Lesion mask from native to template space

[Sharadhi Bharadwaj]

Hello Dr. Yeh,

We had had a conversation over email about being able to import the lesion mask from the native space to template space since most of our analysis is in the template space. 

Thank you so much for your help with that, while importing it is working when I do not do any corrections on my data, I noticed that if I do any sort of TopUp/Eddy corrections and motion correction, the lesion mask no longer right. 

Not making any corrections gives me the desired result, where the mask imported rightly aligns with the fib file.

From your suggestions, I only change I made was do TOPUP/EDDY corrections before running the QSDR reconstruction.

Your help in this would be greatly appreciated. 

1. Drawing Lesions:

The lesion drawing should be delineated on the high-resolution structure images (i.e., FSPGR). First create a GQI FIB file (DSI Studio will ask to resample to 2mm isotropic, click yes). Open the FIB in Step T3 Fiber tracking, and insert slices->select FSPGR. Draw a lesion on the inserted FSPGR slices, and the lesion ROI should have the same dimension/resolution as the FSPGR.

2. Load lesion in QSDR FIB file.

Use the updated version of DSI Studio to load the SRC, and use [QSDR][Attach image] to attach the FSPGR image. Then run QSDR reconstruction to create the QSDR FIB file. Then open the QSDR FIB in Step T3 Fiber tracking, and you can load the native FSPGR lesion here for fiber tracking.

If there are any follow-up questions, please post them to the DSI Studio forum. 

The dataset can be uploaded using the private upload link.

[DSI Studio]

Sorry for the delayed replay:
DSI Studio will crop out the background to speed up topup/eddy.

To avoid this, you may assign a mask covering the entire image (e.g. use threshold=0). 

This should make the lesion mask align with the DWI.

Best,

Frank