Hello Bruce,

this seems to be an issue with the documentation. I am using the following syntax:

mri_compute_volume_fractions reg_file input_volume out_stem

That is not included in the documentation. I attempted to use the flags --reg in front of the reg_file_name, --o in front of the out_stem_name, and did not find anything for the input file. Sorry, that got me confused and was basically caused by a type-o in the syntax that I outlined above. It could be usefull to include the above syntax into the documentation. I did not use mri_compute_volume_fractions for a while and thought something would have been changed meanwhile.

Thanks Joerg ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, June 10, 2019 12:42 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions input volume

Hi Joerg

can you give us more information than that? Why do you say it is not possible? It should be

cheers Bruce On Mon, 10 Jun 2019, Pfannmoeller, Joerg Peter wrote:

Hello,

I always used mri_compute_volume_fractions to compute the volume fractions in my GE-EPI images (percentage of gm,wm, and csf in each voxel). That does not seem to be possible anymore. I can still define a registration matrix and an outstem but no input execpt of the standard FreeSurfer anatomical input. Can you help me with that?

Best Joerg

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