hcp_asl
hcp_asl#
- qx_utilities.hcp.process_hcp.hcp_asl(sinfo, options, overwrite=False, thread=0)#
hcp_asl [... processing options]
hcpa [... processing options]
Runs the HCP ASL Pipeline (https://github.com/physimals/hcp-asl).
Warning
The code expects the first three HCP preprocessing steps (hcp_pre_freesurfer, hcp_freesurfer and hcp_post_freesurfer) to have been run and finished successfully.
Parameters
- --batchfile (str, default ''):
The batch.txt file with all the sessions information.
- --sessionsfolder (str, default '.'):
The path to the study/sessions folder, where the imaging data is supposed to go.
- --parsessions (int, default 1):
How many sessions to run in parallel.
- --overwrite (str, default 'no'):
Whether to overwrite existing data (yes) or not (no). Note that previous data is deleted before the run, so in the case of a failed command run, previous results are lost.
- --hcp_suffix (str, default ''):
Specifies a suffix to the session id if multiple variants are run, empty otherwise.
- --logfolder (str, default ''):
The path to the folder where runlogs and comlogs are to be stored, if other than default.
- --hcp_gdcoeffs (str, default ''):
Path to a file containing gradient distortion coefficients, alternatively a string describing multiple options (see below) can be provided.
- --hcp_asl_mtname (str, default ''):
Filename for empirically estimated MT-correction scaling factors.
- --hcp_asl_territories_atlas (str, default ''):
Atlas of vascular territories from Mutsaerts.
- --hcp_asl_territories_labels (str, default ''):
Labels corresponding to territories_atlas.
- --hcp_asl_cores (int, default 1)
Number of cores to use when applying motion correction and other potentially multi-core operations.
- --hcp_asl_use_t1 (flag, optional):
If specified, the T1 estimates from the satrecov model fit will be used in perfusion estimation in oxford_asl. The flag is not set by default.
- --hcp_asl_interpolation (int, default 1):
Interpolation order for registrations corresponding to scipy’s map_coordinates function.
- --hcp_asl_nobandingcorr (flag, optional):
If this option is provided, MT and ST banding corrections won’t be applied. The flag is not set by default.
- --hcp_asl_stages (str)
A comma separated list of stages (zero-indexed) to run. All prior stages are assumed to have run successfully.
Output files
The results of this step will be present in the ASL folder in the sessions's root hcp folder.
Notes
- Gradient coefficient file specification:
--hcp_gdcoeffs parameter can be set to either "NONE", a path to a specific file to use, or a string that describes, which file to use in which case. Each option of the string has to be divided by a pipe "|" character and it has to specify, which information to look up, a possible value, and a file to use in that case, separated by a colon ":" character. The information too look up needs to be present in the description of that session. Standard options are e.g.:
institution: Yale device: Siemens|Prisma|123456
Where device is formatted as <manufacturer>|<model>|<serial number>.
If specifying a string it also has to include a default option, which will be used in the information was not found. An example could be:
"default:/data/gc1.conf|model:Prisma:/data/gc/Prisma.conf|model:Trio:/data/gc/Trio.conf"
With the information present above, the file /data/gc/Prisma.conf would be used.
- Mapping of QuNex parameters onto HCP ASL pipeline parameters:
Below is a detailed specification about how QuNex parameters are mapped onto the HCP ASL parameters.
QuNex parameter
HCP ASL parameter
hcp_gdcoeffs
grads
hcp_asl_mtname
mtname
hcp_asl_territories_atlas
territories_atlas
hcp_asl_territories_labels
territories_labels
hcp_asl_use_t1
use_t1
hcp_asl_nobandingcorr
nobandingcorr
hcp_asl_interpolation
interpolation
hcp_asl_cores
cores
hcp_asl_stages
stages
Examples
Example run:
qunex hcp_asl \ --sessionsfolder="<path_to_study_folder>/sessions" \ --batchfile="<path_to_study_folder>/processing/batch.txt"
Run with scheduler, while bumping up the number of used cores:
qunex hcp_asl \ --sessionsfolder="<path_to_study_folder>/sessions" \ --batchfile="<path_to_study_folder>/processing/batch.txt" \ --hcp_asl_cores="8" \ --scheduler="SLURM,time=24:00:00,mem-per-cpu=16000"