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.