Hello Freesurfers, Lately I've been scratching my head about image orientation problems. What I do here is take the DICOM images and use mri_convert to convert them into SPM Analyze format. The command I use is:
mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \ "path/to/subj/dir/image" --out_type spm
So the output files we get are imageXXX.{hdr,img,mat}. So, I assume these truly are Analyze format and not NIfTI (if i'm incorrect please tell me, this would be very important). There are weird things SPM does concerning image orientation, so it's *very* important that I get this right (we do functional imaging on surgery candidates):
*Does mri_convert flip the images in any way?*
That is, if my DICOM images are in radiological convention, will the imageXXX images still be in radiological convention? I've been searching far and wide and have hit a wall. With patients, we can see the water pill on the right side of the forehead easily, but with the EPI functional images for our research subjects it's pretty much impossible to tell.
Thanks very much, Chris Watson
Watson, Christopher wrote:
Hello Freesurfers, Lately I've been scratching my head about image orientation problems. What I do here is take the DICOM images and use mri_convert to convert them into SPM Analyze format. The command I use is:
mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \ "path/to/subj/dir/image" --out_type spm
So the output files we get are imageXXX.{hdr,img,mat}. So, I assume these truly are Analyze format and not NIfTI (if i'm incorrect please tell me, this would be very important).
Yes, analyze format, but they include the .mat, which has orientation info but is not part of the analyze spec but spm will read them and act on them.
There are weird things SPM does concerning image orientation, so it's *very* important that I get this right (we do functional imaging on surgery candidates):
*Does mri_convert flip the images in any way?*
No.
That is, if my DICOM images are in radiological convention, will the imageXXX images still be in radiological convention? I've been searching far and wide and have hit a wall. With patients, we can see the water pill on the right side of the forehead easily, but with the EPI functional images for our research subjects it's pretty much impossible to tell.
Thanks very much, Chris Watson
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Watson, Christopher