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BIC-MNI / minc-toolkit

Metaproject uniting all the available minc tools
GNU General Public License v3.0
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does minc-tolkit provide the MNI deps for freesurfer? #34

Closed TheChymera closed 8 years ago

TheChymera commented 8 years ago

Fresurfer bundles quite a few of its deps.

MNI is one of them. Does the minc-toolkit provide the same files?

vfonov commented 8 years ago

minc-toolkit works with minc files, if that's the question. MNI - is Montreal Neurological Institute

TheChymera commented 8 years ago

Sorry for not being more specific.

the README at this address: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/src/mni.srcbuild.June2015.README.txt

describes a number of (bundled) dependencies of Freesurfer that are collectively named mni.srcbuild. I am unsure what the overlap between that and mni-toolkit is. Does the mni-toolktit provide all of:

?

Also, in how far should I be mindful of the versions? do you know whether Freesurfer works with the currently provided dependency versions of minc-toolkit?

rdvincent commented 8 years ago

The current minc-toolkit is a superset of the MINC code shipped with FS. The version included with FreeSurfer is over ten years old. I would guess that FreeSurfer might function with the newer MINC tools, but the actual results would differ materially. However, we do not test our code against FreeSurfer, so it might not function at all. On Oct 12, 2015 10:54 AM, "Horea Christian" notifications@github.com wrote:

Sorry for not being more specific.

the README at this address: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/src/mni.srcbuild.June2015.README.txt

describes a number of (bundled) dependencies of Freesurfer that are collectively named mni.srcbuild. I am unsure what the overlap between that and mni-toolkit is. Does the mni-toolktit provide all of:

  • MINC v1.5.1
  • NetCDF v3.6.0-p1
    • MNI Perllib v0.07
    • N3 v1.12.0
    • EBTKS v1.6.4
    • Getopt-Tabular v0.3
    • MNI autoreg v0.99.6
    • MNI models v1.1

Also, in how far should I be mindful of the versions? do you know whether Freesurfer works with the currently provided dependency versions of minc-toolkit?

— Reply to this email directly or view it on GitHub https://github.com/BIC-MNI/minc-toolkit/issues/34#issuecomment-147423320 .

TheChymera commented 8 years ago

@rdvincent So all the packages I listed are also contained in minc-toolkit (and then some)? For instance I cannot find “Getopt-Tabular” and “MNI models” in the package list of minc-toolkit.

rdvincent commented 8 years ago

Minc-toolkit should contain a version of getopt-tabular. The models are in a separate Github project, bic-mni-models.

In any case, I can't recommend using newer MINC tools with FreeSurfer. Nobody has tested this, to the best of my knowledge.

-bert

On Oct 12, 2015 12:20 PM, "Horea Christian" notifications@github.com wrote:

@rdvincent https://github.com/rdvincent So all the packages I listed are also contained in minc-toolkit (and then some)? For instance I cannot find “Getopt-Tabular” and “MNI models” in the package list of minc-toolkit.

— Reply to this email directly or view it on GitHub https://github.com/BIC-MNI/minc-toolkit/issues/34#issuecomment-147450982 .

vfonov commented 8 years ago

https://github.com/BIC-MNI/minc-toolkit/tree/master/perl-modules/Getopt-Tabular-0.3