fMRIPREP - Layout object

Joan_Carreras_Diaz · February 5, 2024, 11:26am

Dear Neurostars team,
I am trying to follow the steps given in the tutorial Functional Neuroimaging Analysis in Python but I am facing some problems when I execute the function layout = bids.BIDSLayout('../data/ds000030/derivatives/fmriprep/', config=['bids','derivatives']). I should have to obtain the list of my subjects once I execute layout.get_subjects()but in order, my result is [ ].

Later in the tutorial, is being said that is necessary to run this function.
If we didn’t configure pyBIDS with config=['bids','derivatives'] then the desc keyword would not work!.
I am adding a screenshot too of my Python file.

Steven · February 5, 2024, 2:02pm

Hi @Joan_Carreras_Diaz,

It would help if we had the BIDS validation report on the BIDS root directory and the tree output of the fmriprep output directory.

Best,
Steven

Joan_Carreras_Diaz · February 5, 2024, 3:39pm

Yes, of course, the tree output of the fmriprep directory is the following one:

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep
├── dataset_description.json
├── desc-aparcaseg_dseg.tsv
├── desc-aseg_dseg.tsv
├── logs
├── sub-ADNI002S0413
└── sub-ADNI002S0413.html

I don’t think I have any file with the BIDS validation report, as I don’t have any index.html file in the BIDS_DIRECTORY folder:

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY
├── README
├── conversion_info
├── dataset_description.json
├── derivatives
├── participants.tsv
└── sub-ADNI002S0413

However, I have run bids-validator /Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY and I have obtained the following message:

bids-validator@1.14.0
(node:15960) [DEP0040] DeprecationWarning: The `punycode` module is deprecated. Please use a userland alternative instead.
(Use `node --trace-deprecation ...` to show where the warning was created)
(node:15960) Warning: Closing directory handle on garbage collection
This dataset appears to be BIDS compatible.
        Summary:                  Available Tasks:        Available Modalities: 
        68 Files, 524.32MB                                MRI                   
        1 - Subject                                       PET                   
        13 - Sessions                                                           


	If you have any questions, please post on https://neurostars.org/tags/bids.

Thank you,
Joan

Steven · February 5, 2024, 3:46pm

What about tree run on the fMRIPrep subject output, that is, tree /Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/

Joan_Carreras_Diaz · February 5, 2024, 4:02pm

The simplification of that would be the following one:

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/
├── anat
├── figures
├── log
├── ses-M000
├── ses-M006
├── ses-M012
├── ses-M024
├── ses-M036
├── ses-M048
├── ses-M060
├── ses-M072
├── ses-M084
├── ses-M096
├── ses-M108
├── ses-M132
└── ses-M162

If you might prefer the entire one it looks like this:

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/
├── anat
│   ├── sub-ADNI002S0413_desc-brain_mask.json
│   ├── sub-ADNI002S0413_desc-brain_mask.nii.gz
│   ├── sub-ADNI002S0413_desc-preproc_T1w.json
│   ├── sub-ADNI002S0413_desc-preproc_T1w.nii.gz
│   ├── sub-ADNI002S0413_desc-ribbon_mask.json
│   ├── sub-ADNI002S0413_desc-ribbon_mask.nii.gz
│   ├── sub-ADNI002S0413_dseg.nii.gz
│   ├── sub-ADNI002S0413_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│   ├── sub-ADNI002S0413_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   ├── sub-ADNI002S0413_from-T1w_to-fsnative_mode-image_xfm.txt
│   ├── sub-ADNI002S0413_from-fsnative_to-T1w_mode-image_xfm.txt
│   ├── sub-ADNI002S0413_hemi-L_desc-reg_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-L_midthickness.surf.gii
│   ├── sub-ADNI002S0413_hemi-L_pial.surf.gii
│   ├── sub-ADNI002S0413_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-L_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-L_sulc.shape.gii
│   ├── sub-ADNI002S0413_hemi-L_thickness.shape.gii
│   ├── sub-ADNI002S0413_hemi-L_white.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_desc-reg_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_midthickness.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_pial.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_sphere.surf.gii
│   ├── sub-ADNI002S0413_hemi-R_sulc.shape.gii
│   ├── sub-ADNI002S0413_hemi-R_thickness.shape.gii
│   ├── sub-ADNI002S0413_hemi-R_white.surf.gii
│   ├── sub-ADNI002S0413_label-CSF_probseg.nii.gz
│   ├── sub-ADNI002S0413_label-GM_probseg.nii.gz
│   ├── sub-ADNI002S0413_label-WM_probseg.nii.gz
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_desc-brain_mask.json
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_dseg.nii.gz
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
│   ├── sub-ADNI002S0413_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
│   └── sub-ADNI002S0413_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
├── figures
│   ├── sub-ADNI002S0413_desc-conform_T1w.html
│   ├── sub-ADNI002S0413_desc-reconall_T1w.svg
│   ├── sub-ADNI002S0413_dseg.svg
│   ├── sub-ADNI002S0413_ses-M000_desc-about_T1w.html
│   ├── sub-ADNI002S0413_ses-M000_desc-summary_T1w.html
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-carpetplot_bold.svg
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-compcorvar_bold.svg
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-confoundcorr_bold.svg
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-coreg_bold.svg
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-rois_bold.svg
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-summary_bold.html
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-carpetplot_bold.svg
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-compcorvar_bold.svg
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-confoundcorr_bold.svg
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-coreg_bold.svg
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-rois_bold.svg
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-summary_bold.html
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-carpetplot_bold.svg
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-compcorvar_bold.svg
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-confoundcorr_bold.svg
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-coreg_bold.svg
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-rois_bold.svg
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-summary_bold.html
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-carpetplot_bold.svg
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-compcorvar_bold.svg
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-confoundcorr_bold.svg
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-coreg_bold.svg
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-rois_bold.svg
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-summary_bold.html
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-carpetplot_bold.svg
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-compcorvar_bold.svg
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-confoundcorr_bold.svg
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-coreg_bold.svg
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-rois_bold.svg
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-summary_bold.html
│   ├── sub-ADNI002S0413_ses-M132_task-rest_desc-validation_bold.html
│   └── sub-ADNI002S0413_space-MNI152NLin2009cAsym_T1w.svg
├── log
│   ├── 20240117-185138_35bcf3be-da65-485c-a6b4-fb456cf9e865
│   │   ├── crash-20240117-201746-root-anat_merge-b67922a0-fe47-4606-bd80-2ff14f427aa1.txt
│   │   └── fmriprep.toml
│   ├── 20240130-152425_78a06a63-ee48-4bc3-b642-63352eaedc34
│   │   └── fmriprep.toml
│   └── 20240201-191731_98442f86-414d-4962-bfe3-cef64248ea16
│       └── fmriprep.toml
├── ses-M000
│   └── anat
│       └── sub-ADNI002S0413_ses-M000_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M006
│   └── anat
│       └── sub-ADNI002S0413_ses-M006_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M012
│   └── anat
│       └── sub-ADNI002S0413_ses-M012_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M024
│   └── anat
│       └── sub-ADNI002S0413_ses-M024_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M036
│   └── anat
│       └── sub-ADNI002S0413_ses-M036_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M048
│   └── anat
│       └── sub-ADNI002S0413_ses-M048_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M060
│   ├── anat
│   │   └── sub-ADNI002S0413_ses-M060_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-ADNI002S0413_ses-M060_task-rest_desc-confounds_timeseries.json
│       ├── sub-ADNI002S0413_ses-M060_task-rest_desc-confounds_timeseries.tsv
│       ├── sub-ADNI002S0413_ses-M060_task-rest_desc-coreg_boldref.json
│       ├── sub-ADNI002S0413_ses-M060_task-rest_desc-coreg_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M060_task-rest_desc-hmc_boldref.json
│       ├── sub-ADNI002S0413_ses-M060_task-rest_desc-hmc_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M060_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-ADNI002S0413_ses-M060_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-ADNI002S0413_ses-M060_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-ADNI002S0413_ses-M060_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│       ├── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
│       └── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── ses-M072
│   ├── anat
│   │   └── sub-ADNI002S0413_ses-M072_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-ADNI002S0413_ses-M072_task-rest_desc-confounds_timeseries.json
│       ├── sub-ADNI002S0413_ses-M072_task-rest_desc-confounds_timeseries.tsv
│       ├── sub-ADNI002S0413_ses-M072_task-rest_desc-coreg_boldref.json
│       ├── sub-ADNI002S0413_ses-M072_task-rest_desc-coreg_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M072_task-rest_desc-hmc_boldref.json
│       ├── sub-ADNI002S0413_ses-M072_task-rest_desc-hmc_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M072_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-ADNI002S0413_ses-M072_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-ADNI002S0413_ses-M072_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-ADNI002S0413_ses-M072_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-ADNI002S0413_ses-M072_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M072_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│       ├── sub-ADNI002S0413_ses-M072_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
│       └── sub-ADNI002S0413_ses-M072_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── ses-M084
│   ├── anat
│   │   └── sub-ADNI002S0413_ses-M084_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-ADNI002S0413_ses-M084_task-rest_desc-confounds_timeseries.json
│       ├── sub-ADNI002S0413_ses-M084_task-rest_desc-confounds_timeseries.tsv
│       ├── sub-ADNI002S0413_ses-M084_task-rest_desc-coreg_boldref.json
│       ├── sub-ADNI002S0413_ses-M084_task-rest_desc-coreg_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M084_task-rest_desc-hmc_boldref.json
│       ├── sub-ADNI002S0413_ses-M084_task-rest_desc-hmc_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M084_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-ADNI002S0413_ses-M084_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-ADNI002S0413_ses-M084_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-ADNI002S0413_ses-M084_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-ADNI002S0413_ses-M084_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M084_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│       ├── sub-ADNI002S0413_ses-M084_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
│       └── sub-ADNI002S0413_ses-M084_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── ses-M096
│   ├── anat
│   │   └── sub-ADNI002S0413_ses-M096_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-ADNI002S0413_ses-M096_task-rest_desc-confounds_timeseries.json
│       ├── sub-ADNI002S0413_ses-M096_task-rest_desc-confounds_timeseries.tsv
│       ├── sub-ADNI002S0413_ses-M096_task-rest_desc-coreg_boldref.json
│       ├── sub-ADNI002S0413_ses-M096_task-rest_desc-coreg_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M096_task-rest_desc-hmc_boldref.json
│       ├── sub-ADNI002S0413_ses-M096_task-rest_desc-hmc_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M096_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-ADNI002S0413_ses-M096_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-ADNI002S0413_ses-M096_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-ADNI002S0413_ses-M096_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-ADNI002S0413_ses-M096_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M096_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│       ├── sub-ADNI002S0413_ses-M096_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
│       └── sub-ADNI002S0413_ses-M096_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── ses-M108
│   └── anat
│       └── sub-ADNI002S0413_ses-M108_from-orig_to-T1w_mode-image_xfm.txt
├── ses-M132
│   ├── anat
│   │   └── sub-ADNI002S0413_ses-M132_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-ADNI002S0413_ses-M132_task-rest_desc-confounds_timeseries.json
│       ├── sub-ADNI002S0413_ses-M132_task-rest_desc-confounds_timeseries.tsv
│       ├── sub-ADNI002S0413_ses-M132_task-rest_desc-coreg_boldref.json
│       ├── sub-ADNI002S0413_ses-M132_task-rest_desc-coreg_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M132_task-rest_desc-hmc_boldref.json
│       ├── sub-ADNI002S0413_ses-M132_task-rest_desc-hmc_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M132_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-ADNI002S0413_ses-M132_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-ADNI002S0413_ses-M132_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-ADNI002S0413_ses-M132_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-ADNI002S0413_ses-M132_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
│       ├── sub-ADNI002S0413_ses-M132_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│       ├── sub-ADNI002S0413_ses-M132_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
│       └── sub-ADNI002S0413_ses-M132_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
└── ses-M162
    └── anat
        └── sub-ADNI002S0413_ses-M162_from-orig_to-T1w_mode-image_xfm.txt

adelavega · February 5, 2024, 4:38pm

Hi Joan!

Can you try this:

layout = bids.BIDSLayout('../data/ds000030/derivatives/fmriprep/', derivatives='../data/ds000030/derivatives/fmriprep/', config=['bids','derivatives'])

If I’m correct, what is happening is that BIDSLayout is looking for derivatives under the ./derivatives folder, but since you are setting the main directory to a derivative, it wont find any.

This is pretty counter intuitive, but pybids was not originally conceived to be run on derivatives as first order folders. Obviously, it’s a sensible use case, however.

Joan_Carreras_Diaz · February 5, 2024, 4:57pm

I don’t really understand your answer, I can’t use this directory as I don’t have these folders. Changing the '../data/ds000030/derivatives/fmriprep/', derivatives='../data/ds000030/derivatives/fmriprep/' for my '/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/' I don’t obtain nothing, but it is because it doesn’t recognize any subject In BIDSLayout.

adelavega · February 5, 2024, 5:05pm

Oh, sorry, I was just copying your directory in your first question, it should be your directory.
It actually sounds like you have a different issue.

What version of pybids do you have?

Joan_Carreras_Diaz · February 5, 2024, 5:16pm

My pybids version is 0.16.4

adelavega · February 5, 2024, 5:55pm

Hmm, I’m not sure what the issue is but can you possibly try the following:

layout = bids.BIDSLayout('/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY', derivatives=True)

Joan_Carreras_Diaz · February 5, 2024, 6:10pm

It has worked! Thank you very much! If there is something else related to this thread I will let you know.

adelavega · February 5, 2024, 6:22pm

Great! You might try this as well, which is a variation of my original suggestion:

fmriprep_dir = '/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep'

layout = bids.BIDSLayout(fmriprep_dir, derivatives=fmriprep_dir)

I’m guessing the config parameter has changed in how it works since the tutorial was writen.

Joan_Carreras_Diaz · February 6, 2024, 10:55am

Yes, it might be this.

When I execute the following commands I don’t notice of any other inconveniences except when I have run the following line that the result is an empty vector:

t1w_func_data = layout.get(datatype='func', desc='preproc', space="T1w")
t1w_func_data

I have noticed that when running the line:

func_data = layout.get(datatype='func', desc='preproc')
func_data

The result is

[<BIDSJSONFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M060/func/sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json'>, 
<BIDSImageFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M060/func/sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>,
 <BIDSJSONFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M072/func/sub-ADNI002S0413_ses-M072_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json'>,
 <BIDSImageFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M072/func/sub-ADNI002S0413_ses-M072_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>,
 <BIDSJSONFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M084/func/sub-ADNI002S0413_ses-M084_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json'>,
<BIDSImageFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M084/func/sub-ADNI002S0413_ses-M084_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>,
 <BIDSJSONFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M096/func/sub-ADNI002S0413_ses-M096_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json'>,
 <BIDSImageFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M096/func/sub-ADNI002S0413_ses-M096_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>,
 <BIDSJSONFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M132/func/sub-ADNI002S0413_ses-M132_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json'>,
 <BIDSImageFile filename='/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M132/func/sub-ADNI002S0413_ses-M132_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>]

As you can see, there is no file named with T1w, however in one of my func folders, there are some files named with T1w:

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Practiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413/ses-M060/func
├── sub-ADNI002S0413_ses-M060_task-rest_desc-confounds_timeseries.json
├── sub-ADNI002S0413_ses-M060_task-rest_desc-confounds_timeseries.tsv
├── sub-ADNI002S0413_ses-M060_task-rest_desc-coreg_boldref.json
├── sub-ADNI002S0413_ses-M060_task-rest_desc-coreg_boldref.nii.gz
├── sub-ADNI002S0413_ses-M060_task-rest_desc-hmc_boldref.json
├── sub-ADNI002S0413_ses-M060_task-rest_desc-hmc_boldref.nii.gz
├── sub-ADNI002S0413_ses-M060_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
├── sub-ADNI002S0413_ses-M060_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
├── sub-ADNI002S0413_ses-M060_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
├── sub-ADNI002S0413_ses-M060_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
├── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
└── sub-ADNI002S0413_ses-M060_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz

adelavega · February 6, 2024, 6:30pm

That is expected behavior.

You asked for files with desc-preproc but the T1w files have desc-coreg.

And at least from this list of files, there are no files with space=T1w.