run_test.sh break at warp_label.sh

[qinqian]

Hi,

It is really nice to know the nice open source analysis pipeline for multi-modality MRIs. We have encountered a problem when running run_test.sh. The errors occurs from the warp_label.sh step, I tried to run it line by line, there is one issue causing by missing files for PCASL:

file ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_brainmask.nii.gz does not exist . Transform file does not exist: ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_1InverseWarp.nii.gz file ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_brainmask.nii.gz does not exist . file ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_aal.nii.gz does not exist . ./warp_labels.sh: line 62: 30895 Segmentation fault (core dumped) ${ANTSPATH}/ImageMath 3 ${SUBJECTPCASLDIR}${SUBJECTID}_PCASL_aal.nii.gz m ${SUBJECTPCASLDIR}${SUBJECTID}_PCASL_aal.nii.gz ${SUBJECTPCASLDIR}${SUBJECTID}_PCASL_brainmask.nii.gz

We checked the output directory for PCASL, which only contains: ../data/output/PEDS012/20131101/PCASL/: PEDS012_20131101_PCASL_CBF.nii.gz PEDS012_20131101_PCASL_SegmentationWarpedToASL.nii.gz PEDS012_20131101_PCASL_CBFWarpedToTemplate.nii.gz PEDS012_20131101_PCASL_TissueStats.csv

It seems that the files are missing, can you help us figure out how to fix the issue.

Thanks so much. Qian

[jeffduda]

Ok, just fixed this. You'll need to update both NeuroBattery and ANTs and then it should be good. -Jeffrey Duda

On Mon, Sep 11, 2017 at 10:03 PM QinQian [email protected] wrote:

Hi,

It is really nice to know the nice open source analysis pipeline for multi-modality MRIs. We have encountered a problem when running run_test.sh. The errors occurs from the warp_label.sh step, I tried to run it line by line, there is one issue causing by missing files for PCASL:

file ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_brainmask.nii.gz does not exist . Transform file does not exist: ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_1InverseWarp.nii.gz file ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_brainmask.nii.gz does not exist . file ../data/output/PEDS012/20131101/PCASL/PEDS012_20131101_PCASL_aal.nii.gz does not exist . ./warp_labels.sh: line 62: 30895 Segmentation fault (core dumped) ${ANTSPATH}/ImageMath 3 ${SUBJECTPCASLDIR}${SUBJECTID}_PCASL_aal.nii.gz m ${SUBJECTPCASLDIR}${SUBJECTID}_PCASL_aal.nii.gz ${SUBJECTPCASLDIR}${SUBJECTID}_PCASL_brainmask.nii.gz

We checked the output directory for PCASL, which only contains: ../data/output/PEDS012/20131101/PCASL/: PEDS012_20131101_PCASL_CBF.nii.gz PEDS012_20131101_PCASL_SegmentationWarpedToASL.nii.gz PEDS012_20131101_PCASL_CBFWarpedToTemplate.nii.gz PEDS012_20131101_PCASL_TissueStats.csv

It seems that the files are missing, can you help us figure out how to fix the issue.

Thanks so much. Qian

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[qinqian]

Thanks so much for the reply! We have updated the NeuroBattery and ANTS, the issue is fixed. However, there are another issue raised from comparison.Rmd.

Quitting from lines 202-272 (comparison.Rmd) Error in antsImageRead(cbf.test, 3): file does not exist Calls: render ... withVisible -> eval -> eval -> as.array ->antsImageRead

Execution halted

Another minor things is in process_modalities.sh, we need to manually remove the ../data/input/PEDS012/20131101/DTI to make the conversion of DWI work. And, many sh should be replaced with bash to make the antsNeuroimagingBattery work.

The system is Ubuntu 16.04, R version is 3.2.3 with latest ANTsR installed.

Best -Qian

[qinqian]

Any updates? The issue seems to be the missing part of the codes in ${ANTSPATH}/antsNeuroimagingBattery and ${ANTSPATH}/antsASLProcessing.R and to generate *meancbf_anatomical.nii.gz and *PCASL_MOCOStatsFramewise.csv.

[jeffduda]

Sorry, this fell off my radar for a bit. Will try to fix this tomorrow or early next week.

On Tue, Sep 26, 2017 at 10:15 PM QinQian [email protected] wrote:

Any updates? The issue seems to be the missing part of the codes in ${ANTSPATH}/antsNeuroimagingBattery and ${ANTSPATH}/antsASLProcessing.R and to generate *meancbf_anatomical.nii.gz and *PCASL_MOCOStatsFramewise.csv.

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[qinqian]

Thanks so much! looking forward to your updates. By the way, the whole brain tractography and connectome in the readme is fantastic, is that plotted through camino or R?

[jeffduda]

OK, think I fixed the issues. I believe I used R for any line plots, ITK-Snap for the brain slices and overlays and Paraview for the streamline image.

[qinqian]

Great! The issues is fixed, we really learn a lot from the nice codes.