Search found 11 matches

by willsnyder12
Tue Feb 05, 2019 10:03 pm
Forum: BrainVISA
Topic: Anatomist could not load .arg or certain .bck files
Replies: 3
Views: 4308

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

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
by willsnyder12
Tue Feb 05, 2019 8:38 pm
Forum: BrainVISA
Topic: Anatomist could not load .arg or certain .bck files
Replies: 3
Views: 4308

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

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 usin...
by willsnyder12
Tue Feb 05, 2019 8:33 pm
Forum: BrainVISA
Topic: Handling dimensions/transformation in Create Sulcus Label Volume Output
Replies: 1
Views: 2908

Handling dimensions/transformation in Create Sulcus Label Volume Output

Hello, I am trying to overlay and operate on NIFTI files of a sulcus tracing outside of BrainVISA, and so I would like to have NIFTI files in the same space as the original T1 MRI. When I use Create Sulcus Label Volume, the NIFTI output will be the sulcus I am interested in, and when I load that NIF...
by willsnyder12
Tue Feb 05, 2019 8:20 pm
Forum: BrainVISA
Topic: Locked files
Replies: 2
Views: 2598

Re: Locked files

Hi Denis,
I could not load those files into scripts that required them as input, but the item.unlockData() worked well (as well as just simply removing the lock file).

Thank you!
Will
by willsnyder12
Sat Dec 08, 2018 9:09 pm
Forum: BrainVISA
Topic: Anatomist could not load .arg or certain .bck files
Replies: 3
Views: 4308

Anatomist could not load .arg or certain .bck files

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...
by willsnyder12
Thu Dec 06, 2018 2:29 am
Forum: BrainVISA
Topic: Locked files
Replies: 2
Views: 2598

Locked files

Hello, I am attempting to convert freesurfer files to those compatible with morphologist using the freezurfer import to morphologist tool. When executing this from the command line using axon-runprocess —enabledb, I will sometimes randomly have outputs become locked, and scripts I use after (such as...
by willsnyder12
Mon Oct 22, 2018 9:31 pm
Forum: BrainVISA
Topic: Problem Downloading from http://brainvisa.info/web/download.html
Replies: 1
Views: 2363

Problem Downloading from http://brainvisa.info/web/download.html

Hello, I have tried to download BrainVISA from Mac and from Linux from http://brainvisa.info/web/download.html, but whenever I click on any of the download hyperlinks, the page is either reloaded or I am redirected to a page that says "The requested URL /packages/4.6.1/osx/brainvisa-installer/b...
by willsnyder12
Wed Jul 11, 2018 3:30 pm
Forum: BrainVISA
Topic: Errors with Sulci Recognition in Morphologist Pipeline
Replies: 2
Views: 2906

Re: Errors with Sulci Recognition in Morphologist Pipeline

Hi Denis, Thank you for the thorough response! I had unchecked a few steps before the brain mask step and also unchecked the brain mask step in BrainVISA Morphologist 2015. I was able to successfully use my own brain mask which helped increase presence of orbitofrontal sulcus tracings. I will likely...
by willsnyder12
Thu Jun 28, 2018 1:15 pm
Forum: BrainVISA
Topic: MRI segmentation using morphologist 2015 error
Replies: 7
Views: 3993

Re: MRI segmentation using morphologist 2015 error

**Correction: brainvisa MRI (not mdi) format
by willsnyder12
Thu Jun 28, 2018 1:14 pm
Forum: BrainVISA
Topic: MRI segmentation using morphologist 2015 error
Replies: 7
Views: 3993

Re: MRI segmentation using morphologist 2015 error

Hi Alexjandro, I've had similar problems before. When you converted to brainvisa mdi format, did you set the voxel type to S16? Try using the Aims Converter tool in BrainVISA (Tools>converters>Aims Converter) and select the output voxel type to be S16. This helped with some errors in the past I have...
by willsnyder12
Wed Jun 27, 2018 9:29 pm
Forum: BrainVISA
Topic: Errors with Sulci Recognition in Morphologist Pipeline
Replies: 2
Views: 2906

Errors with Sulci Recognition in Morphologist Pipeline

Hello, I am trying to use the Morphologist Pipeline (non-UI) (from BrainVISA version 4.5) on a Mac (OSX 10.9), and I am running into a few errors. I am not using the UI because the T1MRI's I have are already preprocessed/masked/skull stripped, and the UI procedure applies another brain mask that cau...

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