wrote:
 > Dear freesurfer users
 >
 > I'm wondering if there is any way of figuring out the
 surface size
 > within a mask image (mask.mgh)
 > which is generated after running a group-level GLM
 analysis (2nd RFX)
 > using mri_glmfit.
 >
 > As I'm thinking, this may be:
 >   number of vertex by dimension of one vertex (1mm).
 >
 > But I could be wrong and let me know if anyone knows
 the solution.
 >
 > -Glen
 >
 > fyi) the group analysis was performed in freesurfer
 sym space.
 >
 >
 >
 > __**_
 > Freesurfer mailing list
  

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Glen Lee]

Got it.
Thanks for the prompt answer!
By the way, I tried mri_segstats with --accumulate flag, but it says option
'--accumulate' is unknown.
I don't seem to find it when I looked up mri_segstas --help either.



On Tue, Jun 11, 2013 at 5:05 PM, Douglas N Greve
wrote:

>
> Right, so in this case, the "NVoxels" column is the number of vertices,
> the "Mean" column is the average surface area of the vertices in the mask.
> You can force it to compute the total surface area by adding the
> --accumulate flag. Or you can multiple the mean by the number of vertices.
> doug
>
>
>
> On 06/11/2013 04:55 PM, Glen Lee wrote:
>
>> Hi Doug --
>> I copied and pasted the summary file below.
>> It looks like mask.mgh was treated as volumetric image.
>> Also I'm not sure how to interpret TableCol.
>>
>>
>>
>> # Title Segmentation Statistics
>> #
>> # generating_program mri_segstats
>> # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks
>> Exp $
>> # cmdline mri_segstats --seg mask.mgh --id 1 --i
>> /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat
>> # sysname  Linux
>> # hostname rage.uphs.upenn.edu 
>>
>> # machine  x86_64
>> # user gel
>> # anatomy_type volume
>> #
>> # SegVolFile mask.mgh
>> # SegVolFileTimeStamp  2013/06/05 14:50:24
>> # InVolFile  /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area
>> # InVolFileTimeStamp  2013/05/22 16:49:43
>> # InVolFrame 0
>> # Only reporting non-empty segmentations
>> # VoxelVolume_mm3 1
>> # TableCol  1 ColHeader Index
>> # TableCol  1 FieldName Index
>> # TableCol  1 Units NA
>> # TableCol  2 ColHeader SegId
>> # TableCol  2 FieldName Segmentation Id
>> # TableCol  2 Units NA
>> # TableCol  3 ColHeader NVoxels
>> # TableCol  3 FieldName Number of Voxels
>> # TableCol  3 Units unitless
>> # TableCol  4 ColHeader Volume_mm3
>> # TableCol  4 FieldName Volume
>> # TableCol  4 Units mm^3
>> # TableCol  5 ColHeader Mean
>> # TableCol  5 FieldName Intensity Mean
>> # TableCol  5 Units unknown
>> # TableCol  6 ColHeader StdDev
>> # TableCol  6 FieldName Itensity StdDev
>> # TableCol  6 Units unknown
>> # TableCol  7 ColHeader Min
>> # TableCol  7 FieldName Intensity Min
>> # TableCol  7 Units unknown
>> # TableCol  8 ColHeader Max
>> # TableCol  8 FieldName Intensity Max
>> # TableCol  8 Units unknown
>> # TableCol  9 ColHeader Range
>> # TableCol  9 FieldName Intensity Range
>> # TableCol  9 Units unknown
>> # NRows 1
>> # NTableCols 9
>> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min
>> Max Range
>>   1   1 8183781837.0  Seg0001 0.3836 0. 0.1297
>>   1.1861 1.0563
>>
>>
>> On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> Did you look in the summary file? If you have questions about
>> that, can you send it?
>> doug
>>
>>
>> On 06/11/2013 11:34 AM, Glen Lee wrote:
>>
>> mri_segstats --seg mask.mgh --id 1 --i
>> /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat
>>
>>
>> On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve
>> > > >
>> >
>> >>
>> wrote:
>>
>> what is your full command line?
>>
>>
>> On 6/11/13 10:04 AM, Glen Lee wrote:
>>
>> thanks Doug.
>> it worked and I got the following result on which I have
>> clarifying questions:
>>
>> --
>> Voxel Volume is 1 mm^3
>> Generating list of segmentation ids
>> Found   1 segmentations
>> Computing statistics for each segmentation
>>   0 1 81837 81837 
>>
>> 
>>
>> 
>>
>> 1) I'm assuming that voxel here refers to vertex since I'm
>> submitting the surface data.
>>
>> 2) what does 'found 1 segmentations mean'?
>>
>> 3) the dimension is 81837mm^2, correct?
>>
>>
>>
>>
>> On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve
>> > > >
>> >
>> >>
>> wrote:
>>
>> It's --sum for this, not --o
>> doug
>>
>>
>> On 6/10/13 4:44 PM, Glen Lee wrote:
>>
>> Thanks Doug!
>>
>> I just tried, but I got an error:
>> mri_segstats --seg mask.mgh --id 1 --i
>> /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area
>> --o sum.dat
>> ERROR: Option --o unknown
>>
>> I don't see --o o