Posted in:

XNAT, the software the CNDA runs on, includes the ability to store arbitrary strings of text, which they call configs. See this page on the XNAT wiki for more in-depth information. Default (global) configs are stored in an area that disregards project, but each project also has its own config space.

The global configs are already setup on the CNDA. They should be reviewed to ensure that the needed scanner and tracer information is stored in them. If not, the CNDA Help Desk should be contacted to have the needed data added. See end of article for file contents.

In order for the PUP pipeline to run properly, there are 2 configuration files that need to be added to the project.
  • MR Scan Types
  • Parameter Defaults

Example: Issuing the following command on a terminal would write a file to the project config space, {path} to be filled in with specific values.

curl -k -u username:password -X PUT -T /path/to/file "{path}?inbody=true"

MR Scan Types
path ={PROJECT}/config/params/mr_scan_types

Determine if any of the subject's MR scans have been registered and had ROI files generated, which would mean the user can run PUP on the Manual ROI path; also need to find all the Freesurfer assessors that are attached to the subject's MR sessions. Judge which sessions are MR sessions by looking at the scan types of their scans. This config stores a CSV list of all the MR scan types. Having more than needed is OK.

Sample MR Scan Types file:

Parameter Defaults
path ={PROJECT}/config/pipelines/PETUnifiedPipeline_default_params

Provides the ability to have different defaults for some of the params based on which processing path the user chose and to
easily add some values the user could pass to the pipeline if the underlying scripts change.

Sample Parameter Defaults file:
{"t1":{"paths":[{"path":"freesurfer","default":"T1.mgz","type":"text"}]},"wmparc":{"paths":[{"path":"freesurfer","default":"wmparc.mgz","type":"text"}]},"roiimg":{"paths":[{"path":"freesurfer","default":"RSFMask","type":"text"},{"path":"customroi","default":"manual","type":"text"},{"path":"templateroi","default":"AV45ROI","type":"text"}]},"rsflist":{"paths":[{"path":"freesurfer","default":"RSFlist.txt","type":"text"}]},"pvc2cflag":{"paths":[{"path":"freesurfer","default":1,"type":"checkbox"}]},"rsfflag":{"paths":[{"path":"freesurfer","default":1,"type":"checkbox"}]},"template_name":{"paths":[{"path":"templateroi","opts":[{"value":"AV45","label":"AV45"}],"default":"AV45","type":"select"}]},"maskroot":{"paths":[{"path":"templateroi","default":"brainmask","type":"text"}]},"filter":{"default":0,"type":"text"},"fwhm":{"default":6.0,"type":"text"},"delay":{"default":0,"type":"text"},"tbl":{"default":300,"type":"text"},"tolmoco":{"default":200,"type":"text"},"tolreg":{"default":200,"type":"text"},"mst":{"default":40,"type":"text"},"mdt":{"default":30,"type":"text"},"model":{"opts":[{"value":"logan","label":"Logan"},{"value":"nonlogan","label":"No model"}],"default":"logan","type":"select"},"k2":{"default":0.16,"type":"text"},"rmf":{"default":"-rm","type":"text"},"mmf":{"default":"-mm","type":"text"},"rbf":{"default":""-rb 8"","type":"text"},"mbf":{"default":""-mb 6"","type":"text"},"modf":{"default":"""","type":"text"},"suvr":{"default":1,"type":"checkbox"}}
These files can be saved as .txt files.

Global file contents for review

Current contents of these files (8/4/2014).

Filter Params:
1.  {"": {"filterz": "5.0", "filterxy": "5.0"}, "null": {"filterz": "5.0", "filterxy": "5.0"}, "1094": {"filterz": "5.5", "filterxy": "5.5"}, "Allegro Body(C)": {"filterz": "3.0", "filterxy": "3.0"}, "Advance": {"filterz": "2.0", "filterxy": "5.0"}, "Biograph 64": {"filterz": "5.5", "filterxy": "5.5"}, "Biograph64": {"filterz": "5.5", "filterxy": "5.5"}, "SOMATOM": {"filterz": "6.0", "filterxy": "5.5"}, "Biograph_mMR": {"filterz": "6.0", "filterxy": "5.5"}, "Biograph 40": {"filterz": "5.5", "filterxy": "5.5"}, "Definition AS_mCT": {"filterz": "6.0", "filterxy": "5.5"}, "Discovery 710": {"filterz": "5.0", "filterxy": "5.5"}, "SOMATOM Definition AS_mCT": {"filterz": 6.0, "filterxy": 5.5}}

Half Life of tracer:
2.  {"F18":"6586.2","FDG":"6586.2","fdg":"6586.2","AV45":"6586.2","florbetapir":"6586.2","Amyvid":"6586.2","amyvid":"6586.2","C11":"1223","PiB":"1223","PIB":"1223","O15":"122.24","O15-water":"122.24","O15-oxygen":"122.24","O15-CO":"122.24"}