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Aswendt-Lab / AIDAmri

Atlas-based Imaging Data Analysis Pipeline (AIDA) for structural and functional MRI of the mouse brain
GNU General Public License v3.0
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Change the labling txt file (naming) #6

Closed arefks closed 7 months ago

arefks commented 1 year ago

Describe the bug What we do in DSI Studio:

1-Loading a fiber tract file with the following naming scheme: (SubjecName.fib.gz) 2- Loading the corresponding atlas of that subject in the form of SubjectName_split_scaled.nii.gz

Situation 1: Windows 11 DSI studio Version: August 2022 Step 1: Works ✅ Step 2: Does not work completely ⚠️ (Loads segmented brain masks, but the region naming is still not correct) image

How we solved the issue When the atlas region names are saved like "SubjectNameSmoothMicoBetAnno_rsfMRISplit_scaled.nii.txt" it won't work. We took out the .nii from the file naming getting "SubjectNameSmoothMicoBetAnno_rsfMRISplit_scaled.txt", then it worked for the DSI-Studio. image

So somewhere in dsi studio it automatically looks for the txt file but it also does some path splitting maybe based on the .nii in the file name, and that's why it would not work. (Maybe also interesting for you @frankyeh, though this is primarily an AIDAmri issue).

@lucaruthe @VictorVeraFrazao @maswendt

frankyeh commented 1 year ago

Thanks for the information. This should be a quick fix to check or both naming conventions. Frank

On Tue, Oct 10, 2023 at 10:24 AM Aref Kalantari @.***> wrote:

Describe the bug What we do in DSI Studio:

1-Loading a fiber tract file with the following naming scheme: (SubjecName.fib.gz) 2- Loading the corresponding atlas of that subject in the form of SubjectName_split_scaled.nii.gz

Situation 1: Windows 11 DSI studio Version: August 2022 Step 1: Works ✅ Step 2: Does not work completely ⚠️ (Loads segmented brain masks, but the file naming is still not correct) [image: image] https://user-images.githubusercontent.com/87692940/273915444-cdb4a5ce-f736-48c2-ab3a-2ea0a064985b.png

How we solved the issue When the atlas region names are saved like "SubjectNameSmoothMicoBetAnno_rsfMRISplit_scaled.nii.txt" it won't work. We took out the .nii from the file naming getting "SubjectNameSmoothMicoBetAnno_rsfMRISplit_scaled.txt", then it worked for the DSI-Studio. [image: image] https://user-images.githubusercontent.com/87692940/273951172-6555e206-5bda-4c32-b53b-7c48b02c857a.png

So somewhere in dsi studio it automatically looks for the txt file but it also does some path splitting maybe based on the .nii in the file name, and that's why it would not work. (Maybe also interesting for you @frankyeh https://github.com/frankyeh, though this is primarily an AIDAmri issue).

@lucaruthe https://github.com/lucaruthe @VictorVeraFrazao https://github.com/VictorVeraFrazao @maswendt https://github.com/maswendt

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