Question about outputs of ASLPrep

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Hi all,

After running ASLprep using the flag to calculate CBF with Basil, I don’t quite understand the outputs. For example, if I want to calculate the mean CBF from gray matter, should I average the CBF across all voxels from the file [_space-]_desc-basilGM_cbf.nii.gz? There are no gray matter or white matter masks but I resampled an MNI mask to match the resolution of CBF outputs.

When I open the file [_space-]_desc-basilGM_cbf.nii.gz I don’t understand why it looks blurry. Perhaps you have further documentation or could point me to relevant papers?

As per the documentation of ASLprep, this is an example of the output files:

sub-<label>/[ses-<label>/]
   perf/
      <source_entities>[_space-<label>]_desc-basil_cbf.nii.gz  # mean CBF computed with BASIL
      <source_entities>[_space-<label>]_desc-basilGM_cbf.nii.gz  # GM partial volume corrected CBF with BASIL
      <source_entities>[_space-<label>]_desc-basilWM_cbf.nii.gz  # WM partial volume corrected CBF with BASIL
      <source_entities>[_space-<label>]_att.nii.gz  # bolus arrival time/arterial transit time (in seconds)
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There should be tissue type files in the anat folder:

<source_entities>[_space-<label>]__dseg.nii.gz
<source_entities>[_space-<label>]_label-CSF_probseg.nii.gz
<source_entities>[_space-<label>]_label-GM_probseg.nii.gz
<source_entities>[_space-<label>]_label-WM_probseg.nii.gz

desc-basilGM is produced via BASIL’s --pvgm parameter, while desc-basilWM is produced with --pvwm. You can find more information about those parameters and the corresponding outputs at BASIL (command) User Guide — BASIL documentation documentation.

That’s up to you. I think it’s reasonable to use the basilGM if you want to focus on GM CBF.

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