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ledigchr / MALPEM

MALPEM whole-brain segmentation framework
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Mask file does not exist #7

Closed rhan93 closed 3 years ago

rhan93 commented 3 years ago

Hi,

I am getting the error that "File does not exist (/malpem/atlas/nmm/mri_masked_scaled/a4.nii.gz)". Are these files supposed to be downloaded during installation?

Best, Runze

Log file: bin/malpem-proot: line 17: locate: command not found WARNING: Didn't find libGL library in /usr/lib/nvid*, offscreen rendering won't work (only relevant for pdf report) Copying file atlas/pincram/limages/full/m100.nii.gz to input directory: cp atlas/pincram/limages/full/m100.nii.gz bin/../lib/care//rootfs/tmp//input//tmp.zq7ZCzlA52/

Command in CARE environment: malpem -i /tmp/input/tmp.zq7ZCzlA52/m100.nii.gz -o /tmp/output/tmp.zq7ZCzlA52/ -t 8

Input file: /tmp/input/tmp.zq7ZCzlA52/m100.nii.gz Output directory: /tmp/output/tmp.zq7ZCzlA52/ Field strength: 1.5T Max. threads: 8 Using input mask: False Using input segmentation: False Using transformation to initialise MNI alignment: False Performing initial bias correction: True Stopping after brain extraction: False Perform another N4 bias correction after the brain extraction: True Create a subdirectory for output: True Create final pdf report: True Will clean up once finished: False

--- ERROR: File does not exist (/malpem/atlas/nmm/mri_masked_scaled/a4.nii.gz): --- Output directory outputDir doesn't exist, creating it Moving results to output directory: outputDir Cleaning up input directory: bin/../lib/care//rootfs/tmp//input//tmp.zq7ZCzlA52

ledigchr commented 3 years ago

Hi Runze,

Yes, those files should be downloaded during installation. Please refer to the installation guide for a default installation: https://github.com/ledigchr/MALPEM/blob/master/README.md#installation

Cheers, Christian

rhan93 commented 3 years ago

Thank you. I didn't realize that one of the packages was not correctly downloaded due to disk space limitation.