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1: [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.
Summary: Available Tasks: Available Modalities:
15 Files, 425.93MB Stroop T1w
1 - Subject T2w
1 - Session bold
events
sbref
fieldmap
 If you have any questions, please post on https://neurostars.org/tags/bids.
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
200323-14:12:41,136 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.5.9:
* BIDS dataset path: /data.
* Participant list: ['01'].
* Run identifier: 20200323-141240_b10fec1f-5ef1-46e0-8c72-9d2cdf31c02a.
200323-14:12:41,571 nipype.utils INFO:
No new version available.
200323-14:12:43,547 nipype.workflow IMPORTANT:
Creating bold processing workflow for "/data/sub-01/ses-01/func/sub-01_ses-01_task-Stroop_run-01_bold.nii.gz" (0.37 GB / 540 TRs). Memory resampled/largemem=1.49/3.50 GB.
200323-14:12:43,575 nipype.workflow IMPORTANT:
Using single-band reference file sub-01_ses-01_task-Stroop_run-01_sbref.nii.gz
200323-14:12:45,754 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
200323-14:12:47,29 nipype.workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
200323-14:12:52,77 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the following boilerplate:
Results included in this manuscript come from preprocessing
performed using *fMRIPrep* 1.5.9
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.4.2
(@nipype1; @nipype2; RRID:SCR_002502).
Anatomical data preprocessing
: The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through
nonlinear registration with `antsRegistration` (ANTs 2.2.0),
using brain-extracted versions of both T1w reference and the T1w template.
The following template was selected for spatial normalization:
*ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym].
Functional data preprocessing
: For each of the 1 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
using a custom methodology of *fMRIPrep*.
A B0-nonuniformity map (or *fieldmap*) was estimated based on two (or more)
echo-planar imaging (EPI) references with opposing phase-encoding
directions, with `3dQwarp` @afni (AFNI 20160207).
Based on the estimated susceptibility distortion, a corrected
EPI (echo-planar imaging) reference was calculated for a more
accurate co-registration with the anatomical reference.
The BOLD reference was then co-registered to the T1w reference using
`bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
Co-registration was configured with six degrees of freedom.
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 5.0.9, @mcflirt].
BOLD runs were slice-time corrected using `3dTshift` from
AFNI 20160207 [@afni, RRID:SCR_005927].
The BOLD time-series, were resampled to surfaces on the following
spaces: *fsaverage5*.
*Grayordinates* files [@hcppipelines], which combine surface-sampled
data and volume-sampled data, were also generated.
The BOLD time-series (including slice-timing correction when applied)
were resampled onto their original, native space by applying
a single, composite transform to correct for head-motion and
susceptibility distortions.
These resampled BOLD time-series will be referred to as *preprocessed
BOLD in original space*, or just *preprocessed BOLD*.
The BOLD time-series were resampled into standard space,
generating a *preprocessed BOLD run in ['MNI152NLin2009cAsym'] space*.
First, a reference volume and its skull-stripped version were generated
using a custom methodology of *fMRIPrep*.
Several confounding time-series were calculated based on the
*preprocessed BOLD*: framewise displacement (FD), DVARS and
three region-wise global signals.
FD and DVARS are calculated for each functional run, both using their
implementations in *Nipype* [following the definitions by @power_fd_dvars].
The three global signals are extracted within the CSF, the WM, and
the whole-brain masks.
Additionally, a set of physiological regressors were extracted to
allow for component-based noise correction [*CompCor*, @compcor].
Principal components are estimated after high-pass filtering the
*preprocessed BOLD* time-series (using a discrete cosine filter with
128s cut-off) for the two *CompCor* variants: temporal (tCompCor)
and anatomical (aCompCor).
tCompCor components are then calculated from the top 5% variable
voxels within a mask covering the subcortical regions.
This subcortical mask is obtained by heavily eroding the brain mask,
which ensures it does not include cortical GM regions.
For aCompCor, components are calculated within the intersection of
the aforementioned mask and the union of CSF and WM masks calculated
in T1w space, after their projection to the native space of each
functional run (using the inverse BOLD-to-T1w transformation). Components
are also calculated separately within the WM and CSF masks.
For each CompCor decomposition, the *k* components with the largest singular
values are retained, such that the retained components' time series are
sufficient to explain 50 percent of variance across the nuisance mask (CSF,
WM, combined, or temporal). The remaining components are dropped from
consideration.
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file.
The confound time series derived from head motion estimates and global
signals were expanded with the inclusion of temporal derivatives and
quadratic terms for each [@confounds_satterthwaite_2013].
Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS
were annotated as motion outliers.
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
transform matrices, susceptibility distortion correction when available,
and co-registrations to anatomical and output spaces).
Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
configured with Lanczos interpolation to minimize the smoothing
effects of other kernels [@lanczos].
Non-gridded (surface) resamplings were performed using `mri_vol2surf`
(FreeSurfer).
Many internal operations of *fMRIPrep* use
*Nilearn* 0.6.1 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
### Copyright Waiver
The above boilerplate text was automatically generated by fMRIPrep
with the express intention that users should copy and paste this
text into their manuscripts *unchanged*.
It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license.
### References
200323-14:17:18,216 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
200323-14:17:18,233 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:18,233 nipype.workflow INFO:
[Node] Running "autorecon1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:18,235 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:18,366 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
200323-14:17:21,613 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
200323-14:17:21,626 nipype.workflow INFO:
[Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted")
200323-14:17:21,630 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
200323-14:17:27,925 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
200323-14:17:27,943 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:27,943 nipype.workflow INFO:
[Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:27,945 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:28,57 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".
200323-14:17:33,804 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
200323-14:17:33,819 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:33,820 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:33,822 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:33,930 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
200323-14:17:35,894 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
200323-14:17:35,908 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:35,909 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:35,910 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:35,997 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
200323-14:17:38,63 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs".
200323-14:17:38,75 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
200323-14:17:38,79 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:38,79 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:38,81 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:38,185 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
200323-14:17:38,188 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
200323-14:17:38,192 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:38,192 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:38,194 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:38,281 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
200323-14:17:38,285 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs".
200323-14:17:39,897 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
200323-14:17:39,907 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:39,908 nipype.workflow INFO:
[Node] Running "cortribbon" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:39,909 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:39,997 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon".
200323-14:17:43,904 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
200323-14:17:43,918 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:43,919 nipype.workflow INFO:
[Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:43,920 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:44,6 nipype.workflow INFO:
[Node] Finished "_parcstats0".
200323-14:17:45,903 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
200323-14:17:45,915 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:45,916 nipype.workflow INFO:
[Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:45,917 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:45,998 nipype.workflow INFO:
[Node] Finished "_parcstats1".
200323-14:17:47,907 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats".
200323-14:17:47,919 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
200323-14:17:47,924 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:47,924 nipype.workflow INFO:
[Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:47,925 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:48,11 nipype.workflow INFO:
[Node] Finished "_parcstats0".
200323-14:17:48,14 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
200323-14:17:48,19 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:48,19 nipype.workflow INFO:
[Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:48,21 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:48,108 nipype.workflow INFO:
[Node] Finished "_parcstats1".
200323-14:17:48,112 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats".
200323-14:17:49,907 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
200323-14:17:49,921 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:49,922 nipype.workflow INFO:
[Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200323-14:17:49,923 nipype.interface INFO:
recon-all complete : Not running
200323-14:17:50,13 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3".
200323-14:17:51,913 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/recon_report".
200323-14:17:51,919 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource".
200323-14:17:51,922 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource".
200323-14:17:51,926 nipype.workflow INFO:
[Node] Running "recon_report" ("smriprep.interfaces.reports.FSSurfaceReport")
200323-14:17:51,931 nipype.workflow INFO:
[Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
200323-14:17:51,942 nipype.workflow INFO:
[Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
200323-14:17:51,953 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource".
200323-14:17:51,958 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource".
200323-14:17:53,924 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces".
200323-14:17:53,933 nipype.workflow INFO:
[Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource")
200323-14:17:53,946 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces".
200323-14:18:03,428 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.recon_report".
200323-14:18:30,221 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness".
200323-14:18:30,232 nipype.workflow INFO:
[Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink")
200323-14:18:30,531 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness".
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