Thanks for your response, Lilla.

Soft links would be an alternative. Thanks for pointing to it.

When would you think you can add the -i flag? if it's reasonably soon, I may wait to use the updated code. (BTW, how can I get the updated code?)

Also, it would be extremely helpful if you could add more explanation to the --help flag. For example:

is the age in days, weeks, or months?

what are the training subjects? are they coming with the infantFS package?

--aparc flag is not clear to me.

what are --gmwm2, --keepelreg, and the rest of unexplained flags?

I understand that this is the beta version but without clear documentation, we can't fully appreciate its potential.

Thank you for your time and all the hard works!

Best,

Mahmoud

On Thu, Jul 11, 2019 at 3:26 PM Lilla Zollei <lzollei@nmr.mgh.harvard.edu> wrote:

Hi Mahmoud

Currently the -i flag is not activated. I can add that in a bit.

Can you create soft links to your input images?

Lilla

On Thu, 11 Jul 2019, Mahmoud wrote:

>
> Hi all,
> I have my data organized in this way:
> study/sub/T1/data.nii.gz
>
> infantFS wants the input as study/sub/mprage.nii.gz.
> Is there a way to feed my data to infantFS without reorganizing/renaming? -i switch seems to not be recognized by infantFS.
>
> Thank you,
> Mahmoud
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer