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CCB SIG-FLOW - Progress and Workflow Status - 11/05/09
Pending Pipeline Workflows
- Bo Sun's Chinese Atlas Project (see 09/14/09 email)
- Yuchun/Robbie Project: Sulcal-landmark-based cortical registration (Shruthi/Alen)
- NIMH Kids skull-stripping project (/ifs/ccb/collabs/Other_CCB_Collabs/NIMH_Gogtay_Thompson_2009)
- Shruthi (Better SSing with MDT atlas, vs. using one subject A3.img)
- SSMA workflow push to production (?!?) - the results of the NIMH kids data SSing were great.
- Shruthi (10/27/09 email to Kelvin)
- Reformatting of the ICBM DTI/fMRI/MRI data in MNC/NiFTI format to include correct origin (starting point (-90x, -126y, -72z)). Revised volumes are in: /ifs/ccb/data/ICBM/Atlases/ICBM_AtlasFix_Oct2009_MNC_NIFTI_HDR
- Shruthi to validate (e.g., using LONI Inspector) that all NIFTI/MNC volumes have the correct starts/origin. Finally ask Amanda to provision these atlases to the web.
- SVPASEG (Sub-Volume Probabilistic Atlas Segmentation) software
- Shruthi to build, test, pipeline, disseminate
- /ifs/ccb/CCB_SW_Tools/VolumeTools/JussiTohka_Cranium/SVPA_2009/
- LPBA-X Project
- Auto Volume Workflows:
- Ivo to make Wiki pages describing these workflows
- Auto Tissue Volume Workflow (auto calculation of total WM GM ICV volumes)
- Shruthi: Testing using SSME skull-stripping preprocessing based on all 104 subjects in the ADNI study and the Trauma postcontrast data
- Automated 56 ROI Volume extraction workflow - Complete!
- Alen validated on ADNI data
- Alen to double check the "TransposeMatrix" module problem for the Trauma data.
- Test with Trauma data (/ifs/collabs/VESPA/CLEANED/***bet_clean.img)
- Global Shape Analysis (GSA)
- Alen/Shruthi will do the final validation of the GSA pipeline workflow on the dev cluster (cerebro-dev) using the 701 subjects from the ICBM data on both PC and Apple. Data will be split into 3 groups. Then Kamen and the Pipeline team will work on the meta-data augmentation project, where results of the pipeline will be used to append the Design-Matrix (meta-data expansion).
- (Alen) Age: up to 30, 31-50, 51+
- (Shruthi): Weight: up to 140lb, 141-180, 181+
- Use latest version of the Pipeline environment: /ifshome/zliu/Pipeline-2278.jar
- Tested with the 104 ADNI dataset (/ifs/ccb/data/ADNI_Data_Feb2009). Results are in: /ifs/ccb/data/ADNI_Data_Feb2009/Results_July2009/ADNI_GSA_Compiled_Results_July13_2009.txt
- Alan modified the workflow to ensure all modules are well described, all file types are appropriate (e.g., output text files should have *.txt extensions) and commit to production for use by the community.
- Alen is added 2 additional flags/options in ShapeReporter to output the Volumes and MeanCurvature? for each shape (in addition to FD, surface-area, shape-index, curvedness).
- Alen included a data-sink for saving the 56ROI labled volumes in LPBA40 atlas, or native, space.
- Craig/Bae-Cheol/Ivo updated the ShapeTools? TTest module to allow outputting the p-values, in addition to the currently outputted T-values!
- Alen updated the ADNI GSA workflow to provide p-values as outputs
- ShapeTools MakeSceneFile Utility:
- Alen put a new module to enable the local/client display of ROIs that are significantly different between 2 populations, based on a user-specified shape-measure.
- Kamen to confirm the final test with the generation of valid Scene files (and display using LONI_Viewer?)
- Ivo will do an activity/tutorial once the workfow is validated and ready for inclusion in the Core library
- Kamen is running tests on the GSA workflow and he will confirm the results soon. Had some problems with the file system.
- Local Shape Analysis (LSA) - BorisGutman took charge of this workflow (returning Sept 25, 2009)
- Wiki-page docs/usage
- Color-mapping (Red: p<=0.05; Green: 0.05<p<=0.1; Blue: p>0.1).
- Alen resent LSA.V.5 integrated with pre-processing.
- 4 similar-functionality branches:
- Mask --> Shape (Boris's tools, as in the current ADNI AD-MCI-NC Pipeline; or using Yonggang's Mask-to-shape converter)
- Using ShapeToolsStats? or via Yonggang's Direct-Shape-Mapping-Stats tools.
- Alen is testing a couple of these branches using 2-5 ROIs:
- 14 162 R_caudate
- 23 163 L_putamen
- 52 165 L_hippocampus
- 4 181 cerebellum
- fMRI/FEAT
- Shruthi: Second (high) level fMRI data analysis (between subjects/groups) using FSL/Feat
- Script to pre-process the 32-bit fMRI data into 8-bit data are here: /loni/dinov/data.dir/fMRI_data.dir/fMRIDC_Buckner_AD_Elderly_NC.dirprocess_protocol.csh
- fMRI Data to post to core Pipeline data library (/loni/dinov/data.dir/fMRI_data.dir/fMRIDC_Buckner_AD_Elderly_NC.dir/data.dir/exp1-1): Data has been posted on the Pipeline library. Buckner's subject - 1 with run A alone has been posted for the Pipeline roadshow in September.
- JackVanHorn? did a SIGPNS demo of the FSL/FEAT functionality/pipeline in August, 2009.
- Direct Hippo Mapping (DHM, YonggangShi) workflow
- Yonggang to make a Wiki page describing each of the modules and the entire pipeline workflow in detail.
- Shruthi to include in Core Library
- This workflow is similar in principal to the Local Shape Analysis (LSA) workflow, but uses different math/algorithms. Need to compare these.
- Minimum Distance Template (MDT), Atlasing
- Wait until Boris/Claus finalize their MDT (Medial Distance Workflow)
- Need final testing and migration to production
- Boris fixed the bugs with random out-of-memory exceptions of the workflow using KL_MI. We need to compare the results with his latest version of the MDT pipeline/protocol.
- Alen - will then test the revised pipeline on kids data (ICBM space, inire: /loni/warp/dinov_warp/WAIR_tests.dir/kidsMRI.dir/AIR_warps.dir/*_Avg_AIR12.hdr) and the old anisotropic data.
- KristiClark LONI DTI Tools Pipelines
- Shruthi - need to provision to production (ref. Kristi's SIG-PNS Pipeline Demo).
- Alen to update the left-right switch in the DTI atlas (Kristi's email).
- NathanHageman: Leviathan/MiND Pipelines
- Upgrade of LONI_Viewer: Ivo emailed Kamen, Scott, Zhizhong and Craig for the re-packaging of the LONI_Viewer to include/replace the new ShapeViewer JAR and latest Debabeler (svn+ssh://svn.loni.ucla.edu/cvs/ccb/LONI_Viewer).
- In the future, perhaps extend the LONI_Viewer to display Text data (CSV, HTML, XML, ASCII). Movies/post-production animation?
- BrainSuite Cortical Surface Extraction Pipeline
- Awaiting David Shattuck's final go-ahead (access permissions to atlas data).
- Bioinformatics Workflow (Alen/Ivo)
Completed Pipeline Workflows
- UCF SEG to MultiTracer converter, mapping, translator
- Pipeline ICBM Data module - missing /usr/local/data ....
- MGH Diffusion ToolKit? (TracViz?) Pipeline modules - need to provision to production.
- Stats Tools Modules
- Last-remaining (low-priority) request: Allowing string/label/qualitative variables (e.g., "male" and "female")
- skipBytes method (Alen/Ivo updates)
- Alen to make another pipeline wrapper with a single directory output where the filenames will indicate the statistics and the regressor associated with the file (e.g., Beta_Regressor=Sex.img/hdr).
- Volume Stats Modules/Pipelines:
- Alen, Kamen, and Ivo resolved the Memory problem with her 400+ subjects analysis.
- Done: New bug - ordering of the regressor variables and the order of the results (T,B,R,P values) based on the regressors.
This has been resolved and the Volume Regressor module is releases to the Pipeline library.
- Done: Thompson-Group request for calculation/reporting of the partial correlation coefficients. (Jason, April, Ivo)
- Done: (/ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics) General stats modules:
- Alen's new work partition: /ifs/ccb/azamanyan azamanya
- Update all Pipeline core library references data, module-descriptions and workflows to avoid links to personal folders (e.g., /ifs/dinov).
- Handbook revisions and expansion
- Shruthi: Send all the updates, description and screenshots of the fMRI first level workflow to Amanda. Rico is working on debugging the workflow.
- Error in FSLStats (version 4.1.0). The error is that when the user specifies a mask (using -k) and also the mean (-m or -M), the program (the actual program, not just the pipeline instantiation) gives different answers for the following:
- fslstats input.img -m -k mask.img
- fslstats input.img -k mask.img -m: This gives the mean for voxels only within the mask (correct), while #1 gives the mean for the whole image, i.e. the mask is not applied to the data at all. However, I am pretty sure this is a bug in the FSL program because there's nothing in the help menu to suggest that the order of arguments matters. Right now I'm figuring out how to report this to the appropriate people at FSL, or to find out if there was a patch released to fix it, but in the meantime, maybe someone could make a change in the way the pipeline converts the arguments into a commandline b/c right now the actual commandline that is run is #1.
- In FSL 3.3 on the pipeline, the module for avwstats points to a file (/usr/local/fsl-3.3.11_64bit/bin/avwstats.sh) that does not exist.
- AIR/Alignlinear module problem (core Pipeline library)
- Alen is checked - there are 2 modules now that convert Float --> Short that need to be used for such data conversions before the AIR tools are invoked.
- Pipeline module descriptions - dichotomy of describing raw executables vs. wrapper shell-scripts. A suggested paragraph for LONI Pipeline User-Guide/FAQs:
- The pipeline environment does not require any modifications, rebuilds, redeployments of existent tools which provide a well-defined command-line executable invocation syntax. However, sometimes it may be helpful or necessary to wrap executable tools via external shell scripts (e.g., tcsh, csh, bash, etc.) Examples of these situations include:
- instances of command-line executable tools that have a well-defined invocation syntaxt, however, output implicit number, types and formats of results/data that can not be inferred a priori. E.g., VolumeMultipleRegression tool
- tools that require customized environmental variable settings, system controls or job-submission parameter settings (e.g., FreeSurfer?, SPM, FSL/FEAT, etc.)
- ShapeTools Modules/Pipelines
- Available in Core Library (Alen/Shruthi), including the ShapeTranslator Module
- Tensor Based Morphometry (TBM), Cal Tech
- Cal Tech collaborators confirmed that they are able to get the results. Current version of the workflow does PermutaitonTest? correction for multiple-comparison, but does not allow FDR correction, because the data and p-values are stored in 16-bit short integer format.
- DIRAC DWI tools (Vishal)
- Datasets and Atlases
- Alen: Available in the Pipeline (under Data), except that the AD atlas needs Analyze headers
- Ilya's Scan/make Analyze header tools should be made available in the Core Library (Alen) (/ifs/ccb/ilya/tools/ilya/anlz_makehdr)
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