Missing clusters after DIFFPREP

Submitted by wylliansvb on Fri, 03/29/2019 - 12:55

Hi guys,

I apologise if I'm posting a question that was already answered.

I'm facing a problem after I run DIFFPREP in one subject of a project I'm collaborating with. I had to create a T2 image from a T1 using fat_proc_imit2w_from_t1w which worked pretty fine. Then I ran the script provided by Taylor for the AFNI bootcamp, that worked fine for all other subjects except for this one.

Empty *_epi_field.nii file after using DIFFPREP

Submitted by jmollink on Mon, 10/15/2018 - 10:50

Hi Tortoise community,


After applying DIFFPREP to process ex-vivo tissue blocks, my final EPI corrected diffusion images should be stored in the EPI_field.nii. While the file is created, it contents remain empty.. I don't get any error messages in my terminal. Any ideas? Possibly the pipeline is a bit different when using non whole-brain data?





Reorienting anatomical images

Submitted by EBHutch on Fri, 09/28/2018 - 12:02

TORTOISE is a very useful tool and I'm pleased to use it to process pre-clinical data from Bruker scanners.

I have noticed however some issues with my anatomical images not matching my reoriented DWIs and I wonder if there is a good solution for this.  In particular, I don't want to use a third party software (e.g. mipav or FSL) to reorient my anatomical images because I'm worried about how it will affect the header information.  Is there a TORTOISE function that is similar to ReorientImage, but for non-DWI data?