Hello,
We have been having difficulties importing GE .MR files into
FreeSurfer.
We have tried a number of methods:
1) directly importing .MR
2) converting to .IMG via BrainVoyager, then importing .IMG with .HDR
3) converting to .IMG via BrainVoyager and creating .MAT using SPM99,
then importing .IMG with .HDR and .MAT
4) renaming .MR to .DCM, then importing .DCM
Here is a summary of our problems:
1) autorecon1 exits with error
2) orig.mgz is in wrong orientation; T1.mgz is in correct orientation
but a "cosine info" error arises when loading in tkmedit; brainmask.mgz
is in wrong orientation; reconstructed surface is in wrong orientation
(i.e. not actually a hemisphere; appears oblique)
3) orig, T1, and brainmask are all in wrong orientation
4) autorecon1 exits with error
(in all cases except reconstructed surface, "wrong orientation" means:
C = axial with anterior to the left and right to the top
H = sagittal upside-down
S = coronal with superior to the left )
Here is a summary of what seems to be the source of our errors, from
corresponding recon-all.log files (I have attached .doc and .txt files
with longer excerpts)
1)
mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz
/home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform
MRIresample(): source matrix has zero determinant; matrix is:
-0.000 0.000 -0.000 0.000;
0.000 0.000 0.000 -15877550310885762478336514187067392.000;
0.000 -0.000 -0.000 -2013832203448376356765696.000;
0.000 0.000 0.000 1.000;
2)
mri_convert
/home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img
/home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz
-----------------------------------------------------------------
INFO: could not find
/home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file
for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse
unflipped
(default).
INFO: if not valid, please provide the information in
/home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file
3)
reading from
/home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img...
WARNING: analyzeRead(): matfile
/home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat
exists but could not read ...
may not be matlab4 mat file ... proceeding without it.
-----------------------------------------------------------------
INFO: could not find
/home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat
file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse
unflipped
(default).
INFO: if not valid, please provide the information in
/home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat
file
4)
mri_convert
/home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm
/home/omid/freesurfer/subjects/IBS_renamed/c1/mri/orig/001.mgz
reading from
/home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm...
genesisRead(): can't determine file name format for
We are now in the thick of attempting to manually import the volume
from
.MR to .MGZ by using the load_mgh.m, load_mgh2.m, save_mgh.m, and
save_mgh.m scripts, but before pursuing that avenue further we would
like to seek some expert advice.
Any thoughts or suggestions would be greatly appreciated. Please let me
know if I can provide any more necessary information.
Thank you for your time,
- Jerry
=============================================================================
1) IBS_raw -> autorecon1 exit with error
=============================================================================
/home/omid/freesurfer/subjects/IBS_raw/csd
mri_convert /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz
mri_convert /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz
reading from /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR...
freadShort: fread failed
No such file or directory
freadShort: fread failed
No such file or directory
fname_format : /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I%d.MR
fname_format2 : /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I%03d.MR
zero frames specified in file - setting to 1
TR=811509.69, TE=811509.69, TI=811509.69, flip angle=0.00
i_ras = (-0, 1, 1.01471e-34)
j_ras = (0, 0, -1)
k_ras = (-0.997933, 0, -0.0642636)
writing to /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Jul 10 11:53:26 EDT 2007
Found 1 runs
/home/omid/freesurfer/subjects/IBS_raw/csd/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 /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz
/home/omid/freesurfer/subjects/IBS_raw/csd
mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform
mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform
MRIresample(): source matrix has zero determinant; matrix is:
-0.000 0.000 -0.000 0.000;
0.000 0.000 0.000 -15877550310885762478336514187067392.000;
0.000 -0.000 -0.000 -2013832203448376356765696.000;
0.000 0.000 0.000 1.000;
reading from /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz...
TR=811509.69, TE=811509.69, TI=811509.69, flip angle=0.00
i_ras = (-0, 1, 1.01471e-34)
j_ras = (0, 0, -1)
k_ras = (-0.997933, 0, -0.0642636)
Original Data has (4.6006e-41, 4.6006e-41, 4.6006e-41) mm size and (256, 256, 124) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 4 to 0 (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
Linux omid-laptop 2.6.17-10-386 #2 Tue Dec 5 22:26:18 UTC 2006 i686 GNU/Linux
recon-all exited with ERRORS at Tue Jul 10 11:53:34 EDT 2007
=============================================================================
2) IBS_fromBV -> mri_convert cosine error:
=============================================================================
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz
-----------------------------------------------------------------
INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file
-----------------------------------------------------------------
reading from /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img...
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 /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Wed May 30 12:51:21 EDT 2007
Found 1 runs
/home/omid/freesurfer/subjects/IBS_fromBV/c1/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 /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz
/home/omid/freesurfer/subjects/IBS_fromBV/c1
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz --conform
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz --conform
reading from /home/omid/freesurfer/subjects/IBS_fromBV/c1/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 (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
Reslicing using trilinear interpolation
writing to /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz...
mri_add_xform_to_header -c /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/transforms/talairach.xfm /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz
INFO: extension is mgz
=============================================================================
3) IBS_fromBV_reO -> mri_convert .MAT, cosine error
=============================================================================
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz
matfile: only read 476 bytes of name (1768711468 specified)
MatlabRead: readHeader returned NULL
reading from /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img...
WARNING: analyzeRead(): matfile /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat exists but could not read ...
may not be matlab4 mat file ... proceeding without it.
-----------------------------------------------------------------
INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file
-----------------------------------------------------------------
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 /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Wed May 30 14:51:26 EDT 2007
Found 1 runs
/home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/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 /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz
/home/omid/freesurfer/subjects/IBS_fromBV_reO/c1
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz --conform
mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz --conform
reading from /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/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 (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
Reslicing using trilinear interpolation
writing to /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz...
mri_add_xform_to_header -c /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/transforms/talairach.xfm /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz
INFO: extension is mgz
=============================================================================
4) IBS_renamed -> autorecon1 exit with error
=============================================================================
mri_convert /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm /home/omid/freesurfer/subjects/IBS_renamed/c1/mri/orig/001.mgz
mri_convert /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm /home/omid/freesurfer/subjects/IBS_renamed/c1/mri/orig/001.mgz
reading from /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm...
genesisRead(): can't determine file name format for /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm
Linux omid-laptop 2.6.17-10-386 #2 Tue Dec 5 22:26:18 UTC 2006 i686 GNU/Linux
recon-all exited with ERRORS at Thu Jun 28 13:00:47 EDT 2007
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