| T O P I C R E V I E W |
| petty |
Posted - Oct 13 2009 : 09:49:57 AM
Hi,
Over the last week I've rolled out the most recent version of the processing pipeline.
Updates include:
- Support for spiral imaging from the new MR750
- Updated sense processing for the new MR750
- removal of the intermediate sense calibration files (PP.*)
- updated file types of sense images to uint16 to prevent overflow on extreme numbers
- nightly QA generation for dicom functionals
- experimenter options read from webserver
- extended availability of experimenter preferences
- using newest BXH-Xcede Tools v1.9.2
About the Preferences:
I've set up the pipeline to support more experimenter preferences. For instance you can request your data in 3D or 4D as well as changing the file type to spm, nifti-gzipped, just nifti, or raw. The spm type will come with header files already generated as well as a BXH header. The niigz data will come as a 4D nii.gz file, with associated BXH. On top of file type you can request your data to come in a specific orientation (ie: LAS instead of the default scanner orientation) ... the goal of these additions was to deliver data ready for your own processing without the creation of multiple copies of data. Preferences can be set seperatly for Pfiles, DICOM-Func, DICOM-Anat. If you're collecting ASL or B0 maps, they can have the same preferences applied as the Functional Pfiles, or they can be ignored and will come as they do now
If there are any questions please let me know. I will be working on an addition to your "Dashboard" so that you can submit preferences to me, but until that is ready, please email me directly.
Also, if you find any oddities please let me know that as well ... If no requests are made for your specific study, then you will continue to receive your data with the default preferences that you have now.
thanks,
-Chris |
| 3 L A T E S T R E P L I E S (Newest First) |
| wang |
Posted - Oct 13 2009 : 10:39:37 AM
Sound great. Thanks!
Lihong |
| petty |
Posted - Oct 13 2009 : 10:37:38 AM
you would continue to do so, unless you get with me to set up your preferences for specific experiments.
everything is currently coming over the same as before, nothing will be different unless i put in a special entry for your specific experiment .. if you wanted your data .nii.gz and in LAS format we would need to set that up for you, THEN you would not need to re-orient. |
| wang |
Posted - Oct 13 2009 : 10:34:08 AM
This sounds really nice Chris. Thanks a lot. We normally have to reorient the images to match the fsl template before we do data preprocessing. Should we continue to do so with your new version pipeline?
Lihong |
|
|
