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Hi Wayne,

Many thanks for your help. I still have few questions after your reply:

1) Do you know what exactly is the name of Mori's  ROIs atlas?  Dr. Mori told me the ROIs atlas is in MNI coordinates and based on your reply I am not sure what to use.
2) If for example the atlas is in the MNI coordinates I still need to do an alignment to my data since the ROI locations may not perfectly define the target structures in my data.
Should I align this ROIs atlas using fnirt to my individual DTI data  before BET but after eddy corrections since based on the FSL instructions FNIRT is more sensitive to errors in brain extraction so  we should not use the BET output?
3) I should align maybe the ROIs to my data after is registered on the MNI?
How I can do this using the FNIRT command?

Many thanks.
Antonella
------------------------------
Antonella Kis, PhD
Research Fellow
Department of Life Sciences
University of Toronto at Scarborough
Phone: 416-208-4869
Fax:   416-287-7642


Date: Mon, 30 Jul 2012 15:18:08 -0700
From: [log in to unmask]
Subject: Re: [FSL] Error with fnirt
To: [log in to unmask]

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]> 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