Issues Extracting mean value

Hello,
I am trying to extract the mean CSF like diffusivity value from a left hippocampal ROI using the following command.

mrstats -mask ${SUBJECTS_DIR}/${subj}.${cond}/lhipp2diff.nii.gz -ignorezero ${SUBJECTS_DIR}/${subj}.${cond}/TC.mif

I have also tried with TC.nii.gz.

mrstats: [ERROR] dimension mismatch between “/Volumes/DANIEL/AES_mrtrix//AES138.Rest/lhipp2diff.nii.gz” and "/Volumes/DANIEL/AES_mrtrix//AES138.Rest/TC.mif"

However, when I look at the images in fsleyes and freeview the image and ROI seem to overlay perfectly.

I have included the two images of the specs of both images to see if someone can help me with this issue.

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I just realized one of the images didn’t go through regrid so that is probably why there is a mismatch in pixel dimensions. Sorry about the unnecessary post.

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:+1: No worries

Just to briefly mention or make sure you got it right: so the values from that map, would be referred to as the (ROI averaged) CSF-like tissue signal fraction, abbreviated as TC. Most important bit here: that’s not a diffusivity. :wink:
Full scientific sources with some explanation: this one (section 2.5), and this one.

The test-retest reliability and long-term stability paper for this metric (and the other 3-tissue signal fractions) just got accepted in MRM, with whole-brain as well as hippocampal results specifically; so probably available online in a matter of days now.

Cheers,
Thijs

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