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Thank you, Dr Greve. I tried it, but it didn't work. By 'didn't work,' I
mean that when I visualized the NIfTI file, I saw a line on the coronal and
sagittal planes, and the whole brain on the axial view. I was able to
generate a NIfTI image with multiple volumes as expected by using the
mri_convert command with the --nslices-override argument, but I'm not sure
if I'm using it correctly.
On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
> Can you try it with --dcm2niix ?
>
> On 3/25/2023 9:43 AM, John Anderson wrote:
>
> External Email - Use Caution
> Dear Dr Doug Greeve,
> For each participant in my dataset, I have 8 mosaic volumes with 36 slices
> each. I am trying to convert the DICOM files to Nifti format using the
> mri_convert command in FreeSurfer version 7.3.2. However, the conversion
> process fails even when using this latest dev version. To resolve this
> issue, I attempted to use the --nslices-override option. It seems working,
> however, I am unsure if I used it correctly, and I was not able to find any
> relevant examples or guidance on how to use this option in the FreeSurfer
> documentation or other websites.
>
> n=({-1..7})
> 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
>
> Thanks for guidance,
> John
>
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