Explicit mask not run

[cmaumet]

Currently the NIDM export of the "explicit mask" test case cannot be performed because the file is not available in the repo. To solve this issue, we need to:

• Include the nifti file used as an explicit mask in the repo (e.g. named "explicit_mask.nii")
• In nidm_export, re-write path to the explicit_mask.

[cmaumet]

@AlexBowring: could you do the first point above? Thanks!

[AlexBowring]

@cmaumet I have put the mask nifti in the spm_explicit_mask directory... "mask.nii". I'm not sure what you meant by 'in nidm_export, re-write...', but this is the same mask file that the batch.m file points to (line 250):

matlabbatch{1}.spm.stats.fmri_spec.mask = {'/storage/essicd/data/NIDM-Ex/Testing/ds000052/RESULTS/Sub02/mask.nii,1'};

[cmaumet]

Thanks @AlexBowring! One minor thing... Could you rename the mask file in "explicit_mask.nii" (rather than "mask.nii" that is typically the name used by SPM for the analysis mask). I will take care of the second point :)

[AlexBowring]

@cmaumet Done! :)

[cmaumet]

Great! Thanks!

[cmaumet]

@AlexBowring: it looks like explicit_mask.nii has been deleted by recent updates (cf. https://github.com/incf-nidash/nidmresults-examples/tree/master/spm_explicit_mask). Could you create a PR to add this file back so that I can implement the test of this variant?

[AlexBowring]

Hi Camille,

I think that file is now called mask.nii. Looking at the history for /master/spm-explicit-mask/ it looks like at one point with the old files I renamed mask.nii to explicit_mask.nii:

[@AlexBowring]https://github.com/AlexBowring

renamed mask.nii to explicit_mask.niihttps://github.com/incf-nidash/nidmresults-examples/commit/17d5080f3964cb2fcc08d5b64a6afb93e77e7938

AlexBowringhttps://github.com/incf-nidash/nidmresults-examples/commits/master/spm_explicit_mask?author=AlexBowring committed on Jan 11

I can rename it again if you would like?

Alex

[cmaumet]

Hi @AlexBowring. mask.nii is the filename used by SPM to store the "analysis mask" automatically created during model fitting. It's a bit confusing to use the same name for the explicit mask in this example. Could you re-run this variant using a separate file and then upload it?

[AlexBowring]

Hi @cmaumet, I've just run this again but I'm not sure I fully understand what you mean. What are you expecting in the results that isn't there? Because I don't think SPM outputs the explicit mask file.

[cmaumet]

SPM indeed does not output the explicit mask file (in fact, this file is an input of the analysis). But, for our use case, where we are planning to get the analysis exported using NIDM-Results, we need to have access to this file. That's why I was asking you to manually add the explicit_mask.nii file in this folder. Does that make sense?

[AlexBowring]

Ah okay, makes sense! I have done this and committed on the new_ground_truths branch as I'm not sure if its okay to go back and start modifying files. I have updated the PR:
#24