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jeffduda / NeuroBattery

Using ANTs to process multiple MR image types for a single subject
http://jeffduda.github.io/NeuroBattery/
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run_test.sh break at warp_label.sh #9

Open qinqian opened 7 years ago

qinqian commented 7 years ago

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 commented 7 years ago

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 notifications@github.com 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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 notifications@github.com 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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Reply to this email directly, view it on GitHub https://github.com/jeffduda/NeuroBattery/issues/9#issuecomment-332388862, or mute the thread https://github.com/notifications/unsubscribe-auth/AAfWiHjoAPQ0lbriY6VoDteNrzAa6XTwks5sma-5gaJpZM4PT_8q .

qinqian commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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