On 4/9/2019 9:45 AM, Georgina Angelopoulou wrote:

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Hello FreeSurfer Developers,

I have compared two groups in area, volume and thickness (using mri_glmfit and mri_glmfit-sim) and I want to extract the total value from each significant cluster so that I can run analysis with behavioural variables in SPSS.

I have found some previous posts with the following command:

mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th13.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat –accumulate.

but also the alternative option in --seg cache.th13.abs.y.ocn.dat.

Could you please tell me: 1. Which is the correct option for -- seg and what is their difference? You can't use a .dat file for seg. It must be in a volume (eg, mgh) format.

2. I tried to run both option and I get the exact same error:

mri_read(): couldn't determine type of file lh.SexStudy_area.glmdir/MN-FM/cache.th13.abs.y.ocn.dat ERROR: loading lh.SexStudy_area.glmdir/MN-FM/cache.th13.abs.y.ocn.dat

Any ideas of how to resolve that? You should not have gotten that error when using the mgh file. Double check

3. Is that command the right one for volume, area and thickness? For volume and area, but probably not for thickness. --accumulate means to sum up all the values rather than computing the mean. mean is better for thickness.

Thank you in advance,

Best, Georgina

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