Hello,
I am trying to create the linear and non-linear transformations for the diffusion data to standard space (MNI152_T1_1mm) using structural anatomic data. I used the Registration tab to get these transformations.
I see that the following log when i do that (pasted below). Why is it that T1_2_MNI152_2mm configuration file being used for fnirt (anatomical to standard) and convertwarp (diff2standard_warp) uses MNI152_T1_2mm reference, even though i chose MNI152_T1_1mm standard space for registration. Wouldnt it go wrong when the fibers are binned in 1mm standard space(using seeds in 1mm standard space) and the transformations that are used, are from 2mm standard space?
coordinate space Aligned Anatomical
Regards
Jay
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/user/local/jay/fsl/bin/flirt -in /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/nodif_brain -ref /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/anat_${name}.nii.gz -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6 -cost corratio -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str
/user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2diff.mat -inverse /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat
/user/local/jay/fsl/bin/flirt -in /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/anat_${name}.nii.gz -ref /user/local/jay/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -cost corratio -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard
/user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2str.mat -inverse /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat
/user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2standard.mat -concat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat
/user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2diff.mat -inverse /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2standard.mat
/user/local/jay/fsl/bin/fnirt --in=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/anat_${name}_struc_cut.nii.gz --aff=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat --cout=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_warp --config=T1_2_MNI152_2mm --iout=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_fnirt
/user/local/jay/fsl/bin/invwarp -w /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_warp -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2str_warp -r /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/nodif_brain_mask
/user/local/jay/fsl/bin/convertwarp -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2standard_warp -r /user/local/jay/fsl/data/standard/MNI152_T1_2mm -m /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat -w /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_warp
/user/local/jay/fsl/bin/convertwarp -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2diff_warp -r /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/nodif_brain_mask -w /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2str_warp --postmat=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2diff.mat
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