Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

AHEAD segmentation in windows #96

Open
navandezande opened this issue Dec 16, 2024 · 0 comments
Open

AHEAD segmentation in windows #96

navandezande opened this issue Dec 16, 2024 · 0 comments

Comments

@navandezande
Copy link

We have a question regarding the Segmentation Analysis Tool in Sepia, with which we are struggling at the moment.
Hopefully, you can help us with that.

We are working on Windows. We downloaded ANTS binary-Windows version (https://sepia-documentation.readthedocs.io/en/latest/getting_started/Sepia-header.html) as well as the AHEAD atlas (https://uvaauas.figshare.com/articles/dataset/The_Amsterdam_Ultra-high_field_adult_lifespan_database_AHEAD_A_freely_available_multimodal_7_Tesla_submillimeter_magnetic_resonance_imaging_database/10007840/1), which we have unzipped.
We changed the ANTS directory in Utility to the correct folder.
We tried the guideline on https://sepia-documentation.readthedocs.io/en/latest/method/segmentation/ahead.html, but ended up with the following error:

Perform image registration to get atlas labels...
The system cannot find the path specified.
The system cannot find the path specified.
There was an error! Please check the command window/error message file for more information.
Error using sepia_handle_panel_analysis_segmentation_AHEAD>PushbuttonStart_Analysis_segmentation_Callback (line 294)
Function GUNZIP was unable to find file
''T:\2021_METC#_shortstudytitle\HDiron_processed_data\programs\ants-2.5.4\AHEAD_intermediate_files\Sepia_Chimap -
original_2T1w.nii.gz''.

Error while evaluating UIControl Callback.

There is no AHEAD_intermediate_files in our downloaded ants-2.5.4 folder.
Another strange thing is that the ‘atlas’ subfolder in the sepia folder gets blocked the moment we press Start.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant