mris_calc currently only works with flat curvature files (eg ?h.curv, ?h.sulc, ?h.area, ?h.thickness, etc) and not on volumes.
------Original Message------ From: Akram Bakkour Sender: freesurfer-bounces@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_calc Sent: Oct 31, 2008 20:13
Hello, I have two thickness files I want to subtract one from the other, so I did:
on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh
#OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache
mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh \
and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' has wrong magic number."
Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A
Gotcha. Thanks! Are there any plans to have this work with all .mgh surface files?
On Oct 31, 2008, at 8:25 PM, rudolph@nmr.mgh.harvard.edu wrote:
mris_calc currently only works with flat curvature files (eg ? h.curv, ?h.sulc, ?h.area, ?h.thickness, etc) and not on volumes.
------Original Message------ From: Akram Bakkour Sender: freesurfer-bounces@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_calc Sent: Oct 31, 2008 20:13
Hello, I have two thickness files I want to subtract one from the other, so I did:
on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh
#OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using - qcache
mris_calc mris_calc -o 010130_vc6126/surf/ lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/ lh_mean.mgh \
and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/ lh.thickness.fsaverage.mgh' has wrong magic number."
Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A
-- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Rudolph,
we store things like thickness in 'volume' formats these days - the volumes are nvertices x 1 x 1. Not sure why it didn't work, I would have thought it would. Not sure. Akram: can you run mri_info on the input files and send along the results?
Bruce
On Sat, 1 Nov 2008 rudolph@nmr.mgh.harvard.edu wrote:
mris_calc currently only works with flat curvature files (eg ?h.curv, ?h.sulc, ?h.area, ?h.thickness, etc) and not on volumes.
------Original Message------ From: Akram Bakkour Sender: freesurfer-bounces@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_calc Sent: Oct 31, 2008 20:13
Hello, I have two thickness files I want to subtract one from the other, so I did:
on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh
#OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache
mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh \
and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' has wrong magic number."
Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A
On Fri, 31 Oct 2008, Bruce Fischl wrote:
Hi Rudolph,
we store things like thickness in 'volume' formats these days - the volumes are nvertices x 1 x 1. Not sure why it didn't work, I would have thought it would.
Errr... I think nonetheless the problem might be the input hack that 'mris_calc' uses. I basically re-coded the MatLAB 'read_curv.m' in C to use as input function for 'mris_calc'... (i.e. I didn't use MRISRead() -- maybe it's time for me to update things a bit).
ahhh. Yes, you should update it On Fri, 31 Oct 2008, Rudolph Pienaar wrote:
On Fri, 31 Oct 2008, Bruce Fischl wrote:
Hi Rudolph,
we store things like thickness in 'volume' formats these days - the volumes are nvertices x 1 x 1. Not sure why it didn't work, I would have thought it would.
Errr... I think nonetheless the problem might be the input hack that 'mris_calc' uses. I basically re-coded the MatLAB 'read_curv.m' in C to use as input function for 'mris_calc'... (i.e. I didn't use MRISRead() -- maybe it's time for me to update things a bit).
Rudolph,
Another suggestion, based on an email on this list earlier this week, is to add 'threshold' options, like fslmaths allows, to allow usage of your mris_calc to create masks from significance files.
Nick
On Fri, 2008-10-31 at 22:01 -0400, Bruce Fischl wrote:
ahhh. Yes, you should update it On Fri, 31 Oct 2008, Rudolph Pienaar wrote:
On Fri, 31 Oct 2008, Bruce Fischl wrote:
Hi Rudolph,
we store things like thickness in 'volume' formats these days - the volumes are nvertices x 1 x 1. Not sure why it didn't work, I would have thought it would.
Errr... I think nonetheless the problem might be the input hack that 'mris_calc' uses. I basically re-coded the MatLAB 'read_curv.m' in C to use as input function for 'mris_calc'... (i.e. I didn't use MRISRead() -- maybe it's time for me to update things a bit).
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