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