[FIX] fix cluster threshold in randomise + change default prefix #2063

jokedurnez · 2017-06-04T01:03:12Z

Changes proposed in this pull request

The base name tbss in randomise is very confusing, so I changed it to randomise (and removed the _, as FSL adds it too).
Also, the cluster thresholds with 2 digits are not read. Not sure about the other thresholds, so I didn't touch those.

mgxd · 2017-06-09T15:30:10Z

@jokedurnez can you run make specs and add the updated auto-test?

satra · 2017-09-11T18:46:22Z

@jokedurnez - it would be great if you can merge master and add the updated auto-test.

jokedurnez · 2017-09-12T19:38:57Z

I believe the tests failed exactly because of one of the changes I made, so I'm not sure what to do. Probably I should change the test as well, but that would require me to take some time to dive into the testing stuff. I'll try, but it won't be tomorrow... :\

oesteban · 2017-10-09T17:57:05Z

Hi @jokedurnez, sorry for joining late to the party.

I think that doing the following will resolve this error:

At your nipype's repo root directory, with your patch-8 branch checked out, run make specs
Then git add nipype/interfaces/fsl/tests/test_auto_Randomise.py
git commit -m 'updated Randomise specs' && git push

- use master branch for caching - replace kaczmarj/nipype with nipype/nipype - reset cache prefixes - use latest docker (v17.10.0-ce) containers and machine - use environment variable to determine whether to pull or build base image - save docker images to tar.gz if on master branch (deploying) - use fastest gzip compression (gives good ratio of speed/compression)

…odocker

ENH: Enable recon-all -FLAIR / -FLAIRpial options

earlier setuptools did not like mixing directories and files

Throw a warning instead.

- do not store dockerfiles in repo - cache base dockerfile in deploy step that was generated in `compare_base_dockerfiles` step - use global `working_directory`

fix: testing for non-developer installation

…visions

…tor-revisions

… last commit)

ENH: generate Dockerfiles with neurodocker + migrate to CircleCI 2.0

…tor-revisions

Reset change to make hash assertion at https://github.com/nipy/nipype/blob/master/nipype/interfaces/base/tests/test_support.py#L60 happy.

[ENH] Extended MRtrix3 interface

[MAINT] Cleaning / simplify Node

… into forwho-DiffusionToolkit_fix

[FIX] Fix surf_reg input trait

STY: deleting tailing spaces and adding missing newlines at end of files

updating dti.py (cont nipy#1653)

codecov-io · 2018-01-10T21:44:00Z

Codecov Report

Merging #2063 into master will decrease coverage by 19.77%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           master    #2063       +/-   ##
===========================================
- Coverage   72.16%   52.39%   -19.78%     
===========================================
  Files        1137      118     -1019     
  Lines       57194    23654    -33540     
  Branches     8194        0     -8194     
===========================================
- Hits        41276    12394    -28882     
+ Misses      14629    11260     -3369     
+ Partials     1289        0     -1289

Flag	Coverage Δ
#smoketests	`52.39% <ø> (-19.78%)`	⬇️
#unittests	`?`

Impacted Files	Coverage Δ
nipype/interfaces/fsl/model.py	`73.36% <ø> (-7.22%)`	⬇️
nipype/pipeline/plugins/callback_log.py	`12% <0%> (-80%)`	⬇️
nipype/workflows/smri/freesurfer/ba_maps.py	`11.11% <0%> (-79.17%)`	⬇️
nipype/workflows/rsfmri/fsl/resting.py	`14.51% <0%> (-70.97%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon2.py	`2.68% <0%> (-68.59%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon3.py	`2.43% <0%> (-66.67%)`	⬇️
nipype/pipeline/plugins/pbsgraph.py	`29.41% <0%> (-64.71%)`	⬇️
nipype/workflows/smri/freesurfer/bem.py	`38.46% <0%> (-61.54%)`	⬇️
nipype/interfaces/utility/csv.py	`42.85% <0%> (-57.15%)`	⬇️
nipype/workflows/smri/freesurfer/recon.py	`9.28% <0%> (-56.43%)`	⬇️
... and 1074 more

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oesteban · 2018-01-11T00:44:42Z

Please follow-up in #2369. I kept your commits (@jokedurnez's and @mgxd's) there.

mgxd added this to the 0.14.0 milestone Oct 18, 2017

effigies and others added 25 commits November 13, 2017 10:18

FIX: T2/FLAIR inputs not mutually exclusive

77f5bd4

regenerate dockerfiles with base nipype/nipype:base

637f033

use nipype/nipype repo instead of kaczmarj/nipype

399fe16

Merge remote-tracking branch 'upstream/master' into enh/circleci-neur…

126831e

…odocker

Merge pull request nipy#2279 from effigies/enh/reconall_flair

68e8ef0

ENH: Enable recon-all -FLAIR / -FLAIRpial options

fix: testing for non-developer installation

38f8b63

fix: missing comma

0f4a190

fix: included testing data

4a6351b

earlier setuptools did not like mixing directories and files

[FIX] Do not break when building profiling summary

e50226e

Throw a warning instead.

generate dockerfiles in ci + rm dockerfiles

28547cc

- do not store dockerfiles in repo - cache base dockerfile in deploy step that was generated in `compare_base_dockerfiles` step - use global `working_directory`

Merge pull request nipy#2280 from mgxd/fix/pytest

c4a249a

fix: testing for non-developer installation

add jakub kaczmarzyk (mit)

56838b9

sty: whitespaces

bba7a7c

enable reuse of resource_monitor.json, write it in base_dir

d7a2d16

Merge branch 'fix/resource-monitor-file' into fix/resource-monitor-re…

58b4905

…visions

Merge remote-tracking branch 'upstream/master' into fix/resource-moni…

75cb366

…tor-revisions

allow disable resource_monitor appending with nipype option

b72f9aa

allow disable resource_monitor appending with nipype option (amend to…

cd46847

… last commit)

improving documentation of new config entry

8e79259

add new [monitoring] section to nipype config

afa63dc

read new monitoring.summary_file option

0100135

Merge pull request nipy#2202 from kaczmarj/enh/circleci-neurodocker

edaf222

ENH: generate Dockerfiles with neurodocker + migrate to CircleCI 2.0

Merge remote-tracking branch 'upstream/master' into fix/resource-moni…

b159b01

…tor-revisions

Merge branch 'master' of git://github.com/nipy/nipype into rel/0.14.0

92974cf

oesteban and others added 24 commits January 7, 2018 11:28

elevate trace to warning

d0e1ec8

add test for cwd

ee7c70b

cleaning pe.utils

459e0ac

finishing pe.nodes cleanup

1725515

finishing pe.nodes - unfinished hashfiles

4e0f6e1

fix Bunch does not have keys()

396aa1e

[skip ci] fix ordering as per @djarecka

bb905b9

[skip ci] Extend docstring as per @djarecka

4e4c670

[skip ci] Update CHANGES

a80c9b1

Reset change to make hash assertion happy

6f7ae71

Reset change to make hash assertion at https://github.com/nipy/nipype/blob/master/nipype/interfaces/base/tests/test_support.py#L60 happy.

FIX: Reset change to make hash assertion happy

132bd89

FIX: updates hash to accept newline in realign_json.json

974ae09

Merge remote-tracking branch 'upstream/master' into enh-mrtrix3

6401e97

Minor fix (test)

c31d7cd

Merge pull request nipy#2338 from matteomancini/enh-mrtrix3

cfcd8f6

[ENH] Extended MRtrix3 interface

Merge pull request nipy#2325 from oesteban/ref/Node-cleanup

9be816e

[MAINT] Cleaning / simplify Node

Merge branch 'DiffusionToolkit_fix' of https://github.com/forwho/nipype…

fb2628e

… into forwho-DiffusionToolkit_fix

updating the auto test

ee06cc8

Merge pull request nipy#2352 from oesteban/fix/vol2surf

17151d6

[FIX] Fix surf_reg input trait

Merge pull request nipy#2355 from miykael/STY_space_correction

6f5b7f7

STY: deleting tailing spaces and adding missing newlines at end of files

Merge pull request nipy#2361 from djarecka/forwho-DiffusionToolkit_fix

8384523

updating dti.py (cont nipy#1653)

[HOTFIX] Incorrect call to warnings.warn

00ef467

fix: doctest

09465cf

fix: randomise autotest

3fedaab

oesteban mentioned this pull request Jan 11, 2018

[FIX] Cluster threshold in randomise + change default prefix #2369

Merged

oesteban closed this Jan 11, 2018

effigies modified the milestones: 0.14.1, 1.0 Jan 25, 2018

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[FIX] fix cluster threshold in randomise + change default prefix #2063

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[FIX] fix cluster threshold in randomise + change default prefix #2063

[FIX] fix cluster threshold in randomise + change default prefix #2063

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