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.
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
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 greve@nmr.mgh.harvard.eduwrote:
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 greve@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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 greve@nmr.mgh.harvard.eduwrote:
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 < greve@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 greve@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.
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
- I'm assuming that voxel here refers to vertex since I'm submitting
the surface data.
what does 'found 1 segmentations mean'?
the dimension is 81837mm^2, correct?
On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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 greve@nmr.mgh.harvard.eduwrote:
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
- I'm assuming that voxel here refers to vertex since I'm submitting
the surface data.
what does 'found 1 segmentations mean'?
the dimension is 81837mm^2, correct?
On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve < greve@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 < greve@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 greve@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <tel:1%20%C2%A0%2081837%20%C2%A081837> ---------------- 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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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 81837 81837.0 Seg0001 0.3836 0.1111 0.1297 1.1861 1.0563
On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve <greve@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 < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 <tel:1%20%C2%A0%2081837%20%C2%**A081837> ---------------- 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@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 <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 http://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 81837 81837.0 Seg0001 0.3836 0.1111 0.1297 1.1861 1.0563
On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <tel:1%2081837%20%2081837> <tel:1%20%C2%A0%2081837%20%C2%A081837> ---------------- 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 greve@nmr.mgh.harvard.eduwrote:
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 http://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 81837 81837.0 Seg0001 0.3836 0.1111 0.1297 1.1861 1.0563
On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@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 <tel:1%2081837%20%2081837> <tel:1%20%C2%A0%2081837%20%C2%**A081837> ---------------- 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu<greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu<greve@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 <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.** harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
oh, it might not be in your version
On 06/11/2013 05:27 PM, Glen Lee wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 <http://rage.uphs.upenn.edu> <http://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 81837 81837.0 Seg0001 0.3836 0.1111 0.1297 1.1861 1.0563 On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <tel:1%2081837%2081837> <tel:1%2081837%20%2081837> <tel:1%20%C2%A0%2081837%20%C2%A081837> ---------------- 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Glen Lee