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 Greve Thu, 28 Jan 2016 09:35:38 -0800

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 

>> <dgwake...@gmail.com>

>> 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

>> <peter.par...@med.uni-heidelberg.de> wrote:

>>> 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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