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RF + DOC: Add MNI template reference. Also import it into the dipy.da… #681

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@arokem
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arokem commented Jul 16, 2015

…ta namespace.

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samuelstjean commented Jul 18, 2015

It would also be a good idea to add the template license in the note (provided thsi is the right one of course).

And the website : http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

License
Copyright (C) 1993–2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The authors and McGill University make no representations about the suitability of this software for any purpose. It is provided “as is” without express or implied warranty. The authors are not responsible for any data loss, equipment damage, property loss, or injury to subjects or patients resulting from the use or misuse of this software package.

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arokem commented Jul 18, 2015

Sure. Added.

As required by this license, the license also gets downloaded together with the files and saved in the same folder as the template files.

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samuelstjean commented Jul 18, 2015

Ah I did not know that. Probably better to put it here also, I doubt that many people will go and read it inside a hidden download folder anyway.

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arokem commented Jul 18, 2015

Yeah - we don't pay for extra lines of docstrings :-)

And it's better to say these things more times than absolutely necessary,
than too few.

On Sat, Jul 18, 2015 at 10:34 AM, Samuel St-Jean notifications@github.com
wrote:

Ah I did not know that. Probably better to put it here also, I doubt that
many people will go and read it inside a hidden download folder anyway.


Reply to this email directly or view it on GitHub
#681 (comment).

@arokem arokem force-pushed the arokem:mni-citation branch from 338dca7 to 88bb115 Aug 5, 2015

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arokem commented Aug 5, 2015

Just rebased this one, so it can be cleanly merged.

"""
folder = pjoin(dipy_home, 'mni_template')
files, folder = fetch_mni_template()
file_dict = {"T1":pjoin(folder, 'mni_icbm152_t1_tal_nlin_asym_09a.nii'),

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@Garyfallidis

Garyfallidis Aug 6, 2015

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Hi @arokem, why do you prefer the ICBM152 2009a version and not the 2009c version?
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Also now that you are on it can you also fetch the rest of the maps PDs etc?
We can definitely use them for other projects like the Tissue classifiers etc.

I would recommend fetching the 1x1x1 atlases but also fetching the 0.5x0.5x0.5
atlases those will be useful for performing high resolution anatomical tracking.

I hope this is not much to ask. It would be great to fetch the IIT atlas too at some point.
I will need to ask permission from Arfanakis for that. But I think it's possible!
Exciting!

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@matthew-brett

matthew-brett Aug 6, 2015

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The 'c' atlas is symmetric, and so does not represent an average brain. It's main use is when you want to compare directly between the two hemispheres, so I don't think it should be the default.

It sounds like the IIT atlas has an inconvenient license, so we should be careful when fetching that.

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@Garyfallidis

Garyfallidis Aug 6, 2015

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I doubt about that @matthew-brett It clearly says in the MNI website
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
that there is a symmetric and asymmetric version of the 'c' atlas.
Look at the last bullet point.

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@Garyfallidis

Garyfallidis Aug 6, 2015

Member

I know well the person who wrote the atlas and I don't think he had the intention to have a hard-boiled license. I will speak to him about that. Maybe they would love to update their license. Or they don't mind fetching it in DIPY.

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@matthew-brett

matthew-brett Aug 6, 2015

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Ah yes - sorry - you are right about 2009c. Then - do you know the difference between 2009a and 2009c? The page mentions only the different version numbers for the intensity correction method and different 'resampling'.

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@arokem

arokem Aug 6, 2015

Member

No rush. The ROIs that we are using for tractography segmentation are all
based on the MNI template anyway.

On Thu, Aug 6, 2015 at 10:18 AM, Samuel St-Jean notifications@github.com
wrote:

In dipy/data/fetcher.py
#681 (comment):

 """
  • folder = pjoin(dipy_home, 'mni_template')
  • files, folder = fetch_mni_template()
    file_dict = {"T1":pjoin(folder, 'mni_icbm152_t1_tal_nlin_asym_09a.nii'),

They also have a seperate license for commercial and non commercial usage,
so maybe you can just point a download link for people while the
re-licensing happens, so that people might have it in the meantime if it's
that important.


Reply to this email directly or view it on GitHub
https://github.com/nipy/dipy/pull/681/files#r36440520.

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@arokem

arokem Aug 6, 2015

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(that might also be the reason we are using 'a')

On Thu, Aug 6, 2015 at 10:20 AM, Ariel Rokem arokem@gmail.com wrote:

No rush. The ROIs that we are using for tractography segmentation are all
based on the MNI template anyway.

On Thu, Aug 6, 2015 at 10:18 AM, Samuel St-Jean notifications@github.com
wrote:

In dipy/data/fetcher.py
#681 (comment):

 """
  • folder = pjoin(dipy_home, 'mni_template')
  • files, folder = fetch_mni_template()
    file_dict = {"T1":pjoin(folder, 'mni_icbm152_t1_tal_nlin_asym_09a.nii'),

They also have a seperate license for commercial and non commercial
usage, so maybe you can just point a download link for people while the
re-licensing happens, so that people might have it in the meantime if it's
that important.


Reply to this email directly or view it on GitHub
https://github.com/nipy/dipy/pull/681/files#r36440520.

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@jyeatman

jyeatman Aug 6, 2015

I have no preference for a as oppose to c. If c is better, let's go with
that

On Thursday, August 6, 2015, Ariel Rokem notifications@github.com wrote:

In dipy/data/fetcher.py
#681 (comment):

 """
  • folder = pjoin(dipy_home, 'mni_template')
  • files, folder = fetch_mni_template()
    file_dict = {"T1":pjoin(folder, 'mni_icbm152_t1_tal_nlin_asym_09a.nii'),

No rush. The ROIs that we are using for tractography segmentation are all
based on the MNI template anyway.
… <#14f040978a952b82_>
On Thu, Aug 6, 2015 at 10:18 AM, Samuel St-Jean <notifications@github.com
javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote: In
dipy/data/fetcher.py <
https://github.com/nipy/dipy/pull/681#discussion_r36440520>: > """ > -
folder = pjoin(dipy_home, 'mni_template') > + files, folder =
fetch_mni_template() > file_dict = {"T1":pjoin(folder,
'mni_icbm152_t1_tal_nlin_asym_09a.nii'), They also have a seperate license
for commercial and non commercial usage, so maybe you can just point a
download link for people while the re-licensing happens, so that people
might have it in the meantime if it's that important. — Reply to this email
directly or view it on GitHub <
https://github.com/nipy/dipy/pull/681/files#r36440520>.


Reply to this email directly or view it on GitHub
https://github.com/nipy/dipy/pull/681/files#r36440755.

Jason D. Yeatman, PhD
Assistant Professor, Institute for Learning & Brain Sciences (I-LABS)
Department of Speech & Hearing Sciences
University of Washington
http://depts.washington.edu/bdelab/

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@arokem

arokem Aug 6, 2015

Member

Presumably the ROIs were made based on 'a'?

On Thu, Aug 6, 2015 at 11:03 AM, Jason D. Yeatman notifications@github.com
wrote:

In dipy/data/fetcher.py
#681 (comment):

 """
  • folder = pjoin(dipy_home, 'mni_template')
  • files, folder = fetch_mni_template()
    file_dict = {"T1":pjoin(folder, 'mni_icbm152_t1_tal_nlin_asym_09a.nii'),

I have no preference for a as oppose to c. If c is better, let's go with
that
… <#14f042e76c609d20_>
On Thursday, August 6, 2015, Ariel Rokem notifications@github.com
wrote: In dipy/data/fetcher.py <
https://github.com/nipy/dipy/pull/681#discussion_r36440755>: > """ > -
folder = pjoin(dipy_home, 'mni_template') > + files, folder =
fetch_mni_template() > file_dict = {"T1":pjoin(folder,
'mni_icbm152_t1_tal_nlin_asym_09a.nii'), No rush. The ROIs that we are
using for tractography segmentation are all based on the MNI template
anyway. … <#14f040978a952b82_> On Thu, Aug 6, 2015 at 10:18 AM, Samuel
St-Jean <notifications@github.com <javascript:_e(%7B%7D,'cvml','
notifications@github.com');>> wrote: In dipy/data/fetcher.py <
https://github.com/nipy/dipy/pull/681#discussion_r36440520>: > """ > -
folder = pjoin(dipy_home, 'mni_template') > + files, folder =
fetch_mni_template() > file_dict = {"T1":pjoin(folder,
'mni_icbm152_t1_tal_nlin_asym_09a.nii'), They also have a seperate license
for commercial and non commercial usage, so maybe you can just point a
download link for people while the re-licensing happens, so that people
might have it in the meantime if it's that important. — Reply to this email
directly or view it on GitHub <
https://github.com/nipy/dipy/pull/681/files#r36440520>. — Reply to this
email directly or view it on GitHub <
https://github.com/nipy/dipy/pull/681/files#r36440755>.
-- Jason D. Yeatman, PhD Assistant Professor, Institute for Learning &
Brain Sciences (I-LABS) Department of Speech & Hearing Sciences University
of Washington http://depts.washington.edu/bdelab/


Reply to this email directly or view it on GitHub
https://github.com/nipy/dipy/pull/681/files#r36445341.

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@Garyfallidis

Garyfallidis Aug 6, 2015

Member

Guys, you can fetch both and check if the ROIs correspond.

@arokem

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arokem commented Aug 6, 2015

Also, this is just a refactor of a previous PR. So, we can do all that other stuff, but on another PR.

@Garyfallidis

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Garyfallidis commented Aug 6, 2015

Sure, no problem.

@Garyfallidis

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Garyfallidis commented Aug 6, 2015

Let's go with 'a' for now and we write another PR for 'c' and the other maps.

Garyfallidis added a commit that referenced this pull request Aug 6, 2015

Merge pull request #681 from arokem/mni-citation
RF + DOC: Add MNI template reference. Also import it into the dipy.da…

@Garyfallidis Garyfallidis merged commit 93ce2ed into nipy:master Aug 6, 2015

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