Re: [FSL] Error with fnirt
I’m afraid JHU is not exactly in the MNI152 coordinates. I thought it was before, but then I found there were some 1-2 pixels shifts. Later I used JHU-ICBM-FA-1mm.nii.gz in the JHU folder instead.
Wayne
On 12-07-30 12:52 PM, "antonella torok" <[log in to unmask]">[log in to unmask]> wrote:
Dear All,
I understood that JHU atlas is already in the MNI152 coordinates.
Since the alignment in MNI152 is based on linear alignment, the ROI locations may not perfectly define the target structures in my data. I want to do non-linear alignment between JHU atlas and my data.
I was running in the mean time a Fdt registration using Fdt GUI and got all the resulting matrices are stored within the xfms subdirectory of the bedpostX directory and named as follows:
- diff2str.mat - from diffusion to structural space
- str2diff.mat - from structural to diffusion space
- diff2standard.mat - from diffusion to standard space
- standard2diff.mat - from standard to diffusion space
- str2standard.mat - from structural to standard space
- standard2str.mat - from standard to structural space
where standard space is MNI152_T1_1mm.
Can you please advise me how I should use this in order to do a non-linear allignment of the JHU atlas to my individual diffusion data which was registered to MNI
through the structural T1?
I was trying to run:
fnirt --ref=/media/2Tra/Antonella_Backup/Antonella_2011/Probab_Tract/Left/NPI02_dti/data.nii.gz --in=/usr/loca/fsl/JHU_WhiteMatter_labels_1mm.nii.gz --aff=/media/2Tra/Antonella_Backup/Antonella_2011/Probab_Tract/Left/NPI02_dti.bedpostX/xfms/diff2standard.mat --iout=fnirted_JHU2NPI02_dti
Thank you .
Antonella
------------------------------
Antonella Kis, PhD
Research Fellow
Department of Life Sciences
University of Toronto at Scarborough
Phone: 416-208-4869
Fax: 416-287-7642
