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Hi Mark, It seems that the transformation is making very little difference to the positions of the ROI. If you overlay both the transformed and untransformed ROI, they are pretty much identical. Also if I overlay the ROI onto the subject's brain, it is not within the brain, let alone on the anatomical areas I am looking for. Here are the exact commands I am using (within the GUI): I initially register the BET subject's structural to the MNI brain, with 12 parameter model. /usr/local/fsl/bin/flirt -in /kki/g1/jgalea1/eike_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out /kki/g1/jgalea1/eike_brain_reg.nii.gz -omat /kki/g1/jgalea1/eike_brain_reg.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear Then invert the transform /usr/local/fsl/bin/convert_xfm -omat /kki/g1/jgalea1/eike_brain_reg_inv.mat -inverse /kki/g1/jgalea1/eike_brain_reg.mat Apply inverted transform onto my ROI (ppc, this was created using the MNI brain), using the subjects head (with skull) as my reference volume /usr/local/fsl/bin/flirt -in /kki/g1/jgalea1/PPC.nii -applyxfm -init /kki/g1/jgalea1/eike_brain_reg_inv.mat -out /kki/g1/jgalea1/eike_PPC.nii -paddingsize 0.0 -interp trilinear -ref /kki/g1/jgalea1/eike_head.nii.gz thanks for any help you may be able to give me, Joe >>> Mark Jenkinson <[log in to unmask]> 03/01/09 3:43 AM >>> Hi, All of these sound fine in principle. I cannot help without more information. What is going wrong? How are you assessing the results? What are the exact commands that you are using? All the best, Mark On 28 Feb 2009, at 20:42, Joe Galea wrote: > On the basis of previous studies I have created 4 regions of > interest using > the MNI brain151_T1_2mm. I want to TMS these areas and so am > attempting to > transform these positions so that they are relative to each individual > subject's high-res structural scan (with skull). For these subjects > I only > have a high-res structural. > > I have attempted several things: > > 1) Use FLIRT to register the MNI brain to the structural brain (with > skull). > Apply this transform to the ROI (with FLIRT transform) > 2) Use FLIRT to register the MNI brain to the structural brain > (without > skull). Apply this transform to the ROI, using the subject's > structural with > skull as the reference volume. > 3) Use FLIRT to register the structural (without skull) to the MNI. > Invert > this transform, and apply this to the ROI, using the structural with > skull > as the reference volume. > 4) Use FLIRT to register the structural (with skull) to the MNI. > Invert this > transform, and apply this to the ROI, using the structural with > skull as the > reference volume. > > None of these seem to make any difference to the position of my > ROIs, and > get me nowhere near the anatomical positions I'm looking for (within > the > parietal cortex). > > Any help would be much appreciated. > > Joe >