Hi John,
Can you try dcmunpack (https://surfer.nmr.mgh.harvard.edu/fswiki/dcmunpack)
instead?
Here is an example usage:
dcmunpack -auto-runseq <format> -src <dicom-dir> -trg <output-dir>
-no-exit-on-error -dcm2niix
You will find the converted images in <output-dir>.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of John Anderson
Sent: Thursday, March 23, 2023 12:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_convert mosaic data
External Email - Use Caution
Thank you.
I would appreciate feedback from developers on two issues.
1) mri_convert in FS v6 is unable to convert any mosaic DICOMs to Nifti format.
In FS 7.3.2, mri_convert was able to convert mosaic DICOMs to Nifti in some
subjects but failed for many others. All subjects were scanned on the same MRI
scanner with the same acquisition parameters, and I am unable to determine the
cause of the issue.
2) I have 8 ASL mosaic volumes (36 slices) for each participant in my data.
When attempting to convert the DICOMs to Nifti using the simple mri_convert
<input.dcm> <output.nii> command, it fails. Is it correct to apply the
following steps?
n=({-1..6})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done
Thank for guidance,
John
On Wed, Mar 15, 2023 at 3:07 PM Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi John,
I’m assuming all 64 DICOM files are in the same directory.
Which Freesurfer version are you using? If you are using 7.3.2, can you try
mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of John Anderson
Sent: Wednesday, March 15, 2023 1:46 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mri_convert mosaic data
External Email - Use Caution
Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and
controls.
I would like to convert each individual DICOM into a separate NIfTI file or a
single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert.
However, when I use the command mri_convert input_dicom output_nifti, the
output does not seem right, as it only displays one slice in the sagittal and
coronal views. Could you please provide guidance on how to properly convert
these DICOM files using mri_convert?
Thanks very much
John
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