NF - added anatomically-constrained tractography (ACT) tissue classifier #414

gabknight · 2014-09-09T23:18:31Z

Anatomically-Constrained Tractography (ACT) from Smith et al. (neuroimage 2012).

I didn't tested it yet with actual white/grey/csf partial volume fraction maps. I will run FSL/Fast on the B0 image of the stanford_hardi dataset to get some maps. Maybe we could added those image to the dataset at some point.

Do we have a T1 image of the stanford_hardi brain?

arokem · 2014-09-09T23:25:07Z

First of all - I haven't looked in any detail, but generally this looks
awesome.

Second - yes - we have T1's and rather good segmentations on that brain.
I'm having a bit of a hectic week, and traveling, so I can't help much. In
the meanwhile look and see whether the data that Bago used in this tutorial
is sufficient (it uses some Freesurfer labels on this brain):

http://nipy.org/dipy/examples_built/streamline_tools.html#example-streamline-tools

The pertinent lines are:

from dipy.data import read_stanford_labels
hardi_img, gtab, labels_img = read_stanford_labels()

Otherwise - I can help you get all of the data, when I am back at my desk
on Thursday.

On Tue, Sep 9, 2014 at 4:18 PM, Gabriel Girard notifications@github.com
wrote:

Anatomically-Constrained Tractography (ACT) from Smith et al. (neuroimage
2012).

I didn't tested it yet with actual white/grey/csf partial volume fraction
maps. I will run FSL/Fast on the B0 image of the stanford_hardi dataset to
get some maps. Maybe we could added those image to the dataset at some
point.

Do we have a T1 image of the stanford_hardi brain?

You can merge this Pull Request by running

git pull https://github.com/gabknight/dipy add_anatomical_stopping_criteria

Or view, comment on, or merge it at:

#414
Commit Summary

NF - added anatomically-constrained tractography (ACT) tissue
classifier

File Changes

M dipy/tracking/local/init.py
https://github.com/nipy/dipy/pull/414/files#diff-0 (4)

M dipy/tracking/local/tissue_classifier.pxd
https://github.com/nipy/dipy/pull/414/files#diff-1 (13)

M dipy/tracking/local/tissue_classifier.pyx
https://github.com/nipy/dipy/pull/414/files#diff-2 (55)

M doc/examples/newApi.py
https://github.com/nipy/dipy/pull/414/files#diff-3 (36)

Patch Links:

https://github.com/nipy/dipy/pull/414.patch

https://github.com/nipy/dipy/pull/414.diff

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#414.

arokem · 2014-09-21T20:32:07Z

Hey @gabknight - thought I would circle back here to check: do you need any help with these data?

stefanv · 2014-09-22T12:37:50Z

dipy/tracking/local/tissue_classifier.pxd

-        double threshold, interp_out_double[1]
-        double[::1]  interp_out_view
-        double[:, :, :] metric_map
+        double interp_out_double[1]


Any reason to make this a MemoryView? Won't double *interp_out_double do?

IIRC This attribute is passed to a function which takes memory views as inputs. A pointer cannot be used here because pointers have not shape info and cannot be coerced into memory-views. An c array does work, but when I profiled it, I noticed that coercing a c array into a memory view adds a lot of overhead. If we can just do it once up front, it makes a noticeable difference in performance.

Perfect, I was just curious (one doesn't normally see arrays of 1).

MrBago · 2014-09-24T22:15:39Z

Sorry for breaking this PR, I rebased tracking_redesign on the latest master so travis could start testing it.

I went ahead and rebased this PR on top of that because it was very easy:

https://github.com/MrBago/dipy/tree/nf_act

gabknight · 2014-10-06T19:53:54Z

Thanks all for your comments. I addressed them. I also added a binary tissue classifier. It is useful if you know where you want to track. e.g. in the tractometer setup or using wm mask from an atlas.

I putted an example in newapi.py. The next thing to do in this PR is to add clear simple examples for the various TC.

MrBago · 2014-10-06T20:02:24Z

dipy/tracking/local/tissue_classifier.pyx

+
+        voxel[0] = int(point[0])
+        voxel[1] = int(point[1])
+        voxel[2] = int(point[2])


Should this be int(round(point))?

yes. thanks. This made me realized that new tc aren't tested well. I will push testing code..

gabknight · 2014-10-09T16:32:15Z

@MrBago I added support for various dtype in TissueClassifer. Let me know what you think.

I also added tests for tissue classifiers.

gabknight · 2014-10-09T17:11:57Z

@Garyfallidis do you have any clue on what is happening with Travis here?

Garyfallidis · 2014-10-09T17:20:37Z

It seems that Travis commited suicide. Lol. @arokem, @matthew-brett any ideas?

arokem · 2014-10-09T17:32:49Z

Rebase on master. This : #437 should
resolve your issue.

Ariel

On Thu, Oct 9, 2014 at 10:20 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

It seems that Travis commited suicide. Lol. @arokem
https://github.com/arokem, @matthew-brett
https://github.com/matthew-brett any ideas?

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#414 (comment).

gabknight · 2014-10-09T19:22:07Z

thx! @MrBago can you rebase PR #341 on master, and tracking_redesign on PR #341?

Almost there - still need to deal with that hard-coded minimum for cases where all the signal is 0. Need to think about that.

And change back the script. Whew!

Website update

Added non-local means in Changelog

From suggestion by Stefan Behnel.

arokem · 2015-01-15T17:27:06Z

@gabknight - where does this stand? Can I help with the WM/GM segmentation? I do have a higher resolution segmentation of the stanford_hardi brain that I can share, if that's helpful. Also, when you get a chance, please rebase this on top of master?

RF: change config variable to C define

@francopestilli

DOC: Link to @francopestilli's matlab implementation of LiFE.

Added option to return the number of voxels fitting the fa threshold

fixed typo

Addresses dipy#560

RF: Clean up functions that refer to non-existing data

…ates

…ates.

gabknight · 2015-01-21T21:17:31Z

This PR was on nipy:tracking_redesig. I rebased on master and created PR #565 on nipy:master.

This PR can be close.

arokem · 2015-01-21T21:26:47Z

Done.

Garyfallidis mentioned this pull request Sep 14, 2014

Traco Redesign #341

Merged

stefanv reviewed Sep 22, 2014
View reviewed changes

MrBago force-pushed the tracking_redesign branch 2 times, most recently from 786f997 to 1e65e56 Compare September 24, 2014 00:33

gabknight force-pushed the add_anatomical_stopping_criteria branch 2 times, most recently from d58f779 to baa866b Compare October 3, 2014 19:11

MrBago reviewed Oct 6, 2014
View reviewed changes

gabknight force-pushed the add_anatomical_stopping_criteria branch from 61862ab to 8ec8737 Compare October 9, 2014 19:01

gabknight force-pushed the add_anatomical_stopping_criteria branch from 8ec8737 to 6435efe Compare October 9, 2014 20:13

arokem added 3 commits December 12, 2014 11:40

RF: simplify this, move setting of min_signal to __init__ function.

ffe3f6c

Almost there - still need to deal with that hard-coded minimum for cases where all the signal is 0. Need to think about that.

BF: Pop that sucker. So that that kwarg doesn't get propagated.

abd0aac

And change back the script. Whew!

Whitespace.

e312b36

Garyfallidis and others added 6 commits January 7, 2015 18:11

DOC: update index about release

c3b4836

DOC: a more precise intro

40d0ab4

Merge pull request dipy#551 from Garyfallidis/website_update_07Jan2015

f313940

Website update

Merge pull request dipy#550 from Garyfallidis/denoise_in_changelog

fee670d

Added non-local means in Changelog

DOC: Link to @francopestilli's matlab implementation of LiFE.

080a123

RF: change config variable to C define

7e8c24d

From suggestion by Stefan Behnel.

stefanv and others added 18 commits January 15, 2015 11:43

Merge pull request dipy#556 from matthew-brett/config-var-define

7096103

RF: change config variable to C define

Merge pull request dipy#554 from arokem/life-matlab

d381453

DOC: Link to @francopestilli's matlab implementation of LiFE.

Added option to return the number of voxels fittign the fa threshold

79e62cc

Added tournier 2004 ref + docstring chnage

9baac33

Merge pull request dipy#561 from samuelstjean/fix_auto_response

1bdc501

Added option to return the number of voxels fitting the fa threshold

fixed typo

c0b11dc

Merge pull request dipy#564 from samuelstjean/patch-1

372fa61

fixed typo

RF: Cleanup functions that refer to some data that no longer exists here

b08a733

Addresses dipy#560

Merge pull request dipy#563 from arokem/remove-multishell-cruft

7f5b34d

RF: Clean up functions that refer to non-existing data

NF - added anatomically-constrained tractography (ACT) tissue classifier

2d13a4b

STYLE - addressed PEP8 comments, added references

da15af9

STYLE - updated error msg

f1a9a8d

NF - added binary tissue classifier.

498e6e0

BF - added a missing round() to map streamline point to voxel coordin…

90bb548

…ates

BF - added a missing round() to map streamline point to voxel coordin…

bd89a81

…ates.

BF - handle various dtype input in tissue classifier

826e283

TST - tests for tissue classifiers

a391aa5

DOC - wip tissue classifier exemple

4a00976

gabknight force-pushed the add_anatomical_stopping_criteria branch from 6435efe to 4a00976 Compare January 21, 2015 21:02

gabknight mentioned this pull request Jan 21, 2015

Adding New Tissue Classifiers #565

Merged

arokem closed this Jan 21, 2015

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NF - added anatomically-constrained tractography (ACT) tissue classifier #414

NF - added anatomically-constrained tractography (ACT) tissue classifier #414

gabknight commented Sep 9, 2014

arokem commented Sep 9, 2014

Do we have a T1 image of the stanford_hardi brain?

arokem commented Sep 21, 2014

stefanv Sep 22, 2014

MrBago Sep 24, 2014

stefanv Sep 24, 2014

MrBago commented Sep 24, 2014

gabknight commented Oct 6, 2014

MrBago Oct 6, 2014

gabknight Oct 6, 2014

gabknight commented Oct 9, 2014

gabknight commented Oct 9, 2014

Garyfallidis commented Oct 9, 2014

arokem commented Oct 9, 2014

gabknight commented Oct 9, 2014

arokem commented Jan 15, 2015

gabknight commented Jan 21, 2015

arokem commented Jan 21, 2015

NF - added anatomically-constrained tractography (ACT) tissue classifier #414

NF - added anatomically-constrained tractography (ACT) tissue classifier #414

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gabknight commented Sep 9, 2014

arokem commented Sep 9, 2014

Do we have a T1 image of the stanford_hardi brain?

arokem commented Sep 21, 2014

stefanv Sep 22, 2014

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gabknight commented Oct 9, 2014

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arokem commented Oct 9, 2014

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arokem commented Jan 15, 2015

gabknight commented Jan 21, 2015

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