Dear Frank,
We have some patients dwi and PET data that we want to use DSI studio for DTI analysis and maybe then some correlational connectometries to clinical or PET scan ROI scores. For that, we thought we would like to do DTI using gqi in native space. The problem is that for our Hammer’s atlas roi to fit on DTI space, we need to coregister to T1 structural and that seems to be a problem since there seems to be an image orientation mismatch. I read in DSI studio website that this is common to problem and can be solved by multiplying by the DICOM orientation matrix with odf_vertices in fib file after recon. The problem now is that we don’t have DICOM rather we have PAR/REC files from Philips. I also tried to extract the orientation matrix from dwi jason file after using mricrogl dcm2nii tool and making third raw of it by X(3,:)=cross(X(1,:),X(2,:)) function in matlab. then I multiplied this matrix by odf_vertices to reorient and saved the workspace to a new fib which I used in DSI later but it failed to fit to T1. We just missed the first step or reconstruction using DICOM table instead of b-table,
any advice? I think it's either not working or we are missing something, MNI reconstruction worked well btw, should we continue then and opt to use MNI reco method instead? in the latter, we should then normalize PET to MNI too, any way doing that together with DTI reco in MNI inside DSI studio?
Thanks in advance and apologies for the lengthy question
Bassam
Thanks in advance
Bassam
PS. read in your shape analysis Neuroimage paper that you also rotate the dti and b table and did quality control for b table rotation! is it pertinent to my question?
On Tuesday, 30 March 2021 at 21:41:42 UTC+2 Bassam Al-Fatly wrote:Wow, great Frank thanks for the update will try it and other patients data and let you know,
Thanks indeedBassamOn Tuesday, 30 March 2021 at 21:39:43 UTC+2 Frank Yeh wrote:I checked your data, and they seem to work on my side:I use GQI reconstruction at all default settings.After getting the FIB file, I open it in step t3 and inserts the T1W using [Slices][InsertT1W/T2W]Then the atlas can be loaded using [Region][Open Region].If the registration is not good at your end, you may use [Slice][Adjust Registration to fix it].Frank
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