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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 dgreve@mgh.harvard.edu wrote:
Can you try it with --dcm2niix ?
On 3/25/2023 9:43 AM, John Anderson wrote:
External Email - Use CautionDear 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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