AHEAD segmentation in windows

[navandezande]

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.

[kschan0214]

Hi, sorry for the late reply. The shell scripts used for subcortical segmentation are created for unix systems. Unfortunately I don't have a Windows machine so I can't adapt (and test) the scripts for Windows. Have you been able to solve the issue?