We are preparing a large dataset for sharing. It has already been processed and edited through freesurfer with the dicom files. We would like to share the MR scans in Nifti format instead of dicom, however we are encountering this difference in results. We are using dcm2niix to convert. We would like to stick with this program for conversion and the BIDS package. Any suggestions on how we can use this nifti output and get similar freesurfer results? Thanks Pamela
Douglas N Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Thu, 28 Jan 2016 09:35:38 -0800http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160128
I suspect that it has to do with the image geometry information. In
nifit, this is stored in quaterion format. In FS, this is converted to
direction cosines. This conversion is not reversible. So when you
mri_convert the DICOMS to nii, mri_convert will get the direction
cosines from the dicom file and convert them to quaternions. When you
run recon-all using the nii file, the quaternions are converted back to
direction cosines. But this does not yield exactly the same as what was
in the dicom file. This conversion does not happen when you start out
with mgz files. In version 6 I changed the code to try to reduce this
effect, but I think it will always be there.
On 01/28/2016 10:49 AM, Bruce Fischl wrote:
can you run mri_diff on the orig.mgz in the two runs and send us the
output?
On Thu, 28 Jan 2016, Parzer, Peter wrote:
mri_convert
Von: freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von dgw
Gesendet: Donnerstag, 28. Januar 2016 15:55
An: Freesurfer support list
Betreff: Re: [Freesurfer] Segmentation depends on image file format
What software did you use to generate the NIFTI files? Many of the
converters do different things to the axes of the data, and this does
affect results.
hth
d
On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter
Hi,
we have brain images stored as DICOM and as NIFTI files. For some time we
used to import the NIFTI files to freesurfer for segmentation. I was
curious if it makes a difference if we would import the DICOM files
directly, and was surprised that it actually did. Here are the commands we
used:
Pamela LaMontagne, PhD Clinical Research Coordinator Washington University School of Medicine Department of Radiology Phone: (314) 362-3487 Voice: (314) 669-4551
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LaMontagne, Pamela