search

APPIAN-PET / APPIAN

APPIAN is an open-source automated software pipeline for analyzing PET images in conjunction with MRI. The goal of APPIAN is to make PET tracer kinetic data analysis easy for users with moderate computing skills and to facilitate reproducible research.
MIT License
40 stars 17 forks source link

brain_mask_space_pet error #38

Open wcoath opened 2 years ago

wcoath commented 2 years ago

Hello,

I'm using APPIAN to run an SUVR pipeline with T1, freesurfer segmentation and static florbetapir PET image that is one single frame of 50-60mins post-injection. I'm using the latest release downloaded from dockerhub on 19th May 2022, running it through singularity on a HPC cluster (as I can't use docker on the HPC).

This is the command that is being run: python3 /opt/APPIAN/Launcher.py -s /appian_test/data -t /appian_test/cerebellum_suvr_10015124_baseline --sub 10015124 --ses baseline --no-group-level --quant-method suvr --start-time 3000 --end-time 3600 --quant-label-img fs-segm --quant-label 7 8 46 47 --quant-labels-ones-only --quant-label-space t1 --no-mri-mask --normalization-type nl --results-label-img fs-segm --results-label-space t1 --threads 4

It fails consistently on the 'brain_mask_space_pet' step after completing normalisation step. I've attached the full log file. Any help working out what is going wrong would be much appreciated! Many thanks - Will

appian_log.txt

tfunck commented 2 years ago

Hi Will,

Thanks for the message! I'm at a conference right now until Thursday and then off on vacation for a week. I'll try to have a look at it before then, but if not I'll check when ai get back in early July. Don't hesitate to email me to remind me if I don't get back to you soon!

Best

Thomas

On Tue, Jun 21, 2022, 15:23 Will Coath @.**@.>> wrote:

Hello,

I'm using APPIAN to run an SUVR pipeline with T1, freesurfer segmentation and static florbetapir PET image that is one single frame of 50-60mins post-injection. I'm using the latest release downloaded from dockerhub on 19th May 2022, running it through singularity on a HPC cluster (as I can't use docker on the HPC).

This is the command that is being run: python3 /opt/APPIAN/Launcher.py -s /appian_test/data -t /appian_test/cerebellum_suvr_10015124_baseline --sub 10015124 --ses baseline --no-group-level --quant-method suvr --start-time 3000 --end-time 3600 --quant-label-img fs-segm --quant-label 7 8 46 47 --quant-labels-ones-only --quant-label-space t1 --no-mri-mask --normalization-type nl --results-label-img fs-segm --results-label-space t1 --threads 4

It fails consistently on the 'brain_mask_space_pet' step after completing normalisation step. I've attached the full log file. Any help working out what is going wrong would be much appreciated! Many thanks - Will

appian_log.txthttps://github.com/APPIAN-PET/APPIAN/files/8949722/appian_log.txt

— Reply to this email directly, view it on GitHubhttps://github.com/APPIAN-PET/APPIAN/issues/38, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABUJ4PEVOUXQ4UIIUPW73C3VQHF5LANCNFSM5ZMRJAXQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>

Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior

Neugierige sind herzlich willkommen am Sonntag, den 21. August 2022, von 10:00 bis 17:00 Uhr. Mehr unter: https://www.tagderneugier.de

wcoath commented 2 years ago

Hi Thomas, Hope you had a good conference and vacation! I'm just wondering if you've had a chance to look at this yet? Cheers! Will

tfunck commented 2 years ago

Hi Will, I did and just pushed the change last night. Can you run it again and let me know how it goes?

Thomas

On Fri, Jul 15, 2022, 05:12 Will Coath @.***> wrote:

Hi Thomas, Hope you had a good conference and vacation! I'm just wondering if you've had a chance to look at this yet? Cheers! Will

— Reply to this email directly, view it on GitHub https://github.com/APPIAN-PET/APPIAN/issues/38#issuecomment-1185345443, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUJ4PD3LZCN2BUYFBPLVRLVUETQNANCNFSM5ZMRJAXQ . You are receiving this because you commented.

Message ID: @.***>