IntendedFor using in Singularity

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1

Dear all,
I add IntendedFor field to the json file. it apply SDC when running on my computer.

However, if I use Singularity (for cluster):
Functional: Susceptibility distortion correction: None

Preprocessing of B0 inhomogeneity mappings: A total of 2 fieldmaps were found available within the input BIDS structure for this particular subject. A B0-nonuniformity map (or fieldmap) was estimated based on two (or more) echo-planar imaging (EPI) references with topup

[environment]
cpu_count = 40
exec_env = “singularity”
free_mem = 334.6
overcommit_policy = “heuristic”
overcommit_limit = “50%”
nipype_version = “1.6.1”
templateflow_version = “0.7.2”
version = “21.0.2”

2

Hello,

It sounds like, based on this statement, that SDC was applied. Does fMRIPrep produce an fmap output folder? If so, that would be proof that it is unwarping using fieldmaps (assuming fMRIPrep is not crashing).

Also, what was your full fMRIPrep command, and are your data BIDS valid?

Best,
Steven

3

Thank you Steven,
Yes, It create fmap output folder and relevant files, but I believe it does not applied it during he functional preprocessing.

in the .html:
Errors
No errors to report!

singularity run --cleanenv $mypath/fmriprep2102.simg  \
    $mypath/Nifti $mypath/preprocessed  participant --participant-label 05  \
    --skip_bids_validation  \
    --fs-no-reconall  \
    --fs-license-file $mypath/FS/license.txt \
    --ignore {t2w,flair}   \
    --dummy-scans 2  \
    --output-spaces MNI152NLin6Asym:res-2  \
    --nthreads 16 --omp-nthreads 16  \
    --mem_mb 10000  \
    --fd-spike-threshold 0.8  \
    --dvars-spike-threshold  3  \
    --stop-on-first-crash  --write-graph'

Preprocessing of B0 inhomogeneity mappings

: A total of 2 fieldmaps were found available within the input
BIDS structure for this particular subject.
A *B0*-nonuniformity map (or *fieldmap*) was estimated based on two (or more)
echo-planar imaging (EPI) references  with `topup` (@topup; FSL 6.0.5.1:57b01774).

Functional data preprocessing

: For each of the 2 BOLD runs found per subject (across all
tasks and sessions), the following preprocessing was performed.
First, a reference volume and its skull-stripped version were generated
by aligning and averaging 1 single-band references (SBRefs).
Head-motion parameters with respect to the BOLD reference
(transformation matrices, and six corresponding rotation and translation
parameters) are estimated before any spatiotemporal filtering using
`mcflirt` [FSL 6.0.5.1:57b01774, @mcflirt].
BOLD runs were slice-time corrected to 0.954s (0.5 of slice acquisition range
0s-1.91s) using `3dTshift` from AFNI  [@afni, RRID:SCR_005927].
The BOLD time-series (including slice-timing correction when applied)
were resampled onto their original, native space by applying
the transforms to correct for head-motion.
These resampled BOLD time-series will be referred to as *preprocessed
BOLD in original space*, or just *preprocessed BOLD*.
The BOLD reference was then co-registered to the T1w reference using
`mri_coreg` (FreeSurfer) followed by `flirt` [FSL 6.0.5.1:57b01774, @flirt]
with the boundary-based registration [@bbr] cost-function.
Co-registration was configured with six degrees of freedom.
First, a reference volume and its skull-stripped version were generated
 using a custom
4

All of this suggests that SDC was applied. In the HTML report do you see the animation of before/after correction? You should see a brain being warped back and forth.

5

No, I don’t… (I did see it when running on my personal computer, not using singularity)

6

I see that you include the --write-graph argument. Does the output workflow graph include SDC?

7

I think it did not create it. Where is it located?

8

I’ve never used that argument so I do not know, perhaps in the subject’s report or log folder?

Another place that might be worth looking is your working directory. I see you did not specify one in your singularity command (it would be the -w argument). I forget where fMRIPrep makes work directory by default. If you can find the working directory, you should look for a folder like this:

$WORKDIR/fmriprep_$VER_wf/single_subject_$SUBID_wf/func_preproc_task_$TASK_run_$RUN_wf/sdc_report/

If the SDC report folder does not exist (but the rest of the usual folders do), then that could suggest it was not run. If it is there, you can see the SDC report including the graphic I mentioned earlier.