Help with ASHS Processing Error at Stage 4 Using UMC Utrecht 7T Atlas #10
Description
Dear ASHS Support Team,
I hope this message finds you well.
I recently downloaded the ashs-fastashs-20170223.zip package and used the UMC Utrecht 7T ASHS Atlas (ashs_atlas_umcutrecht_7t_20170810) to analyze my hippocampal data. For preprocessing, I ran the following command:
bash
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$ASHS_ROOT/bin/ashs_main.sh -I sub12004
-a /home/lan/ASHS/ashs_atlas_umcutrecht_7t_20170810
-g /home/lan/ASHS/data_test/sub-12004_desc-preproc_T1w.nii.gz
-f /home/lan/ASHS/data_test/sub-12004_Hippo.nii
-w /home/lan/ASHS/data_test/result12004
However, the process consistently fails at Stage 4, with an error indicating missing files. I’m not sure if the problem stems from incorrect input data or if it's an issue with my Linux environment.
- bash /home/lan/ASHS/ashs-fastashs_beta/bin/ashs_default_hook.sh progress 0.894231 0.9 1
====================================
PROGRESS: 0.894231
====================================
**************** !! ERROR !! *******************
Validity check at end of stage 4 detected
missing files.
(bootstrap/tseg_left_train000/greedy_warp.nii.gz
and 132 other files).
Here are a few details that might help in diagnosing the issue:
I’ve tried two different versions of the ASHS tool.
I’ve tested both skull-stripped and non-stripped versions of the T1-weighted image.
My T2-weighted image has a voxel resolution of [0.4375, 0.4375, 1.1].
Given that the atlas T2 resolution is 0.35 × 0.35 × 0.35 mm³ (interpolated), I was wondering:
Should I manually resample my T2 image to match the atlas resolution before running ASHS, or does the pipeline handle this interpolation internally?
I would be truly grateful for any insights or recommendations you could provide. Thank you so much in advance for your support and time!
Warm regards,
Lan