External Email - Use Caution
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
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
External Email - Use Caution
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
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Hi Mahmoud,
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?)
I am waiting for another feature to be added to this stream, so it might not happen within a couple of days. Please, go ahead with the links.
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?
Sure. I will work on that. For now age is in months.
what are the training subjects? are they coming with the infantFS package?
Yes, they are provided in the download.
--aparc flag is not clear to me.
The stream will produce parcellations as well. As the download email specifies "Currently, the parcellation information (aparc) is provided only for the sake of completeness, but has not been fully validated. It is a projected version of the adult atlas, so it does not originate from the infant training data set directly!"
what are --gmwm2,
You would want to use this flag if you wanted to make sure that GMWm information is for sure propagated via the tarining subjects. There are scnarios where this does not happen due to the fact that some of the tarining subjects do not have a GMWM separation.
--keepelreg, and the rest of unexplained flags?
I think this is a cvs registration flag and not an infant_recon one.
Best, Lilla
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
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