Anatomist could not load .arg or certain .bck files

Questions about BrainVisa usage and installation

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willsnyder12
Posts: 11
Joined: Tue Jun 05, 2018 6:34 pm

Anatomist could not load .arg or certain .bck files

Postby willsnyder12 » Sat Dec 08, 2018 9:09 pm

Hello,

I wrote a script to run morphologist on some brains from the command line, and I am now trying to view the resulting sulci graph (*.arg). The anatomist application stops responding after, and I figured something was wrong with the .data files. I could individually load all the .bck files from the .data folder, except for ss_Bucket.bck and plidepassage_Bucket.bck, and when I delete these files, I am able to now view the *.arg sulci graph (however, some of the buckets I expected to have values did not when viewing this image, presumably from the deleted .bck files).

Why is it that these two .bck files are not able to load in anatomist? I have not had trouble viewing these in the past with other datasets, so I feel it is not anatomist but rather something about these two .bck files that is wrong. I ran Brainvisa using axon-runprocess --enabled from the command line, and the last part of my script clears out all other morphologist output files except for those typically necessary to view sulci graphs (*.arg, *.arg.minf, *.data). Could it be that moving around these files somehow corrupted them? I'm not sure what is going on here. Any help will be greatly appreciated.

Thank you,
Will

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riviere
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Re: Anatomist could not load .arg or certain .bck files

Postby riviere » Sun Dec 16, 2018 9:11 pm

Hi,
Well it's difficult to answer without more information... Anatomist should be able to read .bck files, so either the files are corrupted, or there is something wrong in bucker reading in anatomist (but as it is using the same IO library as every tool in morphologist, it should not be specific to anatomist).
You can try sending me one of the buckets (ss_bucket for instance), so I can see if the file is OK or not. I suspect not. Then we have to understand why it is not.
Denis

willsnyder12
Posts: 11
Joined: Tue Jun 05, 2018 6:34 pm

Re: Anatomist could not load .arg or certain .bck files

Postby willsnyder12 » Tue Feb 05, 2019 8:38 pm

Hello again,

Since I last responded I have run Morphologist on 580 subjects and now have lots of tracing data to work with. While I haven't manually quality-checked all 580 brains, all of the files seemed to open well in Anatomist, however in the case that this issue does occur again while I am using the data, I am curious how it may be avoided. Attached I have the ss_bucket file that would not load in Anatomist. Let me know if there is anyway to edit/uncorrupt this file or whether it is better to just run the pipeline on the same brain again.

Best,
Will

willsnyder12
Posts: 11
Joined: Tue Jun 05, 2018 6:34 pm

Re: Anatomist could not load .arg or certain .bck files

Postby willsnyder12 » Tue Feb 05, 2019 10:03 pm

I am having difficulty attaching a .bck file to the forum post, let me know if you would like me to email it to you.

Best,
Will


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