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merrill
Starting Member
USA
9 Posts |
 Posted - Sep 22 2004 : 4:24:57 PM
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I hope there is a simple answer to this - I recently encountered some problems using the dicom2spm.m program. We ran a couple of pilot subjects and, for each subject, collected 2 3D high res anatomical scans. The scans differed from each other slightly in terms of voxel size, FOV, and slice thickness. When I ran dicom2spm, it only worked for one scan per subject. For the other, it appeared to run fine, but the resulting image was empty and the dimensions read "256 256 0". I can see no obvious problems with the *.dcm files themselves - anyone know what would cause this?
Kari |
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 22 2004 : 4:28:38 PM
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| Where did you get the program dicom2spm? Do you mean dicom2bxh? Is this a MATLAB program? |
Edited by - charles.michelich on Sep 22 2004 4:29:17 PM |
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merrill
Starting Member
USA
9 Posts |
Posted - Sep 23 2004 : 1:11:52 PM
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Chuck-
It's a matlab program (not dicom2bxh)- I downloaded it a while ago (around the time when the switch from Signa to the dicom format at BIAC occurred), but I'm pretty sure I got it from the Programs on Gall (although I can't find it there now). If there is some newer program that will do the same thing, convert the anatomicals to SPM format and create a header, let me know, although I'm still puzzled as to why I'm suddenly having this problem with dicom2spm.
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 23 2004 : 1:21:38 PM
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I haven't heard of dicom2spm before.
The easiest way that I know of to translate your DICOM files into Analyze 7.5 files is to use Syam's bxh2analyze program to convert the images using the BXH headers that are automatically generated. The tool is available on golgi or on any BIAC windows computer (see this post.) |
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melissa.slavin
BIAC Alum
Australia
44 Posts |
Posted - Sep 23 2004 : 2:08:15 PM
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Hi Kari,
I've never heard of dicom2spm either. I must admit we're still a little old fashioned and actually create a header using SPM99 (I don't know why they removed that utility in SPM2!) so that we can process the images in SPM2. This might be easier for you as you are not on-site at BIAC.
Melissa |
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merrill
Starting Member
USA
9 Posts |
Posted - Sep 27 2004 : 08:25:42 AM
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I used bxh2analyze, and it seemed to work (the files are all there and the images looked ok in SPM), but I got the following message when I ran it:
WARNING: Not a supported Analyze orientation -- labeling as transverse unflipped (0) anyway
What does that mean and is it a problem?
Thanks |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Sep 27 2004 : 08:59:08 AM
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quote:
Originally posted by merrill
WARNING: Not a supported Analyze orientation -- labeling as transverse unflipped (0) anyway
This warning is generally harmless, unless the orientation is non-axial and labeling it as such in the Analyze header is important to you. Unfortunately the Analyze 7.5 header does not support all orientations that DICOM does, which is why you get the warning. If you are only going to be using these files with SPM, consider the --spmhdr option to bxh2analyze, it will use SPM-specific fields and also provide orientation information in .mat files. |
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dicom to spm problem
