Direction of effects inverted

1

Hi there,

I am encountering an issue where I ran out of options.

I am using nistats for 1/2 level analysis and the results are exactly inverted to my expectation in multiple investigations. Most prominent is the negative activation for a button press condition in relation to baseline (no other button press condition in all of the experiment), using the left hand, in the right motor cortex. Please see

catch_trails_baselinecontrast
catch_trails_baselinecontrast.jpg1474×408 198 KB

I used the following code for contrast coding and plotting

zmap = second_level_model.compute_contrast(first_level_contrast='CATCH')
plotting.plot_glass_brain(zmap, colorbar=True, threshold=norm.isf(0.001),
                          title='CATCH (unc p<0.001)',
                          plot_abs=False, display_mode='lyrz')

the fitted models had the following form

FirstLevelModel(drift_model='cosine', drift_order=1, fir_delays=[0],
        hrf_model='glover', mask=None, memory=Memory(cachedir=None),
        memory_level=1, min_onset=-24, minimize_memory=True, n_jobs=1,
        noise_model='ar1', period_cut=128, signal_scaling=True,
        slice_time_ref=0.0, smoothing_fwhm=8.0, standardize=False,
        subject_label='3IK02', t_r=2.25, target_affine=None,
        target_shape=None, verbose=0)

using the first_level_models_from_bids function.

In addition, I used fMRIprep for preprocessing and Dcm2niix to convert my dicoms to niftis.

Any suggestions/ideas where this might originate from?
Thanks in advance.
Best wishes,
Benjamin

2

Still working on this issue …
More information can be found here: https://github.com/nistats/nistats/issues/274

in addition I used the following command lines for fMRIprep, could it be the case that this would lead to the inversion of the BOLD signal?

docker run --rm -it -v /…/BIDS/:/data:ro -v /…/Data_output/:/out -v /…/license.txt:/opt/freesurfer/license.txt poldracklab/fmriprep:1.0.0 /data /out participant --participant_label sub-YBA08

singularity run /…/poldracklab_fmriprep_latest-2018-04-16-d35305e5bdb8.img \ /…/BIDS/ /…/Data_output/ --fs-license-file /…/license.txt \ participant \ --participant-label BHK18

Thanks in advance,
Best wishes,
Benjamin

3

I cannot see how FMRIPREP could lead to such issue. It’s most likely a bug in model definition.

4

Thanks for clarification.