Hello FreeSurfers,
I am trying to run autorecon-1 on data (nifti) downloaded from the NIH MRI Study of Normal Brain Development (Pediatric MRI Study) Repository. However, the command exited with errors mentioning that the source matrix has a zero determinant. I've read past e-mail conversations on this issue, but I did not see any ways of solving this issue.
My main goal at the moment is just to perform intensity normalization and skull strip on these data (thus that is why i did not run -notalairach.) When I ran the command listed below on other non-NIH Pediatric MRI data, it performed without any errors.
Here is what I ran:
ubuntu:~> *recon-all -autorecon1 -notalairach -s 1433_v1 -i $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii -force* INFO: /usr/local/freesurfer/subjects/1433_v1 exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 todd todd 17815 Oct 28 12:00 /usr/local/freesurfer/subjects/1433_v1/scripts/recon-all.log Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010 x86_64 GNU/Linux /usr/local/freesurfer/subjects/1433_v1
mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 28 12:01:59 PDT 2010 Found 1 runs /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz
/usr/local/freesurfer/subjects/1433_v1
mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform *MRIresample(): source matrix has zero determinant; matrix is:* $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) Original Data has (0.976562, 0.976562, 0) mm size and (256, 256, 1) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation 0.977 0.000 -0.000 -136.512; 0.000 -0.977 -0.000 133.512; 0.000 0.000 0.000 -73.100; 0.000 0.000 0.000 1.000; Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010 x86_64 GNU/Linux
recon-all -s 1433_v1 exited with ERRORS at Thu Oct 28 12:02:02 PDT 2010
When I tried to open 001.mgz in tkmedit, as imagined, an error appeared as well:
ubuntu:~> tkmedit 1433_v1 001.mgz mghRead(/usr/local/freesurfer/subjects//1433_v1/mri/001.mgz, -1): could not open file
Error: Loading volume 001.mgz
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
Any help would be greatly appreciated.
Thank you in advance.
Best, Lisa Akiyama ____________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
There is something wrong with the header of that nifti file. Can you send the result of:
mri_info *deface_1433_V1_t1w_slice0.nii
doug * Lisa F. Akiyama wrote:
Hello FreeSurfers,
I am trying to run autorecon-1 on data (nifti) downloaded from the NIH MRI Study of Normal Brain Development (Pediatric MRI Study) Repository. However, the command exited with errors mentioning that the source matrix has a zero determinant. I've read past e-mail conversations on this issue, but I did not see any ways of solving this issue.
My main goal at the moment is just to perform intensity normalization and skull strip on these data (thus that is why i did not run -notalairach.) When I ran the command listed below on other non-NIH Pediatric MRI data, it performed without any errors.
Here is what I ran:
ubuntu:~> *recon-all -autorecon1 -notalairach -s 1433_v1 -i $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii -force* INFO: /usr/local/freesurfer/subjects/1433_v1 exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 todd todd 17815 Oct 28 12:00 /usr/local/freesurfer/subjects/1433_v1/scripts/recon-all.log Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010 x86_64 GNU/Linux /usr/local/freesurfer/subjects/1433_v1 mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 28 12:01:59 PDT 2010 Found 1 runs /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz /usr/local/freesurfer/subjects/1433_v1 mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform *MRIresample(): source matrix has zero determinant; matrix is:* $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) Original Data has (0.976562, 0.976562, 0) mm size and (256, 256, 1) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation 0.977 0.000 -0.000 -136.512; 0.000 -0.977 -0.000 133.512; 0.000 0.000 0.000 -73.100; 0.000 0.000 0.000 1.000; Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010 x86_64 GNU/Linux recon-all -s 1433_v1 exited with ERRORS at Thu Oct 28 12:02:02 PDT 2010When I tried to open 001.mgz in tkmedit, as imagined, an error appeared as well:
ubuntu:~> tkmedit 1433_v1 001.mgz mghRead(/usr/local/freesurfer/subjects//1433_v1/mri/001.mgz, -1): could not open file Error: Loading volume 001.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.Any help would be greatly appreciated.
Thank you in advance.
Best, Lisa Akiyama ____________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Here's the result of mri_info:
ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii INFO: using NIfTI-1 qform Volume information for /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii type: nii dimensions: 256 x 256 x 1 voxel sizes: 0.9766, 0.9766, 0.0000 type: FLOAT (3) fov: 250.000 dof: 0 xstart: -125.0, xend: -125.0 ystart: -125.0, yend: -125.0 zstart: -0.0, zend: -0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = -0.0000, c_r = -11.5117 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 8.5118 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -73.1000 Orientation : RPS Primary Slice Direction: axial
voxel to ras transform: 0.9766 0.0000 -0.0000 -136.5116 0.0000 -0.9766 -0.0000 133.5117 0.0000 0.0000 0.0000 -73.1000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0
ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER!
Thank you.
Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington lrisa87@uw.edu
P Please consider the environment before printing this e-mail.
On Thu, Oct 28, 2010 at 4:25 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
mri_info *deface_1433_V1_t1w_slice0.nii
The problem is that the slice thickness is 0. BTW, I don't know what you are planning to do with this in freesurrfer, but it's not going to work with only one slice.
doug
Lisa F. Akiyama wrote:
Hi Doug,
Here's the result of mri_info:
ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii INFO: using NIfTI-1 qform Volume information for /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii type: nii dimensions: 256 x 256 x 1 voxel sizes: 0.9766, 0.9766, 0.0000 type: FLOAT (3) fov: 250.000 dof: 0 xstart: -125.0, xend: -125.0 ystart: -125.0, yend: -125.0 zstart: -0.0, zend: -0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = -0.0000, c_r = -11.5117 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 8.5118 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -73.1000 Orientation : RPS Primary Slice Direction: axial
voxel to ras transform: 0.9766 0.0000 -0.0000 -136.5116 0.0000 -0.9766 -0.0000 133.5117 0.0000 0.0000 0.0000 -73.1000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0
ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER!
Thank you.
Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
P Please consider the environment before printing this e-mail.
On Thu, Oct 28, 2010 at 4:25 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
mri_info *deface_1433_V1_t1w_slice0.nii
Hi Doug,
There are approximately 40~45 slices of each individual's brain, each saved as separate nifti files. I'm trying to use FreeSurfer for the Non-uniform intensity normalization and skull strip functions. So, if I edit the header of each nifti file so that the slice thickness isn't 0, recon-all -autorecon1 should work?
Thanks.
Best, Lisa
______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
P Please consider the environment before printing this e-mail.
On Fri, Oct 29, 2010 at 10:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
The problem is that the slice thickness is 0. BTW, I don't know what you are planning to do with this in freesurrfer, but it's not going to work with only one slice.
doug
Lisa F. Akiyama wrote:
Hi Doug,
Here's the result of mri_info:
ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii INFO: using NIfTI-1 qform Volume information for /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii type: nii dimensions: 256 x 256 x 1 voxel sizes: 0.9766, 0.9766, 0.0000 type: FLOAT (3) fov: 250.000 dof: 0 xstart: -125.0, xend: -125.0 ystart: -125.0, yend: -125.0 zstart: -0.0, zend: -0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = -0.0000, c_r = -11.5117 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 8.5118 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -73.1000 Orientation : RPS Primary Slice Direction: axial
voxel to ras transform: 0.9766 0.0000 -0.0000 -136.5116 0.0000 -0.9766 -0.0000 133.5117 0.0000 0.0000 0.0000 -73.1000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0
ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER!
Thank you.
Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
P Please consider the environment before printing this e-mail.
On Thu, Oct 28, 2010 at 4:25 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
mri_info *deface_1433_V1_t1w_slice0.nii
-- 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
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.
You would have to take all 45 slices and put them into one volume. It won''t work slice-by-slice. It is probably the case that this won't work either as we usually use high res data. For intensity normalization, maybe it will work.
doug
Lisa F. Akiyama wrote:
Hi Doug,
There are approximately 40~45 slices of each individual's brain, each saved as separate nifti files. I'm trying to use FreeSurfer for the Non-uniform intensity normalization and skull strip functions. So, if I edit the header of each nifti file so that the slice thickness isn't 0, recon-all -autorecon1 should work?
Thanks.
Best, Lisa
Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
P Please consider the environment before printing this e-mail.
On Fri, Oct 29, 2010 at 10:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The problem is that the slice thickness is 0. BTW, I don't know what you are planning to do with this in freesurrfer, but it's not going to work with only one slice. doug Lisa F. Akiyama wrote: Hi Doug, Here's the result of mri_info: ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii INFO: using NIfTI-1 qform Volume information for /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii type: nii dimensions: 256 x 256 x 1 voxel sizes: 0.9766, 0.9766, 0.0000 type: FLOAT (3) fov: 250.000 dof: 0 xstart: -125.0, xend: -125.0 ystart: -125.0, yend: -125.0 zstart: -0.0, zend: -0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = -0.0000, c_r = -11.5117 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 8.5118 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -73.1000 Orientation : RPS Primary Slice Direction: axial voxel to ras transform: 0.9766 0.0000 -0.0000 -136.5116 0.0000 -0.9766 -0.0000 133.5117 0.0000 0.0000 0.0000 -73.1000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0 ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! Thank you. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing this e-mail. On Thu, Oct 28, 2010 at 4:25 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: mri_info *deface_1433_V1_t1w_slice0.nii -- 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> 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,
Thanks for the tips. I will look into putting all the slices into one volume.
Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington lrisa87@uw.edu
P Please consider the environment before printing this e-mail.
On Fri, Oct 29, 2010 at 11:53 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
You would have to take all 45 slices and put them into one volume. It won''t work slice-by-slice. It is probably the case that this won't work either as we usually use high res data. For intensity normalization, maybe it will work.
doug
Lisa F. Akiyama wrote:
Hi Doug,
There are approximately 40~45 slices of each individual's brain, each saved as separate nifti files. I'm trying to use FreeSurfer for the Non-uniform intensity normalization and skull strip functions. So, if I edit the header of each nifti file so that the slice thickness isn't 0, recon-all -autorecon1 should work?
Thanks.
Best, Lisa
Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington
P Please consider the environment before printing this e-mail.
On Fri, Oct 29, 2010 at 10:55 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The problem is that the slice thickness is 0. BTW, I don't know what you are planning to do with this in freesurrfer, but it's not going to work with only one slice.
doug
Lisa F. Akiyama wrote:
Hi Doug, Here's the result of mri_info: ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii INFO: using NIfTI-1 qform Volume information for/usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii type: nii dimensions: 256 x 256 x 1 voxel sizes: 0.9766, 0.9766, 0.0000 type: FLOAT (3) fov: 250.000 dof: 0 xstart: -125.0, xend: -125.0 ystart: -125.0, yend: -125.0 zstart: -0.0, zend: -0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = -0.0000, c_r = -11.5117 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 8.5118 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -73.1000 Orientation : RPS Primary Slice Direction: axial
voxel to ras transform: 0.9766 0.0000 -0.0000 -136.5116 0.0000 -0.9766 -0.0000 133.5117 0.0000 0.0000 0.0000 -73.1000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0 ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! Thank you. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing this e-mail. On Thu, Oct 28, 2010 at 4:25 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: mri_info *deface_1433_V1_t1w_slice0.nii-- 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
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 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 -
Lisa F. Akiyama