On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -f mm103184/stats/ lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot
Any suggestions?
Thanks, Cate
On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote:
Hi Cate,
I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen.
mris_anatomical_stats usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>]
This program measures a variety of anatomical properties
valid options are:
-i <low thresh> <hi thresh> - only consider thicknesses in the specified range. -l <label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <annotation file> - compute properties for each label in the annotation file separately -b - tabular output -f tablefile - table output to a file (different format than -b) -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it
Jenni On Fri, 11 May 2007, Catherine Hartley wrote:
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ?h.aparc.splitcingulate.stats file.
It generates and outputs summary statistics, but it does not write a .stats file to the stats directory:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/ mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume = 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate%
Thanks for your help!
-Cate
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I have parcellations that I've manually edited, and want to recompute the aparc.stats and aparc+aseg.mgz files to reflect what I've done. From the help file, I'm guessing the correct command for that is something like below, but wanted to verify:
recon-all -parcstats2 -aparc2aseg -subjid Name
Also, is there anyway to specify input and output names for the files, since I'd like to hold on to the unaltered data as well?
Thanks,
-Aaron-
You are probably going to want to run mri_aparc2aseg manually, somthing like:
mri_aparc2aseg --s subject --o youraparc+aseg.mgz --ribbon --annot youraparc.annot
One problem you are going to run into is that the names in the FreeSurferColorsLUT.txt will not match up with your new areas. I'm working on a fix, but it will probably be a few weeks.
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi,
I have parcellations that I've manually edited, and want to recompute the aparc.stats and aparc+aseg.mgz files to reflect what I've done. From the help file, I'm guessing the correct command for that is something like below, but wanted to verify:
recon-all -parcstats2 -aparc2aseg -subjid Name
Also, is there anyway to specify input and output names for the files, since I'd like to hold on to the unaltered data as well?
Thanks,
-Aaron-
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Cate,
As wacky as this may seem, you have to put the flagged options first, then the required items, otherwise the flagged options will be blindly ignored (it took me a while to figure this out in the code). So try:
mris_anatomical_stats \ -f mm103184/stats/lh.aparc.splitcingulate.stats \ -a mm103184/label/lh.aparc.splitcingulate.annot \ mm103184 lh inflated
Nick
On Fri, 2007-05-11 at 13:39 -0400, Catherine Hartley wrote:
On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -f mm103184/stats/ lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot
Any suggestions?
Thanks, Cate
On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote:
Hi Cate,
I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen.
mris_anatomical_stats usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>]
This program measures a variety of anatomical properties
valid options are:
-i <low thresh> <hi thresh> - only consider thicknesses in the specified range. -l <label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <annotation file> - compute properties for each label in the annotation file separately -b - tabular output -f tablefile - table output to a file (different format than -b) -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it
Jenni On Fri, 11 May 2007, Catherine Hartley wrote:
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ?h.aparc.splitcingulate.stats file.
It generates and outputs summary statistics, but it does not write a .stats file to the stats directory:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/ mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume = 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate%
Thanks for your help!
-Cate
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
Thanks, Nick!
That seemed to be working fine until it tried to write the file, and then I got the same bus error that I emailed about before. Is there something I need to do with the color table when I create a new parcellation.
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats -f mm103184/stats/lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot mm103184 lh inflated computing statistics for each annotation in mm103184/label/ lh.aparc.splitcingulate.annot. reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form...reading colortable from annotation file... CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Bus error [catemac:freesurfer/subjects/reruns] cate%
-Cate
On May 11, 2007, at 2:32 PM, Nick Schmansky wrote:
Cate,
As wacky as this may seem, you have to put the flagged options first, then the required items, otherwise the flagged options will be blindly ignored (it took me a while to figure this out in the code). So try:
mris_anatomical_stats \ -f mm103184/stats/lh.aparc.splitcingulate.stats \ -a mm103184/label/lh.aparc.splitcingulate.annot \ mm103184 lh inflated
Nick
On Fri, 2007-05-11 at 13:39 -0400, Catherine Hartley wrote:
On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -f mm103184/stats/ lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot
Any suggestions?
Thanks, Cate
On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote:
Hi Cate,
I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen.
mris_anatomical_stats usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>]
This program measures a variety of anatomical properties
valid options are:
-i <low thresh> <hi thresh> - only consider thicknesses in the specified range. -l <label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <annotation file> - compute properties for each label in the annotation file separately -b - tabular output -f tablefile - table output to a file (different format than -b) -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it
Jenni On Fri, 11 May 2007, Catherine Hartley wrote:
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ?h.aparc.splitcingulate.stats file.
It generates and outputs summary statistics, but it does not write a .stats file to the stats directory:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/ lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/ mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume = 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate%
Thanks for your help!
-Cate
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
Cate,
I can't seem to reproduce that bus error on our Intel Mac with plain data. Can you send me that subject in a tarball?
tar cvf mm103184.tar mm103184/ gzip mm103184.tar
You can upload it to me via our secure file drop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Fri, 2007-05-11 at 14:41 -0400, Catherine Hartley wrote:
Thanks, Nick!
That seemed to be working fine until it tried to write the file, and then I got the same bus error that I emailed about before. Is there something I need to do with the color table when I create a new parcellation.
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats -f mm103184/stats/lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot mm103184 lh inflated computing statistics for each annotation in mm103184/label/ lh.aparc.splitcingulate.annot. reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form...reading colortable from annotation file... CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Bus error [catemac:freesurfer/subjects/reruns] cate%
-Cate
On May 11, 2007, at 2:32 PM, Nick Schmansky wrote:
Cate,
As wacky as this may seem, you have to put the flagged options first, then the required items, otherwise the flagged options will be blindly ignored (it took me a while to figure this out in the code). So try:
mris_anatomical_stats \ -f mm103184/stats/lh.aparc.splitcingulate.stats \ -a mm103184/label/lh.aparc.splitcingulate.annot \ mm103184 lh inflated
Nick
On Fri, 2007-05-11 at 13:39 -0400, Catherine Hartley wrote:
On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -f mm103184/stats/ lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot
Any suggestions?
Thanks, Cate
On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote:
Hi Cate,
I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen.
mris_anatomical_stats usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>]
This program measures a variety of anatomical properties
valid options are:
-i <low thresh> <hi thresh> - only consider thicknesses in the specified range. -l <label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <annotation file> - compute properties for each label in the annotation file separately -b - tabular output -f tablefile - table output to a file (different format than -b) -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it
Jenni On Fri, 11 May 2007, Catherine Hartley wrote:
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ?h.aparc.splitcingulate.stats file.
It generates and outputs summary statistics, but it does not write a .stats file to the stats directory:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/ lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/ mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume = 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate%
Thanks for your help!
-Cate
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
Cate,
It looks like the problem you are encountering with mris_anatomical_stats is one where the labels were created with a dev version of a utility, which uses a newer different colortable format. So you will need to use the 'dev' version of mris_anatomical_stats, found here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev
Copy the file to your /Applications/freesurfer/bin directory, then type:
cd /Applications/freesurfer/bin chmod a+x mris_anatomical_stats
It seems to work on the data that you sent me.
Nick
On Fri, 2007-05-11 at 14:41 -0400, Catherine Hartley wrote:
Thanks, Nick!
That seemed to be working fine until it tried to write the file, and then I got the same bus error that I emailed about before. Is there something I need to do with the color table when I create a new parcellation.
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats -f mm103184/stats/lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot mm103184 lh inflated computing statistics for each annotation in mm103184/label/ lh.aparc.splitcingulate.annot. reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form...reading colortable from annotation file... CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Bus error [catemac:freesurfer/subjects/reruns] cate%
-Cate
On May 11, 2007, at 2:32 PM, Nick Schmansky wrote:
Cate,
As wacky as this may seem, you have to put the flagged options first, then the required items, otherwise the flagged options will be blindly ignored (it took me a while to figure this out in the code). So try:
mris_anatomical_stats \ -f mm103184/stats/lh.aparc.splitcingulate.stats \ -a mm103184/label/lh.aparc.splitcingulate.annot \ mm103184 lh inflated
Nick
On Fri, 2007-05-11 at 13:39 -0400, Catherine Hartley wrote:
On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -f mm103184/stats/ lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot
Any suggestions?
Thanks, Cate
On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote:
Hi Cate,
I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen.
mris_anatomical_stats usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>]
This program measures a variety of anatomical properties
valid options are:
-i <low thresh> <hi thresh> - only consider thicknesses in the specified range. -l <label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <annotation file> - compute properties for each label in the annotation file separately -b - tabular output -f tablefile - table output to a file (different format than -b) -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it
Jenni On Fri, 11 May 2007, Catherine Hartley wrote:
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ?h.aparc.splitcingulate.stats file.
It generates and outputs summary statistics, but it does not write a .stats file to the stats directory:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/ lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/ mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume = 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate%
Thanks for your help!
-Cate
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
freesurfer@nmr.mgh.harvard.edu
-
Catherine Hartley -
Doug Greve -
Goldman, Aaron (NIH/NIMH) [C] -
Nick Schmansky