It looks like there are several (102 to be exact) that do not have any voxels in your parcellation. Eg, #82:
82 82 ic4.tri_vertex_82 0
So the problem appears to be with mris_make_face_parcellation, not with mri_segstats. doug
On 09/10/2012 10:56 AM, Linda Douw wrote:
Hi Doug, Output and sumfile are attached. Any ideas? Linda
Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To: freesurfer@nmr.mgh.harvard.edu Message-ID:50295BA1.8090307@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Linda, can you send the terminal output for mri_segstats? Can you also send the summary file? doug
On 08/13/2012 10:59 AM, Linda Douw wrote:
Hi Doug,
I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface):
mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot
Then I extract the waveforms using mri_segstats
mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum
Hope this clarifies the problem! Linda
Message: 25 Date: Fri, 10 Aug 2012 11:18:38 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To: freesurfer@nmr.mgh.harvard.edu Message-ID:5025264E.3030801@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
what are your command lines? doug
On 08/09/2012 01:21 PM, Linda Douw wrote:
Dear Freesurfers,
I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something?
Thanks,
Hi Doug,
I see. I'm trying to compare fMRI to MEG, so it would be very helpful if the same parcellation (i.e. with all 2562 labels) could be used.
How could I investigate why mris_make_face_parcellation skips a bunch of labels? The problem is not fsaverage5, because doing the analysis in native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in mris_make_face_parcellation?
Thanks again, Linda
On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote:
It looks like there are several (102 to be exact) that do not have any
voxels in your parcellation. Eg, #82:
82 82 ic4.tri_vertex_82 0
So the problem appears to be with mris_make_face_parcellation, not with
mri_segstats.
doug
On 09/10/2012 10:56 AM, Linda Douw wrote:
Hi Doug, Output and sumfile are attached. Any ideas? Linda
Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:50295BA1.8090307@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Linda, can you send the terminal output for mri_segstats? Can you
also send the summary file?
doug On 08/13/2012 10:59 AM, Linda Douw wrote:
Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are
morphed to fsaverage5 surface):
mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot
fsaverage5c rh ico4 --sum ico4_rh.sum
Hope this clarifies the problem! Linda
Message: 25 Date: Fri, 10 Aug 2012 11:18:38 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:5025264E.3030801@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed what are your command lines? doug On 08/09/2012 01:21 PM, Linda Douw wrote:
Dear Freesurfers, I'm trying to extract the average waveforms from all 2562 ROIs in
an
annotation constructed using mris_make_face_parcellation with ico4.
However, I get only 2460 waveforms after doing mri_segstats, and the
summary files show that several ROIs are 'skipped' for some reason.
Am
I missing something? Thanks,
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi Linda, I'd need the same type of information, ie what is you mris_make_face_parcellation command line and what is the terminal output. doug
On 09/10/2012 01:17 PM, Linda Douw wrote:
Hi Doug,
I see. I'm trying to compare fMRI to MEG, so it would be very helpful if the same parcellation (i.e. with all 2562 labels) could be used.
How could I investigate why mris_make_face_parcellation skips a bunch of labels? The problem is not fsaverage5, because doing the analysis in native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in mris_make_face_parcellation?
Thanks again, Linda
On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote:
It looks like there are several (102 to be exact) that do not have any
voxels in your parcellation. Eg, #82:
82 82 ic4.tri_vertex_82 0
So the problem appears to be with mris_make_face_parcellation, not with
mri_segstats.
doug
On 09/10/2012 10:56 AM, Linda Douw wrote:
Hi Doug, Output and sumfile are attached. Any ideas? Linda
Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:50295BA1.8090307@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Linda, can you send the terminal output for mri_segstats? Can you
also send the summary file?
doug On 08/13/2012 10:59 AM, Linda Douw wrote:
Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are
morphed to fsaverage5 surface):
mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot
fsaverage5c rh ico4 --sum ico4_rh.sum
Hope this clarifies the problem! Linda
Message: 25 Date: Fri, 10 Aug 2012 11:18:38 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:5025264E.3030801@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed what are your command lines? doug On 08/09/2012 01:21 PM, Linda Douw wrote: > Dear Freesurfers, > I'm trying to extract the average waveforms from all 2562 ROIs in
an
> annotation constructed using mris_make_face_parcellation with ico4.
However, I get only 2460 waveforms after doing mri_segstats, and the
> summary files show that several ROIs are 'skipped' for some reason.
Am
> I > missing something? > Thanks,
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Command was: mris_make_face_parcellation /cluster/neuromind/douw/scans/controls/nmr00541_FS/surf/lh.inflated $FREESURFER_HOME/lib/bem/ic4.tri native.ico4.annot
Output was: parcellating hemisphere into 2562 units parcellation took 0 minutes and 3 seconds.
I've attached the created .annot for your information.
On Mon, September 10, 2012 1:36 pm, Douglas N Greve wrote:
Hi Linda, I'd need the same type of information, ie what is you mris_make_face_parcellation command line and what is the terminal
output.
doug
On 09/10/2012 01:17 PM, Linda Douw wrote:
Hi Doug, I see. I'm trying to compare fMRI to MEG, so it would be very helpful
if
the same parcellation (i.e. with all 2562 labels) could be used. How
could I investigate why mris_make_face_parcellation skips a bunch of
labels? The problem is not fsaverage5, because doing the analysis in
native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in
mris_make_face_parcellation? Thanks again, Linda On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote:
It looks like there are several (102 to be exact) that do not have any
voxels in your parcellation. Eg, #82:
82 82 ic4.tri_vertex_82 0 So the problem appears to be with mris_make_face_parcellation, not
with
mri_segstats.
doug On 09/10/2012 10:56 AM, Linda Douw wrote:
Hi Doug, Output and sumfile are attached. Any ideas? Linda
Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:50295BA1.8090307@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Linda, can you send the terminal output for mri_segstats? Can you
also send the summary file?
doug On 08/13/2012 10:59 AM, Linda Douw wrote:
Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data
are
morphed to fsaverage5 surface):
mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot
fsaverage5c rh ico4 --sum ico4_rh.sum
Hope this clarifies the problem! Linda > ------------------------------ > Message: 25 > Date: Fri, 10 Aug 2012 11:18:38 -0400 > From: Douglas N Grevegreve@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To:
freesurfer@nmr.mgh.harvard.edu
> Message-ID:5025264E.3030801@nmr.mgh.harvard.edu > Content-Type: text/plain; charset=ISO-8859-1; format=flowed what
are your command lines?
> doug > On 08/09/2012 01:21 PM, Linda Douw wrote: >> Dear Freesurfers, >> I'm trying to extract the average waveforms from all 2562 ROIs in
an
>> annotation constructed using mris_make_face_parcellation with ico4.
However, I get only 2460 waveforms after doing mri_segstats, and the
>> summary files show that several ROIs are 'skipped' for some reason.
Am
>> I >> missing something? >> Thanks,
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Thanks Linda. BTW, please don't attach big image files, use the file drop instead. Thanks! doug
On 09/10/2012 02:02 PM, Linda Douw wrote:
Command was: mris_make_face_parcellation /cluster/neuromind/douw/scans/controls/nmr00541_FS/surf/lh.inflated $FREESURFER_HOME/lib/bem/ic4.tri native.ico4.annot
Output was: parcellating hemisphere into 2562 units parcellation took 0 minutes and 3 seconds.
I've attached the created .annot for your information.
On Mon, September 10, 2012 1:36 pm, Douglas N Greve wrote:
Hi Linda, I'd need the same type of information, ie what is you mris_make_face_parcellation command line and what is the terminal
output.
doug
On 09/10/2012 01:17 PM, Linda Douw wrote:
Hi Doug, I see. I'm trying to compare fMRI to MEG, so it would be very helpful
if
the same parcellation (i.e. with all 2562 labels) could be used. How
could I investigate why mris_make_face_parcellation skips a bunch of
labels? The problem is not fsaverage5, because doing the analysis in
native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in
mris_make_face_parcellation? Thanks again, Linda On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote:
It looks like there are several (102 to be exact) that do not have any
voxels in your parcellation. Eg, #82:
82 82 ic4.tri_vertex_82 0So the problem appears to be with mris_make_face_parcellation, not
with
mri_segstats.
doug On 09/10/2012 10:56 AM, Linda Douw wrote:
Hi Doug, Output and sumfile are attached. Any ideas? Linda
Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:50295BA1.8090307@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Linda, can you send the terminal output for mri_segstats? Can you
also send the summary file?
doug On 08/13/2012 10:59 AM, Linda Douw wrote: > Hi Doug, > I first parcellate fsaverage5 using ico4 (all my functional data
are
morphed to fsaverage5 surface):
> mris_make_face_parcellation /fsaverage5/rh.inflated > $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot > Then I extract the waveforms using mri_segstats > mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot
fsaverage5c rh ico4 --sum ico4_rh.sum
> Hope this clarifies the problem! > Linda >> ------------------------------ >> Message: 25 >> Date: Fri, 10 Aug 2012 11:18:38 -0400 >> From: Douglas N Grevegreve@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To:
freesurfer@nmr.mgh.harvard.edu
>> Message-ID:5025264E.3030801@nmr.mgh.harvard.edu >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed what
are your command lines?
>> doug >> On 08/09/2012 01:21 PM, Linda Douw wrote: >>> Dear Freesurfers, >>> I'm trying to extract the average waveforms from all 2562 ROIs in
an
>>> annotation constructed using mris_make_face_parcellation with ico4.
However, I get only 2460 waveforms after doing mri_segstats, and the
>>> summary files show that several ROIs are 'skipped' for some reason.
Am
>>> I >>> missing something? >>> Thanks,
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi Linda, I have tracked down several problems.
Problem 1: it was sometimes merging several parcellation units into effectively a single unit. These could have been spread out over space. This has been fixed.
Problem 2: the documentation suggested using the inflated surface. This is mostly likely not the surface you want to use. Instead, use sphere or sphere.reg based on these criteria:
sphere: units will be approximately equal size within subject but not in correspondence across subjects sphere.reg: units will be different sizes within subject but in correspondence across subjects
These changes will be in the next release, but you can get a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
let me know how it goes
doug
On 09/10/2012 02:02 PM, Linda Douw wrote:
Command was: mris_make_face_parcellation /cluster/neuromind/douw/scans/controls/nmr00541_FS/surf/lh.inflated $FREESURFER_HOME/lib/bem/ic4.tri native.ico4.annot
Output was: parcellating hemisphere into 2562 units parcellation took 0 minutes and 3 seconds.
I've attached the created .annot for your information.
On Mon, September 10, 2012 1:36 pm, Douglas N Greve wrote:
Hi Linda, I'd need the same type of information, ie what is you mris_make_face_parcellation command line and what is the terminal
output.
doug
On 09/10/2012 01:17 PM, Linda Douw wrote:
Hi Doug, I see. I'm trying to compare fMRI to MEG, so it would be very helpful
if
the same parcellation (i.e. with all 2562 labels) could be used. How
could I investigate why mris_make_face_parcellation skips a bunch of
labels? The problem is not fsaverage5, because doing the analysis in
native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in
mris_make_face_parcellation? Thanks again, Linda On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote:
It looks like there are several (102 to be exact) that do not have any
voxels in your parcellation. Eg, #82:
82 82 ic4.tri_vertex_82 0So the problem appears to be with mris_make_face_parcellation, not
with
mri_segstats.
doug On 09/10/2012 10:56 AM, Linda Douw wrote:
Hi Doug, Output and sumfile are attached. Any ideas? Linda
Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To:
freesurfer@nmr.mgh.harvard.edu
Message-ID:50295BA1.8090307@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Linda, can you send the terminal output for mri_segstats? Can you
also send the summary file?
doug On 08/13/2012 10:59 AM, Linda Douw wrote: > Hi Doug, > I first parcellate fsaverage5 using ico4 (all my functional data
are
morphed to fsaverage5 surface):
> mris_make_face_parcellation /fsaverage5/rh.inflated > $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot > Then I extract the waveforms using mri_segstats > mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot
fsaverage5c rh ico4 --sum ico4_rh.sum
> Hope this clarifies the problem! > Linda >> ------------------------------ >> Message: 25 >> Date: Fri, 10 Aug 2012 11:18:38 -0400 >> From: Douglas N Grevegreve@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To:
freesurfer@nmr.mgh.harvard.edu
>> Message-ID:5025264E.3030801@nmr.mgh.harvard.edu >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed what
are your command lines?
>> doug >> On 08/09/2012 01:21 PM, Linda Douw wrote: >>> Dear Freesurfers, >>> I'm trying to extract the average waveforms from all 2562 ROIs in
an
>>> annotation constructed using mris_make_face_parcellation with ico4.
However, I get only 2460 waveforms after doing mri_segstats, and the
>>> summary files show that several ROIs are 'skipped' for some reason.
Am
>>> I >>> missing something? >>> Thanks,
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Linda Douw