it might be. That override was for a particular experimental case, but
if it works, it works
On 3/27/2023 2:06 PM, John Anderson wrote:
External Email - Use Caution
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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