Exploring Preprocessed fMRI Data from fMRIPREP

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Dear Neurostars team,
I have been trying to preprocess the fMRI data from fMRIPREP following the tutorial given in this page: Functional Neuroimaging Analysis in Python . However, once I try to execute the command preproc_T1 = layout.get(datatype='anat', desc='preproc', extension=".nii.gz") it does not seem to happen anything.

On the other hand, I don’t have exactly the same results as in the tutorial, obtaining different files and results in the fmriprep folder. Even I get one Error in the fMRIPREP conversion, as it can be seen in here.
Errors.txt (25.6 KB)

I am unaware if this error is significative and it is the main cause of my problems. If not, how could I obtain the desired results as in the tutorial with my data?

The tree of the fmriprep folder is the following one:

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Pràctiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep
├── dataset_description.json
├── logs
├── sub-ADNI002S0413
└── sub-ADNI002S0413.html

/Users/joancarrerasdz/Desktop/CARPETES/UdG/Pràctiques/Dades_ADNI/BIDS_DIRECTORY/derivatives/fmriprep/sub-ADNI002S0413
├── figures
│   ├── sub-ADNI002S0413_desc-conform_T1w.html
│   ├── sub-ADNI002S0413_ses-M000_desc-about_T1w.html
│   ├── sub-ADNI002S0413_ses-M000_desc-summary_T1w.html
│   ├── sub-ADNI002S0413_ses-M060_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M072_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M084_task-rest_desc-validation_bold.html
│   ├── sub-ADNI002S0413_ses-M096_task-rest_desc-validation_bold.html
│   └── sub-ADNI002S0413_ses-M132_task-rest_desc-validation_bold.html
├── log
│   └── 20240117-185138_35bcf3be-da65-485c-a6b4-fb456cf9e865
│       ├── crash-20240117-201746-root-anat_merge-b67922a0-fe47-4606-bd80-2ff14f427aa1.txt
│       └── fmriprep.toml
├── ses-M060
│   └── func
│       ├── 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-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
├── ses-M072
│   └── func
│       ├── 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-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
├── ses-M084
│   └── func
│       ├── 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-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
├── ses-M096
│   └── func
│       ├── 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-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
└── ses-M132
    └── func
        ├── 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-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

Thank you.

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2 posts were merged into an existing topic: fMRIprep dependency problem (Python installation)

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