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 > 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 > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 gr...@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 The information in this e-mail is intended only for the person to whom it is addressed. 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