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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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