Connectome / connectivity map generating command in QSIRecon?

Summary of what happened:

Hi Experts,

I am exploring the connectivity maps generated by the QSIRecon. For this I make use of the sub-OAS30003_ses-d3731_space-ACPC_connectivity.mat file stored in the derivatives…/…/…/dwi directory and load in Matlab for visualization. Now, I am searching for the possible tck2connectome command used in this process if this is used.
Can you please point me to the command and it’s location used for this purpose?

Thanks and regards,
Suhail

Command used :

apptainer run --containall --writable-tmpfs \
  --bind ${DATA}:/data \
  --bind ${APP_DERIV_DIR}:/outputs \
  --bind ${WORK_DIR}:/work \
  --bind ${LIC}:/lic \
  --bind ${fssubj}:/fssubj \
  --bind ${atlases}:/atlasT \
  ${APP} /data /outputs participant \
  --participant-label ${Subject} \
  --work-dir /work \
  --nthreads 16 --omp-nthreads 16 \
  --fs-license-file /lic/license.txt \
  --recon-spec mrtrix_singleshell_ss3t_ACT-hsvs \
  --datasets /atlasT \
  --atlases THOMASCORT8 \
  --fs-subjects-dir /fssubj \
  -v -v


Hi @suhail,

The tck2connectome command used can be found in the qsirecon working directory. You should see it in a folder called connectivity, corresponding to the node name in the recon spec (qsirecon/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_ACT-hsvs.yaml at main · PennLINC/qsirecon · GitHub).

Best,
Steven

Thank you Steven
The link was very useful as I could see the specifications of the tck2connectome command.

Hi @Steven,

I have few more questions with the same command.

Q1. a) We have Thalamic nuclei labels segmented using THOMAS segmentation technique using native space T1w images. Why is that we need to warp these labels to MNI space for compatibility with QSIRecon?
b) Can we still use the native space segmentation labels for generating the connectivity maps?
c) Also, fiber tracts generated by the QSIRecon we believe are in AC-PC space?

Q2. Where does the AC-PC to MNI warps located in the QSIPrep or QSIRecon output directories?

Thanks & regards,
Suhail

Hi @suhail,

QSIRecon uses the MNI-to-subject warp to put atlases into subject space.

QSIRecon is built around standard space atlases. Although, I suppose it is possible to make an MNI version of each subject’s segmentation, and make each one a “separate” atlas. At that point though, you might just be better off running tck2connectome separately from QSIRecon.

Yes, all postprocessed data are in DWI space (which is ACPC after QSIPrep) unless otherwise specified (e.g., with the scalar stats template mapper as in qsirecon/qsirecon/data/pipelines/hbcd_scalar_maps.yaml at main · PennLINC/qsirecon · GitHub)

QSIPrep anatomical outputs.

Best,
Steven

Hi @Steven

Thank you very much clarifications and details.

Suhail