Questions copied from the slicer-users mailing list, originally posted by Sandya Venugopal.


-------- Original Message --------
Subject: [slicer-users] Questions regarding White Matter Lesion Module
on Slicer
Date: Sat, 15 Jan 2011 10:43:55 -0800
From: sandya venugopal
To: slicer-users@bwh.harvard.edu



I had originally addressed this email to Mr.Bockholt and Mr.Scully, however I have not had any response so far, hence posting it on the user forum. I am a new Slicer user. I want to use "Longitudinal Lesion Comparison" on my datasets. However I am not exactly sure how the initial images are generated for it. I have gone through the "White Matter Lesion Detection in Lupus" tutorial, but am still at a loss to understand how the initial images are generated. Using tutorial datasets to obtain expected results has been very easy, but translating that into
analyzing my own data has been quite difficult.

I do not have a programming background (I am a physician), so if someone could kindly send me an "idiot-proof" version of how to perform pre-processing, including co-registration, brain extraction, bias correction, and intensity standardization, in order to obtain the reg+bias.nii and brain_mask.nii files from T1, T2 and FLAIR DICOM images, I would be very grateful.

1. Can I do the preprocessing on Slicer, if not what program should I use, or is there a script I need to run on Linux?
2. T1, T2, FLAIR-Do I have to convert DICOM images to nrrd format first-I know how to do that?
3. How do I generate the brain mask dataset?
4. Where do I find the supporting model files?
5. In the Lupus tutorial, lupus003 seems to be the patient's dataset, and lupus002 seems to be the reference volume. How do I obtain reference volumes for TBI datasets? Do I create them myself? If so, how?
6. Kindly also clarify any other point I might not have thought about.

Once the above questions are clarified, generating the Predict Lesion volume appears quite straight forward as per the tutorials. My understanding is that the lesion volume map generated through this step is the input for the longitudinal lesion comparison module. Kindly correct me if I am wrong please. Other questions I have are:

7. How are Change Tracker and Longitudinal Lesion Comparison modules different? The former seems to be only for tumors from what I've read, or can it be used for every pathology?
8. Can you please explain how to co-register the Predict lesion map with DTI images to assess diffusion deficits? Do I use our FLIRT corrected Nifti images as DTI input? Or something else?
9. Is it possible to do a group comparison of longitudinal lesion changes? Or is it only possible to do it for a single individual?
10. Any other answers I should know to successfully run the above modules, but have not been able to think of it, would be immensely helpful.

Looking forward to your guidance with anticipation.

Thanks and kind regards,

Dr.Sandya Venugopal
Postdoc Research Fellow
Neuroradiology, UCSF, SF, CA