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It is a volume based study so I will continue to use mgx .25. Thank you! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298

On Mon, Feb 25, 2019 at 1:42 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

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:

...

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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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