ENH: Add flags dictionary input to spm.Level1Design #2861
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## master #2861 +/- ##
==========================================
- Coverage 67.39% 67.02% -0.38%
==========================================
Files 341 343 +2
Lines 43428 44798 +1370
Branches 5396 5848 +452
==========================================
+ Hits 29270 30026 +756
- Misses 13461 13983 +522
- Partials 697 789 +92
Continue to review full report at Codecov.
|
This was referenced Feb 20, 2019
Merged
Co-Authored-By: hstojic <hrvoje.stojic@protonmail.com>
effigies
approved these changes
Feb 24, 2019
yarikoptic
added a commit
to yarikoptic/nipype
that referenced
this pull request
Mar 15, 2019
1.1.9 (February 25, 2019) Full changelog: https://github.com/nipy/nipype/milestone/30?closed=1 * FIX: Make positional arguments to LaplacianThickness require previous argument (nipy#2848) * FIX: Import math and csv modules for bids_gen_info (nipy#2881) * FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (nipy#2739) * ENH: Allow afni.MaskTool to take multiple input files (nipy#2892) * ENH: Add flags dictionary input to spm.Level1Design (nipy#2861) * ENH: Threshold stddev once only in TSNR (nipy#2883) * ENH: Add workbench.CiftiSmooth interface (nipy#2871) * DOC: Replace initialism typo in comment with intended phrase (nipy#2875) * DOC: Fix typos in ANTs Registration input documentation (nipy#2869) * tag '1.1.9': (34 commits) MNT: Update changelog MNT: Add Katherine Bottenhorn, Paul Mihai to Zenodo MNT: Add kchawla-pi to Zenodo, update mailmap and ordering add to zenodo MNT: Update zenodo ordering Update .zenodo.json afni utils.py - masktool - InputMultiPath for in_file argument MNT: Update .zenodo ordering MNT: Add Oliver Contier name to .zenodo.json Update nipype/interfaces/spm/model.py ENH: Add zenodo updating script MNT: Update mailmap to avoid renames in script MNT: Update .mailmap, .zenodo.json MNT: Version 1.1.9 DOC: 1.1.9 changelog ENH: minor - compute non degenerate stddev map once BF: regenerated test_auto_LaplacianThickness using wonderfully long running tools/checkspecs.py TEST: Thorough test of LaplacianThickness requirement cascade FIX: Requires error text was backwards import math and csv modules for bids_gen_info ...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Summary
One common thing in SPM is to change the default masking threshold in the
stats.fmri_specpart. It is set to 0.8 which is quite high if you are interested in midbrain regions, OFC etc that have lower signal. At the moment I don't see how to set this default and a correct way seemed to be to addflagsoption, similar to the one implemented in theEstimateModelfunction. I tried it out on my local version and it does work correctly, it adds a correct line to the .m file created by Nipype for this job. and resulting images correspondingly change.If some additional files with documentation should be changed, do let me know.
Re Run
make check-before-commitbefore submitting the PR. Where can I find info about libraries that I need to install to run this? If I run it on basic Ubuntu OS terminal it complains about missing libraries.List of changes proposed in this PR (pull-request)
flagsargument inLevel1DesignfunctionAcknowledgment