I see. I'll defer to Doug on this.
On Wed, 21 Feb 2007, Martin Kavec wrote:
Hi Bruce,
On Wednesday 21 February 2007 20:25, Bruce Fischl wrote:
Hi Martin,
what is IOD? We use multiframe images (multiecho) all the time using:
IOD stands for Information Object Definition, but is it not that
important. What is important is that my 3D volume is not stored in a
directory with one slice per file, but all the slices in ONE single file.
The DICOM header is in this case composed of
SharedAtributes+ConcatenatedPerFrameAttributes+PixelData
mri_convert -nth $echono <input dicom series> output_echo${echono}.mgz
what error do you get?
It's actually warning, but the geometry of the image is not determined
correctly and therefore tkmedit refuses to display the image:
$mri_conver IM-0001-0001.dcm IM-0001-0001.mgz
mri_convert IM-0001-0001.dcm IM-0001-0001.mgz
reading from IM-0001-0001.dcm...
1 DICOM 3.0 files in list
Found 1 DICOM Files
WARNING: NumberOfFrames 0 != Found Count of slices 1.
reading DICOM image...
-------------------------------------------------
DICOM meta-header
file name /Users/kavec/tmp8/IM-0001-0001.dcm
Date and time
study date 20070206
study time 105754
series time 121550.04000
acquisition time 121550.04000
Identification
patient name TEST JONES
manufacturer Philips Medical Systems
Dimensions
number of rows 288
number of columns 288
number of frames 1
pixel width not found
pixel height not found
slice thickness 1
field of view 0
image number 1 (might be not reliable)
transfer syntax UID 1.2.840.10008.1.2.1
Acquisition parameters
echo time not found
repetition time not found
inversion time not found
echo number not found
flip angle not found
bits allocated 16
Spatial information
first image position notfound
last image position notfound
image orientation notfound
-------------------------------------------------
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1.10422e-42, 1.10422e-42, 7.02051e-43)
j_ras = (-1.99546, 4.25209e-40, 2.32459e-40)
k_ras = (0, -1.4013e-42, 2.20284e-42)
writing to IM-0001-0001.mgz...
$ tkmedit -f ./IM-0001-0001.mgz
MRIresample(): source matrix has zero determinant; matrix is:
0.000 -0.000 0.000 0.000;
0.000 0.000 -0.000 0.000;
0.000 0.000 0.000 0.000;
0.000 0.000 0.000 1.000;
Error: Loading volume ./IM-0001-0001.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.
Thanks in advance
Bruce
On Wed, 21 Feb 2007, Martin Kavec wrote:
Hi,
our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image
file. When I try to use this format with FreeSurfer mri_convert fails. I
assume it is not designed for this type of images, isn't it? Anybody
knows a workaround?
Thanks in advance for help (and great software),
Martin
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