Can you try it with --dcm2niix ?

On 3/25/2023 9:43 AM, John Anderson wrote:

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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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