QSIPrep problem about custom atlas:

1

I am trying to use a custom atlas to calculate connectivity.
I have already resampled my atlas to the LPS+ and same FOV as described in the [documentation]
(Reconstruction — qsiprep version documentation).

However, I don’t understand why and how to zero-out the sform. Is it necessary, and how do I do it? (I have checked the Neurostar and github, but didn’t found a clear answer.)

Now, I am trying to replicate the qform and sform of the QSIPrep atlas template using below code. However, I am still not sure if it is correct.

The QSIPrep atals:
filename aal116MNI_lps_mni.nii.gz

image
image1012×722 84.7 KB

My code:

import nibabel as nib
qsi_atlas = '/mnt/workdir/DCM/Docs/Reference/qsirecon_atlases/aal116MNI_lps_mni.nii.gz'
qsi_atlas_img = nib.load(qsi_atlas)
sform = qsi_atlas_img.header.get_sform()
sform_code = qsi_atlas_img.header._structarr['sform_code']
print(sform)
print(sform_code)

my_atlas = r'/mnt/workdir/DCM/Docs/Mask/DMN/DMN_atlas/DMN_atlas_lps.nii.gz'
dmn_img = nib.load(my_atlas)
print(dmn_img.header.get_sform())
qform = dmn_img.header.get_qform()
print(qform)

# zero_out the sform
dmn_img.header.set_sform(sform, int(sform_code))
dmn_img.header.set_qform(qform, int(1))
dmn_img.to_filename('/mnt/workdir/DCM/Docs/Mask/DMN/DMN_atlas/DMN_atlas_lps_zero-

After this, I got the sform and qform in my atlas as below:

image
image982×682 79.6 KB

2

Now, my QSIPrep procedure have been stuck at the step “tck_sift2” for 20h. The log shows: “230830-11:25:20,267 nipype.workflow INFO: [Node] Finished “tck_sift2”, elapsed time 476.22031s.”

As far as I know, after “tck_sift2”, QSIPrep should proceed to calculate the connectome. Could this issue be related to my atlas?

3

It’s not necessary to zero out the sform, your custom parcellation should be good!

If qsiprep ever gets stuck on a step for this long, it’s likely that something crashed earlier in the pipeline. What was your command?

4

@mattcieslak This is my command, here you are:

qsiprep-docker /mnt/workdir/DCM/BIDS /mnt/workdir/DCM/BIDS/derivatives/qsiprep participant 
--participant_label 202 203 204 205  --output-resolution 2
--recon_input /mnt/workdir/DCM/BIDS/derivatives/qsiprep 
--recon_spec mrtrix_multishell_msmt_ACT-hsvs 
--fs-license-file /mnt/data/license.txt 
--freesurfer-input /mnt/workdir/DCM/BIDS/derivatives/freesurfer 
-w /mnt/workdir/DCM/working 
--custom_atlases /mnt/workdir/DCM/Docs/Reference/qsirecon_atlases 
--nthreads 100 
--gpus all

This is my atlas directory:
The “atlas_config.json” and “DMN_atlas_lps.nii.gz” both in the directory:

image
image982×268 19.5 KB

image
image1054×972 118 KB

5

I found a crash file. The content in this file is :

Node: qsirecon_wf.sub-070_mrtrix_multishell_msmt_hsvs.sub_070_dir_PA_space_T1w_desc_preproc_recon_wf.qsirecon_anat_wf.get_atlases
Working directory: /scratch/qsirecon_wf/sub-070_mrtrix_multishell_msmt_hsvs/sub_070_dir_PA_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/get_atlases

Node inputs:

atlas_names = [‘schaefer100’, ‘schaefer200’, ‘schaefer400’, ‘brainnetome246’, ‘aicha384’, ‘gordon333’, ‘aal116’]
forward_transform = /out/qsiprep/sub-070/anat/sub-070_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
reference_image = /out/qsiprep/sub-070/dwi/sub-070_dir-PA_space-T1w_desc-preproc_dwi.nii.gz
space = T1w

Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py”, line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node get_atlases.

Traceback:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/utils.py”, line 46, in _run_interface
atlas_configs = get_atlases(atlas_names)
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/utils/atlases.py”, line 26, in get_atlases
raise Exception(“Atlas %s not found in atlas_config.json” % atlas_name)
Exception: Atlas schaefer200 not found in atlas_config.json

6

Maybe I know the reason for this. To aceelated the speed of reconstruction, I remove the default atlas from the atlas_config.json. But the QSIPrep read the atlas name from the pipeline json file. It still only contains the default atlas but not my custom atlas.
So, to fulfill my requirement, I also need change the pipeline json file as the input of QSIPrep command?

7

Hi @YukunQu,

Yes, please make your own recon spec json that is a copy of the json file (https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/pipelines/mrtrix_multishell_msmt_ACT-hsvs.json) but with your atlas in the atlases field. Then pass that modified json into the —recon-spec argument.

Best,
Steven

1 Like