Danny

TractSeg bedpostX out of memoryy

5

In the following bedpostX folder, I tried running `TractSeg -i dyads1.nii.gz`.  However, the following error was output : ``` BedpostX dyads detected. Will automatically combine dyads1+2[+3]. Loading weights from:...

Way to use MNI Pediatric Template?

5

I was wondering if there is a way to use MNI Pediatric template, like how `--infant` option can be used to use the MNI infant template instead of the adult...

Various `autorecon` errors

1

When running dwi preprocessing on BIDS compatible data, 10% of the subjects gave out crash errors, which could be divided into three categories: 1. `autorecon30` error 2. `autorecon_surfs1` error 3....

Running `recon_only` without doing tck2connectome

3

I want to perform reconstruction only using a similar reconstruction pipeline as the default `mrtrix_multishell_msmt_hsvs` JSON but without doing the `tck2connectome`. The JSON file was named `new_workflow` and is posted...

QSIprep recon_only is stuck at "plot_connectivity"

2

When I ran the following QSIprep code, `time qsiprep-docker /scratch/connectome/dyhan316/dwMRI/UKB_sample/sub_02_INPUT_4/ /scratch/connectome/dyhan316/dwMRI/time_it/outputs/recon_variety/multi_msmt_noACT/ participant --output_resolution 1.2 --recon_only --recon_input /scratch/connectome/dyhan316/dwMRI/UKB_sample/sub_02_INPUT_4/ --recon_spec mrtrix_multishell_msmt_noACT --fs-license-file /scratch/connectome/dyhan316/dwMRI/license.txt --skip_bids_validation --nthreads 48 --omp_nthreads 24 --stop_on_first_crash` to only do...

 As the picture below shows, the description states that `kcoreness_centrality_bu` outputs an integer as its second output. However, as the code shows, it actually outputs a vector.

How to properly crop the freesurfer images

1

**Task** (what are you trying to do/register?) I am trying to prepare my data to be used as according to the README.md, but I am stuck in knowing how/where to...

Question regarding the native T1w to ACPC alignment matrix in qsiprep version 18.0

6

When the qsiprep version 18.0 is run, for the anat results, we get something like ``` dyhan316@node1: ~.../QSIPREP/qsiprep/sub-130917/anat$ ls sub-130917_desc-aseg_dseg.nii.gz sub-130917_desc-brain_mask.nii.gz sub-130917_desc-preproc_T1w.nii.gz sub-130917_dseg.nii.gz sub-130917_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 sub-130917_from-orig_to-T1w_mode-image_xfm.txt sub-130917_from-T1wACPC_to-T1wNative_mode-image_xfm.mat sub-130917_from-T1wNative_to-T1wACPC_mode-image_xfm.mat sub-130917_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 ``` We...

Hello experts, I want to run qsiprep on infant data. It seems that I should use --infant with --dwi-only so that the infant template is used. However, what should the...

I believe that `input = torch.stack([item[0] for item in data]).view((input_window,batch_len,1))` should be changed to `input = torch.stack([item[0] for item in data]).T.unsqueeze(-1)`. This is because the orders are not correct if...