Data formatted according to a validatable standard? Please provide the output of the validator:
ExperimentalWarning: The fs.promises API is experimental
1: [WARN] Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest". (code: 25 - EVENTS_TSV_MISSING)
... and 28 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=EVENTS_TSV_MISSING for existing conversations about this issue.
2: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
... and 23 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.
3: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
4: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Relevant log outputs (up to 20 lines):
Screenshots / relevant information:
I do not have a pic of the erroneous outputs at this moment as I gave deleted them but I can try to upload them later. In any case,
I am attaching the BOLD file and fieldmap:
I have relabeled your post as Software Support and added the corresponding post template, please fill in the other requested information by editing your so we an best help. Also, in the Screenshots section, please post the SDC images from the HTML report.
hi @Steven@Chris_Rorden, thank you. I have populated the related fields in the form, except the picture of the output from preprocessing. I deleted that previously but should be able to upload it later. Otherwise, I have provided all required information.
Note 1: The difference of contrast in image for correction version of v20.2.6 vs v23 is that in fmriprep v20.2.6, I used the SBref image as reference, whereas for fmriprep v23, I ignored the SBref.
Note 2: In fact in fmriprep v23, I did not proved a masked 'phasediffimage but the phasediff`image was well masked when I looked at it in the working directory. The issue seems to be coming in the creation of the field coefficient, with B-Spline functions. Here is the look at the fieldmap applied for fmriprep v23:
Thanks @jsein, and apologies for not being more clear. I did use the latest version:
fMRIPrep version: 23.0.2
fMRIPrep command: /opt/conda/bin/fmriprep /home/cmccabe/data/NTR/data/NTR0019_bids /home/cmccabe/data/NTR/data/work participant --participant-label NTR0019 --fs-license-file /home/wgraves/software/freesurfer/license.txt
Date preprocessed: 2023-05-04 09:30:50 -0400
Thank you @wwgraves for sharing this example of SDC going wrong with fmriprep v 23.0.2! Do you confirm that the SDC correction method used in your case by fmriprep v23.0.2 is the “phase difference” case?
May you try with fmriprep v20.2.7 and confirm that the SDC correction is still much better with this earlier version?
Yes, as far as I know it’s a “phase difference” case. I used the field map sequence that came with our Siemens Prisma. Using dcm2bids output two magnitude images, and one phase image, where the phase image had two echo times. That’s why I assume it’s a phase difference map. Please let me know if there’s a better way to verify.
I’m running fMRIPrep v20.2.7 now. I’ll post here once I’ve gotten a chance to take a look at the results!
@jsein@Steven Replying to confirm that phasediff fieldmap correction is still providing incorrect distortion correction in the latest fmriprep versions. Only version 20.2.7 seems to work with phasediff fieldmap input.
@wwgraves@jsein@Steven So far only solution seems to be to convert the phasediff + magnitude fieldmap into a rad/s fieldmap (and appropriately name it as per direct fieldmap under BIDS convention) before feeding it to fmriprep.