Hi everybody,
We're doing a structural VBM bicentric cross cultural study, using
Freesurfer v5.0.0. on 2 computers :
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 9.8.0 i386
FREESURFER_HOME: /home/scnlab/Desktop/
freesurfer
Build stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0
Debian version: squeeze/sid
Kernel info: Linux 2.6.32-29-generic i686
freesurfer@nmr.mgh.harvard.edu
Successful reconstructions have been realized for some of the subjects from
one of the 2 centers, using their DICOMS (Siemens Trio), but we seem to be
unable to use any DICOM from the other center (Siemens Allegra).
It seems that the same problem has already been submitted to the mailing
list, without any available solution :
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01354.html
We get the following error messages (same on both computers):
[wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert
1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz
mri_convert 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
001.mgz
file not found or unknown file type for file
1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
[wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert --in_type
siemens_dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
001.mgz
mri_convert --in_type siemens_dicom
1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm...
ERROR (ScanSiemensSeries):
/Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
is not a Siemens DICOM file
ERROR: could not find any files (SeriesList==NULL)
[wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert
--in_type dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
001.mgzmri_convert --in_type dicom
1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm...
Starting DICOMRead2()
dcmfile =
/Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
dcmdir = /Users/SPLab/Desktop/OK-J-01/structural
ERROR:
/Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
is not a dicom file
[wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert
--in_type siemens --out_type mgz
1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz
mri_convert --in_type siemens --out_type mgz
1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm...
ERROR: could not parse
/Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
ERROR: siemensRead():
/Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm
- When trying to convert them with the MRI Convert software I get the
following error message : Unable to find series UID
- I can however convert them to nifti using SPM8 and MIPAV, and then
successfully run mri_convert and auto-recon1. I also tried to save as
dicoms in MIPAV, but it didn't change anything.
Here are headers as given by MIPAV :
Dimension 256
Dimension 256
Dimension 192
Type Unsigned Short
Min 0.0
Max 1654.0
Orientation Axial
Pixel resolution 0 0.75
Pixel resolution 1 0.75
Pixel resolution 2 1.0
Unit of measure Millimeters per pixel
Transformation Matrix
1. 0. 0. 0.
0. 1. 0. 0.
0. 0. 1. 0.
0. 0. 0. 1.
(0002,) File Meta Information Group Length 206
(0002,0001) File Meta Information Version 1
(0002,0002) Media Storage SOP Class UID 1.2.840.10008.5.1.4.1.1.4
(0002,0003) Media Storage SOP Instance UID
1.3.12.2.1107.5.2.7.20409.300703080442501872322
(0002,0010) Transfer Syntax UID 1.2.840.10008.1.2
(0002,0012) Implementation Class UID 1.2.804.114118.3
(0002,0013) Implementation Version Name eFilm/UCDavisLib
(0002,0016) Source Application Entity Title
(0008,0005) Specific Character Set ISO_IR 100
(0008,0008) Image Type ORIGINAL, PRIMARY, M, ND
(0008,0016) SOP Class UID 1.2.840.10008.5.1.4.1.1.4
(0008,0018) SOP Instance UID
1.3.12.2.1107.5.2.7.20409.300703080442501872322
(0008,0020) Study Date 20070308
(0008,0021) Series Date 20070308
(0008,0022) Acquisition Date 20070308
(0008,0023) Content (formerly Image) Date 20070308
(0008,0030) Study Time 142430.328000
(0008,0031) Series Time 153343.484000
(0008,0032) Acquisition Time 152244.074999
(0008,0033) Content (formerly Image) Time 153344.937000
(0008,0050) Accession Number 06H17
