Abhijit Guha Roy

@shayansiddiqui Please take a look into the recent release

Hi, There is a quick pre-processor using FreeSurefer before segmentation. You need to execute this command from terminal: mri_convert (input_vol_name) (out_vol_name) --conform This resamples and also performs some global contrast...

If I got it right, your data is 256x256x130 (1mmx1mmx1.3mm). In that case only use the predictions from coronal network (If your 130, 256x256 slices corresponds to coronal slices). The...

It seems the problem is with the reader 'MRIread'. You can try any other reader and pass the volume directly as Data (matrix of size 256x256x130) in [Predictions, SegTime] =...

Are you overlaying the MRI and segmentation properly? Coronal axis predictions looks ok-ish to me, just misaligned (Might be a problem with header files). If possible drop me an e-mail...

Hi, There is also some global contrast enhancement made during this step. Unfortunately this is not very clear in FreeSurfer documentation. https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert

Hi Donghuan, 1. Rows were zero padded to size of 512 (power of 2), for the ease of using encoder-decoder architecture with max-pooling layer, which reduces the resolution by 2....