I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for each
segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
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.
Try using the full path to the file
On Sep 1, 2010, at 12:16 PM, corinna bauer corinnab83@gmail.com wrote:
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
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.
Then I get this error:
ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Try using the full path to the file
On Sep 1, 2010, at 12:16 PM, corinna bauer corinnab83@gmail.com wrote:
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote:
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for
each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
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.
what is your full command line? On Wed, 1 Sep 2010, corinna bauer wrote:
Then I get this error:
ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Try using the full path to the file
On Sep 1, 2010, at 12:16 PM, corinna bauer corinnab83@gmail.com wrote:
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote:
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for
each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
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.
mris_anatomical_stats -t /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh
On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what is your full command line?
On Wed, 1 Sep 2010, corinna bauer wrote:
Then I get this error:
ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Try using the full path to the file
On Sep 1, 2010, at 12:16 PM, corinna bauer corinnab83@gmail.com wrote:
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu> fischl@nmr.mgh.harvard.edu> wrote:
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for
each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
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.
can you run
mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh
and send us the output?
On Wed, 1 Sep 2010, corinna bauer wrote:
mris_anatomical_stats -t /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh
On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what is your full command line?
On Wed, 1 Sep 2010, corinna bauer wrote:
Then I get this error:
ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Try using the full path to the file
On Sep 1, 2010, at 12:16 PM, corinna bauer corinnab83@gmail.com wrote:
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu> fischl@nmr.mgh.harvard.edu> wrote:
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for
each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message:
reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight?
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.
Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh type: MGH dimensions: 1 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 1.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 58340.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 58340.5000 0.0000 0.0000 1.0000 11.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 58340.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -11.0254 0.0000 0.0000 0.0000 1.0000
On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
can you run
mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh
and send us the output?
On Wed, 1 Sep 2010, corinna bauer wrote:
mris_anatomical_stats -t
/home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh
On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
what is your full command line?
On Wed, 1 Sep 2010, corinna bauer wrote:
Then I get this error:
ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu
wrote:
Try using the full path to the file
On Sep 1, 2010, at 12:16 PM, corinna bauer corinnab83@gmail.com wrote:
Hi Bruce, When I use the -t flag, I get this message in the output:
mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file
I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh
Corinna
On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu> fischl@nmr.mgh.harvard.edu> wrote:
Hi Corinna,
the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try:
mris_anatomical_stats -t lh.gwratio.mgh
and the rest as normal. Note that it will report the values as "thickness"
cheers Bruce
On Mon, 30 Aug 2010, corinna bauer wrote:
I am trying to get an output with average gray/white ratio values for
each > segmentation. I tried using the gwratio.mgh file as the input for > mris_anatomical_stats, but got the following error message: > > reading input surface > /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... > ERROR: MRISread: file > '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 > vertices! > > Any insight? > > > > 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.
Something went very wrong with the creation of that file. It only has one voxel/vertex.
doug
corinna bauer wrote:
Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh type: MGH dimensions: 1 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 1.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 58340.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 58340.5000 0.0000 0.0000 1.0000 11.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 58340.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -11.0254 0.0000 0.0000 0.0000 1.0000
On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
can you run mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh and send us the output? On Wed, 1 Sep 2010, corinna bauer wrote: mris_anatomical_stats -t /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>wrote: what is your full command line? On Wed, 1 Sep 2010, corinna bauer wrote: Then I get this error: ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0 On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> wrote: Try using the full path to the file On Sep 1, 2010, at 12:16 PM, corinna bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com>> wrote: Hi Bruce, When I use the -t flag, I get this message in the output: mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh Corinna On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna, the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try: mris_anatomical_stats -t lh.gwratio.mgh and the rest as normal. Note that it will report the values as "thickness" cheers Bruce On Mon, 30 Aug 2010, corinna bauer wrote: I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message: reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices! Any insight? 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do you have any idea as to what may have gone wrong? Both files that went into creating the ratio have dimensions: 151243 x 1 x 1. In matlab I did this:
rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; paths=dir([rootdir,'/*']);
num=numel(paths) for ii=428:num fprintf('----- Processing %i of %i -----\n', ii, length(paths)); if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && ~strcmp(paths(ii).name,'..'));
pathgray=fullfile(rootdir,paths(ii).name,'mri/rh.white.projfrac.pos35.mgh'); gray = MRIread(pathgray);
pathwhite=fullfile(rootdir,paths(ii).name,'mri/rh.white.projdist.neg1.mgh'); white = MRIread(pathwhite);
gwratio = gray; gwratio.vol = gray.vol/white.vol;
pathratio=fullfile(rootdir,paths(ii).name,'mri','rh.gwratio.mgh'); MRIwrite(gwratio, pathratio);
On Wed, Sep 1, 2010 at 4:43 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Something went very wrong with the creation of that file. It only has one voxel/vertex.
doug
corinna bauer wrote:
Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh type: MGH dimensions: 1 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 1.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 58340.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 58340.5000 0.0000 0.0000 1.0000 11.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 58340.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -11.0254 0.0000 0.0000 0.0000 1.0000
On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto: fischl@nmr.mgh.harvard.edu> wrote:
can you run
mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh
and send us the output?
On Wed, 1 Sep 2010, corinna bauer wrote:
mris_anatomical_stats -t /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>wrote: what is your full command line? On Wed, 1 Sep 2010, corinna bauer wrote: Then I get this error: ERROR: number of vertices in/home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> wrote: Try using the full path to the file On Sep 1, 2010, at 12:16 PM, corinna bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com>> wrote: Hi Bruce, When I use the -t flag, I get this message in the output: mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh Corinna On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna, the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try: mris_anatomical_stats -t lh.gwratio.mgh and the rest as normal. Note that it will report the values as "thickness" cheers Bruce On Mon, 30 Aug 2010, corinna bauer wrote: I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message: reading input surface/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file
'/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices!
Any insight? 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.
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi Corinna
I think most likely it's the division operator ( / ) you used in the line
gwratio.vol = gray.vol/white.vol;
Element-wise division in MATLAB is achieved by a ./ . I think the line should be
gwratio.vol = gray.vol./white.vol
You could debug it by placing a
size(gwratio.vol)
immediately following the line and see if it agrees with the sizes of gray.vol and white.vol
See this : http://www.mathworks.com/access/helpdesk/help/techdoc/ref/mldivide.html for more information
-Krish
On Sep 2, 2010, at 1:48 PM, corinna bauer wrote:
Do you have any idea as to what may have gone wrong? Both files that went into creating the ratio have dimensions: 151243 x 1 x 1. In matlab I did this:
rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; paths=dir([rootdir,'/*']);
num=numel(paths) for ii=428:num fprintf('----- Processing %i of %i -----\n', ii, length(paths)); if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && ~ strcmp (paths (ii ).name,'..')); pathgray=fullfile(rootdir,paths(ii).name,'mri/ rh.white.projfrac.pos35.mgh'); gray = MRIread(pathgray); pathwhite=fullfile(rootdir,paths(ii).name,'mri/ rh.white.projdist.neg1.mgh'); white = MRIread(pathwhite);
gwratio = gray; gwratio.vol = gray.vol/white.vol;pathratio=fullfile(rootdir,paths(ii).name,'mri','rh.gwratio.mgh'); MRIwrite(gwratio, pathratio);
On Wed, Sep 1, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Something went very wrong with the creation of that file. It only has one voxel/vertex.
doug
corinna bauer wrote: Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/ mri/lh.gwratio.mgh type: MGH dimensions: 1 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 1.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 58340.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 58340.5000 0.0000 0.0000 1.0000 11.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 58340.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -11.0254 0.0000 0.0000 0.0000 1.0000
On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
can you run
mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh
and send us the output?
On Wed, 1 Sep 2010, corinna bauer wrote:
mris_anatomical_stats -t /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>wrote: what is your full command line? On Wed, 1 Sep 2010, corinna bauer wrote: Then I get this error: ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/ lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0
On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> wrote: Try using the full path to the file On Sep 1, 2010, at 12:16 PM, corinna bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com>> wrote: Hi Bruce, When I use the -t flag, I get this message in the output: mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh Corinna On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna, the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try: mris_anatomical_stats -t lh.gwratio.mgh and the rest as normal. Note that it will report the values as "thickness" cheers Bruce On Mon, 30 Aug 2010, corinna bauer wrote: I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message: reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/ lh.gwratio.mgh' has 0 vertices!
Any insight? 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.
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It could be that the input files (eg, mghrh.white.projfrac.pos35) were created, then the subject was edited (which would change the number of vertices), but the input files were not re-created. Check the creation dates on the files.
doug
corinna bauer wrote:
Do you have any idea as to what may have gone wrong? Both files that went into creating the ratio have dimensions: 151243 x 1 x 1. In matlab I did this:
rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; paths=dir([rootdir,'/*']);
num=numel(paths) for ii=428:num fprintf('----- Processing %i of %i -----\n', ii, length(paths)); if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && ~strcmp(paths(ii).name,'..'));
pathgray=fullfile(rootdir,paths(ii).name,'mri/mghrh.white.projfrac.pos35.'); gray = MRIread(pathgray);
pathwhite=fullfile(rootdir,paths(ii).name,'mri/rh.white.projdist.neg1.mgh'); white = MRIread(pathwhite);
gwratio = gray; gwratio.vol = gray.vol/white.vol;pathratio=fullfile(rootdir,paths(ii).name,'mri','rh.gwratio.mgh'); MRIwrite(gwratio, pathratio);
On Wed, Sep 1, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Something went very wrong with the creation of that file. It only has one voxel/vertex. doug corinna bauer wrote: Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh type: MGH dimensions: 1 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 1.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 58340.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 58340.5000 0.0000 0.0000 1.0000 11.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 58340.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -11.0254 0.0000 0.0000 0.0000 1.0000 On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: can you run mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh and send us the output? On Wed, 1 Sep 2010, corinna bauer wrote: mris_anatomical_stats -t /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>wrote: what is your full command line? On Wed, 1 Sep 2010, corinna bauer wrote: Then I get this error: ERROR: number of vertices in /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not match surface (1,116670)structure is "/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white" number of vertices = 116670 total surface area = 76860 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.112 folding index = 2190 intrinsic curvature index = 223.0 On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Try using the full path to the file On Sep 1, 2010, at 12:16 PM, corinna bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>>> wrote: Hi Bruce, When I use the -t flag, I get this message in the output: mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file I tried: mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh Corinna On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Corinna, the gwratio.mgh is a scalar field over the surface, *not* a surface (i.e. it has no topology information). Try: mris_anatomical_stats -t lh.gwratio.mgh and the rest as normal. Note that it will report the values as "thickness" cheers Bruce On Mon, 30 Aug 2010, corinna bauer wrote: I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message: reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices! Any insight? 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. ------------------------------------------------------------------------ _______________________________________________ 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 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
corinna bauer -
Douglas N Greve -
Krish Subramaniam