When you specify the --seg, just use gtmseg.mgz and not the whole path.
For mgx, I'd need to know what you intend to do with it. Is it a
surface-based study? If so, then I'd go with .01 in stead of .25

On 2/25/19 11:05 AM, Daniel Callow wrote:
>
>         External Email - Use Caution
>
> Hello,
>
> I am currently trying to run PVC for my adc images using the following
> script.
>
> mri_gtmpvc --i
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc-masked.nii.gz
> --reg
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.lta
> --psf 0 --seg
> /Applications/freesurfer/subjects/Freesurfer_output/${subj}.${cond}.fsoutput/mri/gtmseg.mgz
> --default-seg-merge --auto-mask PSF .01 --mgx .25 --o
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc.gtmpvc.output
> --no-rescale
>
>
> What would I need to change in order to accurately perform PVC on FA
> images? Would the --mgx flag need to be changed?
>
>
>
> Best,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>_
> 443-254-6298
>
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