Visualization of QSIprep and further analysis of the results

Ziyun-li · November 30, 2022, 6:10pm

Hi everyone,

I am new to using QSIprep and working with DWI data, and I have a few problems when working with DWI data using QSIprep:

The output does not produce a visual report, and the figure file is empty. Below is the result file.
I want to know what software can open the generated fiber file and observe the results in the picture.
I have observed that QSIprep can only be used for preprocessing and reconstruction. If I want to further analyze the reconstructed fiber, for example, to study the FA of a certain fiber, what software should I use?
Any help would be greatly appreciated.

Many thanks,
Ziyun Li

1669831147955

├─qsiprep
│  │  dataset_description.json
│  │  dwiqc.json
│  │  sub-01.html
│  │
│  ├─logs
│  │      CITATION.html
│  │      CITATION.md
│  │      CITATION.tex
│  │
│  └─sub-01
│      ├─anat
│      │      sub-01_desc-brain_mask.nii.gz
│      │      sub-01_desc-preproc_T1w.nii.gz
│      │      sub-01_dseg.nii.gz
│      │      sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│      │      sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│      │      sub-01_label-CSF_probseg.nii.gz
│      │      sub-01_label-GM_probseg.nii.gz
│      │      sub-01_label-WM_probseg.nii.gz
│      │      sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│      │      sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
│      │      sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
│      │      sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
│      │      sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
│      │      sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
│      │
│      ├─figures
│      └─ses-001
│          ├─anat
│          │      sub-01_ses-001_run-001_from-orig_to-T1w_mode-image_xfm.txt
│          │
│          └─dwi
│                  sub-01_ses-001_confounds.tsv
│                  sub-01_ses-001_desc-ImageQC_dwi.csv
│                  sub-01_ses-001_desc-SliceQC_dwi.json
│                  sub-01_ses-001_dwiqc.json
│                  sub-01_ses-001_space-T1w_desc-brain_mask.nii.gz
│                  sub-01_ses-001_space-T1w_desc-eddy_cnr.nii.gz
│                  sub-01_ses-001_space-T1w_desc-preproc_dwi.b
│                  sub-01_ses-001_space-T1w_desc-preproc_dwi.bval
│                  sub-01_ses-001_space-T1w_desc-preproc_dwi.bvec
│                  sub-01_ses-001_space-T1w_desc-preproc_dwi.nii.gz
│                  sub-01_ses-001_space-T1w_dwiref.nii.gz
│
└─qsirecon
    │  dwiqc.json
    │  sub-01.html
    │
    ├─logs
    │      CITATION.html
    │      CITATION.md
    │      CITATION.tex
    │
    └─sub-01
        ├─figures
        └─ses-001
            └─dwi
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aal116_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aal116_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aal116_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aal116_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aicha384_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aicha384_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aicha384_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-aicha384_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-brainnetome246_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-brainnetome246_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-brainnetome246_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-brainnetome246_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-csfFODmtnormed_ss3tcsd.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-csfFOD_ss3tcsd.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-exemplarbundles_dhollanderconnectome.zip
                    sub-01_ses-001_space-T1w_desc-preproc_desc-gmFODmtnormed_ss3tcsd.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-gmFOD_ss3tcsd.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-gordon333_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-gordon333_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-gordon333_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-gordon333_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-mtinliermask_ss3tcsd.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-mtnorm_ss3tcsd.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer100_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer100_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer100_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer100_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer200_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer200_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer200_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer200_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer400_atlas.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer400_atlas.nii.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer400_mrtrixLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-schaefer400_origLUT.txt
                    sub-01_ses-001_space-T1w_desc-preproc_desc-siftweights_ifod2.csv
                    sub-01_ses-001_space-T1w_desc-preproc_desc-tracks_ifod2.tck
                    sub-01_ses-001_space-T1w_desc-preproc_desc-wmFODmtnormed_ss3tcsd.mif.gz
                    sub-01_ses-001_space-T1w_desc-preproc_desc-wmFOD_ss3tcsd.txt
                    sub-01_ses-001_space-T1w_desc-preproc_dhollanderconnectome.mat

Steven · November 30, 2022, 6:48pm

Hi, and welcome to neurostars!

Some general questions that will help us best answer your question:

What were your commands for preprocessing and reconstruction?
What version of QSIPrep did you use?
Did you encounter any errors / crashes?

It looks like you used an MRtrix workflow. These outputs can be visualized with MRview (part of MRtrix3). The HTML from reconstruction will mainly just report the ODF plot which you can use to make sure the fiber orientations look correct.

Many software packages can do this. I would recommend DIPY or MRTrix3, since both tools are used in QSIPrep, are open-source, and have supportive communities to help answer questions.

Best,
Steven

Ziyun-li · December 1, 2022, 3:28am

Hi，

Thank you for the reply! Your reply has been very helpful to me, and I will try to learn MRTrix3.

For the first question, I used the QSIprep version: 0.16.1, and added my commands below. The program can run smoothly and produce output results, and no errors seem to occur，but there are only words in HTML without pictures. I guess whether there are commands that can control the output of visual images.

Many thanks,
Ziyun Li

sudo docker run --rm -it -v /home/li/test/Nifti:/data:ro -v /home/li/test/out:/out pennbbl/qsiprep:0.16.1 \
/data /out participant -v /home/li/test/license.txt：/opt/freesurfer/license.txt：ro \
--output_resolution 1.2 --recon_spec mrtrix_singleshell_ss3t_noACT

Steven · December 1, 2022, 1:54pm

Most of the pictures are in the preprocessing folder (e.g. BIDS/derivatives/qsiprep), not the reconstruction folder (BIDS/derivatives/qsirecon).

Ziyun-li · December 2, 2022, 3:18pm

Yes, I looked at the figures file under the derivatives/qsiprep path, but it was empty.

harrison-huan-liu · September 10, 2024, 5:24am

I am wondering if there are any options that I can choose to produce figures for the HTML report?

Thank you so much!