WIP: Dmri nipype #609

baothien · 2013-07-15T18:36:00Z

No description provided.

chrisgorgo · 2013-07-15T18:41:56Z

examples/dmri_tractography.py

+
+from dmri_classInterfaces import BrainExtraction, EddyCorrection, ResampleVoxelSize, TensorModel, Tracking
+
+path ='/home/bao/tiensy/Nipype_tutorial/data/dmri/temp6/'


Please use Datasink for storing results instead of setting abs paths for output files. See http://nipy.sourceforge.net/nipype/users/grabbing_and_sinking.html#datasink

chrisgorgo · 2013-07-15T18:53:30Z

Looks like a very valuable contribution, but there are still a few glitches to fix. @Garyfallidis care to have a look?

Garyfallidis · 2013-07-26T18:29:59Z

Many apologies, for my delayed answer. I was running with different things. I will look at this during the weekend and get back to you. In short, there are many nice things that you can add in this pipeline e.g. constrained deconvolution etc. Best wishes.

chrisgorgo · 2013-09-10T07:57:06Z

@baothien any chances that you could finish working on this before the next release? ETA 2 weeks

chrisgorgo · 2013-09-13T12:17:16Z

Thanks for addin the datasink. We are almost there. There are still some issues remaining (see comments above).

Garyfallidis · 2013-09-14T15:35:48Z

nipype/interfaces/dmri_preprocessing.py

+Pre-processing dMRI data, including 03 steps
+1. Brain extraction
+2. Eddy current correction
+3. Resample data to isotrophy, usually to voxel size (2.,2.,2.)


Typo: to isotropic

Garyfallidis · 2013-09-14T15:41:38Z

Hi guys, apologies for the delay and thank you for the effort and the feedback. I have a general question. What is the purpose of this dMRI pipeline? dMRI is a very general term. From what I see you only use Tensors and deterministic tracking here. Is that correct? Also the .dpy file format is still experimental and few people will have access to HDF5 that is required for that. You may want to save things in Trackvis or a different format.

chrisgorgo · 2013-12-19T11:42:17Z

Any progress on this? It would be great to see it being part of nipype soon...

oesteban · 2013-12-28T18:35:15Z

Dear all, I'm very interested on this issue. I will take a look on it starting on January and see if I can give a hand.

Anyways, I totally agree with @Garyfallidis:

we should define the scope of this pipeline,
the term dMRI might not be very appropriate for interfaces... but I let this question for the nipype experts. I don't think this is crucial, though.
we should also use trackvis, as it is the most standard format currently

So, what do you think?

Garyfallidis · 2013-12-28T19:10:07Z

@chrisfilo let's organize I hangout by the beginning of the year. I will be back in the office after the 10th of January. I think we can help each other and create some very nice pipelines using dipy. But let's talk first.

baothien · 2013-12-28T20:25:21Z

Hi Chris and all,

Sorry for late reply. I am in travelling from 16-Dec.
It would be great if we can have a talk first, and then decide what to do
next. Currently, the pipeline works well with input in .nifti format and
the tractography output in .dpy format. However, it is correct that the
trackvis is more popular and if it is necessary we can use .trk format for
output.

Regards,

T.Bao

On Sat, Dec 28, 2013 at 8:10 PM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

@chrisfilo https://github.com/chrisfilo let's organize I hangout by the
beginning of the year. I will be back in the office after the 10th of
January. I think we can help each other and create some very nice pipelines
using dipy. But let's talk first.

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/609#issuecomment-31302733
.

Nguyen Thien Bao

NeuroInformatics Laboratory (NILab), Fondazione Bruno Kessler (FBK),
Trento, Italy
Centro Interdipartimentale Mente e Cervello (CIMeC), Universita degli Studi
di Trento, Italy
Surgical Planning Laboratory (SPL), Department of Radiology, BWH, Harvard
Medical School, USA
Email: bao at bwh.harvard.edu or tbnguyen at fbk.eu or ntbaovn at gmail.com
Fax: +39.0461.283.091
Cellphone: +1. 857.265.6408 (USA)
+39.345.293.1006 (Italy)
+84.996.352.452 (VietNam)

chrisgorgo · 2014-01-02T10:17:09Z

Happy new year everybody!

I'm back and happy to arrange a google hangout whenever everybody is ready.

Best,
Chris

On Sat, Dec 28, 2013 at 9:25 PM, baothien notifications@github.com wrote:

Hi Chris and all,

Sorry for late reply. I am in travelling from 16-Dec.
It would be great if we can have a talk first, and then decide what to do
next. Currently, the pipeline works well with input in .nifti format and
the tractography output in .dpy format. However, it is correct that the
trackvis is more popular and if it is necessary we can use .trk format for
output.

Regards,

T.Bao

On Sat, Dec 28, 2013 at 8:10 PM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

@chrisfilo https://github.com/chrisfilo let's organize I hangout by
the
beginning of the year. I will be back in the office after the 10th of
January. I think we can help each other and create some very nice
pipelines
using dipy. But let's talk first.

—
Reply to this email directly or view it on GitHub<
https://github.com/nipy/nipype/pull/609#issuecomment-31302733>
.

Nguyen Thien Bao

NeuroInformatics Laboratory (NILab), Fondazione Bruno Kessler (FBK),
Trento, Italy
Centro Interdipartimentale Mente e Cervello (CIMeC), Universita degli
Studi
di Trento, Italy
Surgical Planning Laboratory (SPL), Department of Radiology, BWH, Harvard
Medical School, USA
Email: bao at bwh.harvard.edu or tbnguyen at fbk.eu or ntbaovn at
gmail.com
Fax: +39.0461.283.091
Cellphone: +1. 857.265.6408 (USA)
+39.345.293.1006 (Italy)
+84.996.352.452 (VietNam)

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/609#issuecomment-31304129
.

baothien · 2014-01-10T14:52:31Z

Dear Chris and all guys,

Hope that all you have good holiday with your family and friends.

I think that it is time for back to work. Do you have any idea for a google
hangout.
How about end of this week?

Wait for your reply.

On Thu, Jan 2, 2014 at 11:17 AM, Chris Filo Gorgolewski <
notifications@github.com> wrote:

Happy new year everybody!

I'm back and happy to arrange a google hangout whenever everybody is
ready.

Best,
Chris

On Sat, Dec 28, 2013 at 9:25 PM, baothien notifications@github.com
wrote:

Hi Chris and all,

Sorry for late reply. I am in travelling from 16-Dec.
It would be great if we can have a talk first, and then decide what to
do
next. Currently, the pipeline works well with input in .nifti format and
the tractography output in .dpy format. However, it is correct that the
trackvis is more popular and if it is necessary we can use .trk format
for
output.

Regards,

T.Bao

On Sat, Dec 28, 2013 at 8:10 PM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

@chrisfilo https://github.com/chrisfilo let's organize I hangout by
the
beginning of the year. I will be back in the office after the 10th of
January. I think we can help each other and create some very nice
pipelines
using dipy. But let's talk first.

—
Reply to this email directly or view it on GitHub<
https://github.com/nipy/nipype/pull/609#issuecomment-31302733>
.

Nguyen Thien Bao

NeuroInformatics Laboratory (NILab), Fondazione Bruno Kessler (FBK),
Trento, Italy
Centro Interdipartimentale Mente e Cervello (CIMeC), Universita degli
Studi
di Trento, Italy
Surgical Planning Laboratory (SPL), Department of Radiology, BWH,
Harvard
Medical School, USA
Email: bao at bwh.harvard.edu or tbnguyen at fbk.eu or ntbaovn at
gmail.com
Fax: +39.0461.283.091
Cellphone: +1. 857.265.6408 (USA)
+39.345.293.1006 (Italy)
+84.996.352.452 (VietNam)

—
Reply to this email directly or view it on GitHub<
https://github.com/nipy/nipype/pull/609#issuecomment-31304129>
.

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/609#issuecomment-31444999
.

Nguyen Thien Bao

NeuroInformatics Laboratory (NILab), Fondazione Bruno Kessler (FBK),
Trento, Italy
Centro Interdipartimentale Mente e Cervello (CIMeC), Universita degli Studi
di Trento, Italy
Surgical Planning Laboratory (SPL), Department of Radiology, BWH, Harvard
Medical School, USA
Email: bao at bwh.harvard.edu or tbnguyen at fbk.eu or ntbaovn at gmail.com
Fax: +39.0461.283.091
Cellphone: +1. 857.265.6408 (USA)
+39.345.293.1006 (Italy)
+84.996.352.452 (VietNam)

Garyfallidis · 2014-01-21T19:22:43Z

Hi Chris and all,

I am available this week on Thursday to speak about Dipy & Nipype.

Is 2 PM EST good for you?
http://wwp.greenwichmeantime.com/time-zone/usa/eastern-time/

Best wishes,
Eleftherios

oesteban · 2014-01-23T15:46:16Z

I'm sorry, I've just checked it out.

I can't make it today, but may I join your meeting if you postpone it for next week?

chrisgorgo · 2014-01-23T16:09:44Z

It would be great if you could join in. Could everyone interested fill in
their availability?
http://app.scheduleonce.com/MP.aspx?param=VD0xLk09MTExNzg3NS5VPS0x

On Thu, Jan 23, 2014 at 4:46 PM, Oscar Esteban notifications@github.comwrote:

I'm sorry, I've just checked it out.

I can't make it today, but may I join your meeting if you postpone it for
next week?

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/609#issuecomment-33135128
.

baothien · 2014-01-28T12:10:55Z

Dear all,

I am very sorry. I would not be able to attend the meeting due to the Lunar
New Year in Vietnam. But I am very appreciated if someone can summarize and
let me know what is the idea for this project.

Thank you in advance and hope to work with all of you.

Regards,

T.Bao

On Thu, Jan 23, 2014 at 11:09 PM, Chris Filo Gorgolewski <
notifications@github.com> wrote:

It would be great if you could join in. Could everyone interested fill in
their availability?
http://app.scheduleonce.com/MP.aspx?param=VD0xLk09MTExNzg3NS5VPS0x

On Thu, Jan 23, 2014 at 4:46 PM, Oscar Esteban notifications@github.comwrote:

I'm sorry, I've just checked it out.

I can't make it today, but may I join your meeting if you postpone it
for
next week?

—
Reply to this email directly or view it on GitHub<
https://github.com/nipy/nipype/pull/609#issuecomment-33135128>
.

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/609#issuecomment-33138148
.

Nguyen Thien Bao

NeuroInformatics Laboratory (NILab), Fondazione Bruno Kessler (FBK),
Trento, Italy
Centro Interdipartimentale Mente e Cervello (CIMeC), Universita degli Studi
di Trento, Italy
Surgical Planning Laboratory (SPL), Department of Radiology, BWH, Harvard
Medical School, USA
Email: bao at bwh.harvard.edu or tbnguyen at fbk.eu or ntbaovn at gmail.com
Fax: +39.0461.283.091
Cellphone: +1. 857.265.6408 (USA)
+39.345.293.1006 (Italy)
+84.996.352.452 (VietNam)

oesteban · 2014-09-05T08:17:20Z

Maybe of your interest: #910

effigies · 2018-01-22T01:45:07Z

This pull request is "orphaned," which means it has been deemed to be abandoned by its original author. Orphaned pull requests have not been rejected, and we hope that if a user sees one that will meet their needs with a little work, that they will fork it and open a new pull request (or, in the case of the original author, reopen the original PR).

We ask that all adopted PRs be updated to merge or rebase the current master. If you would like to adopt a PR and need help getting started, any of a number of contributors will be happy to help.

baothien added 2 commits July 15, 2013 20:16

workflow for reconstructing tractography from dmri data

4c3585c

preprocessing and tracking interfaces

fe1fb13

chrisgorgo reviewed Jul 15, 2013
View reviewed changes

remove brain extraction class and unecessary code

965777d

Add DataSink node for storing the results

9515c9e

Garyfallidis reviewed Sep 14, 2013
View reviewed changes

chrisgorgo changed the title ~~Dmri nipype~~ WIP: Dmri nipype Sep 29, 2014

effigies closed this Jan 21, 2018

effigies added the orphaned label Jan 21, 2018


		from dmri_classInterfaces import BrainExtraction, EddyCorrection, ResampleVoxelSize, TensorModel, Tracking

		path ='/home/bao/tiensy/Nipype_tutorial/data/dmri/temp6/'

WIP: Dmri nipype #609

WIP: Dmri nipype #609

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baothien commented Jul 15, 2013

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baothien commented Jan 28, 2014

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effigies commented Jan 22, 2018

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