BRC Pipeline Frequently Asked Questions

1. What MRI data do I need to use the BRC Pipelines?

• For structural analysis, one needs a high-resolution 3D (<=1mm) T1w image and either a high-resolution 3D (<=1mm) T2w image or a high-resolution 3D (<=1mm) FLAIR image. Higher than 1mm resolution is recommended if possible.

• For functional analysis, one needs an fMRI time-series (if the scans are multi-band), it is highly recommended to save the single-band reference scan or a spin echo field map (two phase encoding direction reversed spin echo volumes with the same geometrical and echo spacing parameters as the fMRI time-series). High spatial (<=2.5mm) and temporal (TR<=1s) resolution fMRI data is recommended.

• For diffusion analysis, one needs phase encoding direction reversed diffusion data. High spatial (<=1.5mm) and angular (>=120 directions) resolution diffusion data is recommended with multiple shells that include a higher b-value (>=1500). NOTE that PosData defines the reference space in 'topup' and 'eddy' AND it is assumed that each scan series begins with a b=0 acquisition so that the reference space in both 'topup' and 'eddy' will be defined by the same (initial b=0) volume.

• Functional and diffusion preprocessing also require the scans needed for structural preprocessing.

2. Examples of the command that you can use for running the pipelines:

As an example, the structural preprocessing pipeline can be run using a command like this:

    $ ./struc_preproc.sh --path /path/to/the/analysis/folder --subject Sub_001 --input /path/to/the/input/T1.nii.gz --t2 /path/to/the/input/T2.nii.gz --subseg

For the diffusion preprocessing pipeline, pipeline can be run using a command like this:

    $ ./dMRI_preproc.sh --path /path/to/the/analysis/folder --subject Sub_001 --input /path/to/the/input/dMRI_1.nii.gz --input_2 /path/to/the/input/dMRI_2.nii.gz --pe_dir 1 --echospacing 0.00078 --slice2vol --slspec /path/to/the/input/diffusion.json --reg

For the fundtional preprocessing pipeline, pipeline can be run using a command like this:

    $ ./fMRI_preproc.sh --path /path/to/the/analysis/folder --subject Sub_001 --input /path/to/the/input/fMRI.nii.gz --echospacing 0.00058 --unwarpdir y- --dcmethod TOPUP --fmrires 3 --mctype EDDY --slice2vol --slspec /path/to/the/input/functional.json --stcmethod 6 --fwhm 3 --intensitynorm --SEPhaseNeg /path/to/the/input/SEPhaseNeg.nii.gz --SEPhasePos /path/to/the/input/SEPhasePos.nii.gz --biascorrection SEBASED --tempfilter 100

For the fundtional group analysis pipeline, pipeline can be run using a command like this:

    $ ./fmri_group_analysis.sh --in /path/to/the/input_list.txt --indir /path/to/the/analysis/folder --outdir /path/to/the/output/folder --parcellation SHEN --fmrires 3 --tr 2 --labels /path/to/the/input_labels.txt --corrtype RCORR --varnorm 1

Note that when you are running the pipeline on the cluster, you don't need to put the ./ on the above examples.

3. What should I do if I get this error "Error"?

• All the pipelines:

    <PATH TO PIPELINE>/BRC_Pipeline/Show_version.sh: Permission denied
  

  This error means that you didn't follow the installation procedure, correctly. In order to make the scripts executable, the following command must be called in the ~/BRC_Pipeline directory:

    $ find . -name "*.sh" -exec chmod 755 {} \;
  

• Diffusion Pipeline:

    TopupFileIO:: msg=TopupDatafileReader::ReadOutTime: Invalid index
  

  NOTE that PosData defines the reference space in 'topup' and 'eddy' AND it is assumed that each scan series begins with a b=0 acquisition so that the reference space in both 'topup' and 'eddy' will be defined by the same (initial b=0) volume.

4. How do I cite the pipeline?

Each version of the pipeline has its own DOI. The shiny badge in README.md shows the DOI of the last version. However, by clicking on this badge, you can find different DOIs of different versions. You can cite all versions by using the DOI 10.5281/zenodo.3624973. This DOI represents all versions, and will always resolve to the latest one.

• Cite as:

    Ali-Reza Mohammadi-Nejad, Stefan Pszczolkowski, Dorothee Auer, Stamatios Sotiropoulos. Multi-modal 
    neuroimaging pipelines for data preprocessing. Zenodo. http://doi.org/10.5281/zenodo.3624973
  

5. How should I know BRC Pipeline finished without error?

After finishing the pre-processing without any error, you should be able to see the following message in the log file:

    ==========================================================================
                                 ===============                              
    ==========================================================================
                             PRODUCT: BRC Pipeline
                               VERSION: Ver1.4.5
                               Subject: Sub_001
                         Type of Analysis: Diffusion
                     End Time: Wed  6 Jan 12:40:51 GMT 2021
                           Run Time (H:M:S): 00:51:03
    ==========================================================================

6. I have a question not listed here about the BRC Pipelines, where do I ask it?

If you don't find the answer from searching, then send a message to the list at [email protected].