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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>
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 <
> 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>
> *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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