stroke MRI, segmentation, file organization

[Joyce Chen]

Hello,

I'm a new user and had a few questions if someone can help:

1. I am working with MRIs of people with stroke - they have variable lesion sizes, some quite small, others noticeable. Is there a way to process these MRIs? I have binarized lesion masks so could 'exclude' the lesion voxels in any analyses, if that is an option? We apply the tDCS to the contralesional hemisphere.

2. How can I check the segmentation outputs. I have worked in FSL and would typically overlay the segmented outputs on the T1 and visually check. Is there a 3D file for each segmented output?

3. Any advice as to how to organize data. For example, for each participant, I will run roast twice. If I then move these data into two separate folders, how can I use reviewRes since the outputs of Roast are in a separate folder from the struct.nii file

This is how I've set things up:

/roast/s01/struct/struct.nii

/roast/s01/struct/C41Fp1-1/outputs of Roast for analysis 1

/roast/s01/struct/C4-1Fp1-1/outputs of Roast for analysis 2

where /roast contains all subject data (s01, s02, etc), and all the matlab files downloaded from your website.

Thank you very much for your time and help. 

Kind regards,

Joyce

 

[Yu (Andy) Huang]

Hi Joyce,

1. I am working with MRIs of people with stroke - they have variable lesion sizes, some quite small, others noticeable. Is there a way to process these MRIs? I have binarized lesion masks so could 'exclude' the lesion voxels in any analyses, if that is an option? We apply the tDCS to the contralesional hemisphere.

ROAST does not process lesioned MRIs. You can use any other toolboxes. One example is the MultiPrior deep neural network for segmenting the lesioned MRIs.

2. How can I check the segmentation outputs. I have worked in FSL and would typically overlay the segmented outputs on the T1 and visually check. Is there a 3D file for each segmented output?

Yes the segmentation is output as a *_masks.nii file. You can open it with any NIFTI file viewer.

3. Any advice as to how to organize data. For example, for each participant, I will run roast twice. If I then move these data into two separate folders, how can I use reviewRes since the outputs of Roast are in a separate folder from the struct.nii file

You don't have to move files by hand. You can keep everything in the same folder. When you run different analyses, give them different tags when calling roast() using the simulationTag option, then all simulations will be automatically managed by the tags. 

Hope this helps. 

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