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
>
> ------------------------------------------------------------------------
>
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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
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