You don’t have to BET FA data, as you should have specified a brain mask when you calculated it. It appears you are using fslmaths instead of cp to copy files, which might not be ideal. I’m not sure why you combine the nodif2highres.mat and the highres2standard warp and then don’t use it in the applywarp command.
Peace,
Matt.
_____
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of xuemei lei
Sent: Thursday, December 02, 2010 7:58 PM
To: [log in to unmask]
Subject: Re: [FSL] register problems from DTI space to MNI space
Hi，experts
I have registered the DTI space to MNI space via b0 and the high resolution 3D. The DTI data are with few slice lack on the top. After registered, the image showed some tines in the place with few top slices lack（the picture are attached in the last email ） .I am a green hand and not sure if these register are acceptable sine the few top slices are lack. Or maybe I made some mistakes in the procedures such as the wrong parameters. And I will use the warpfield to register the MNI space (AAL and HarvardOxford-cort-maxprob atlases) to individual DTI space. I am not sure these are right。
On the other hand, I take the suggestions from Matt and use the FA image instead of b0 image to do the register from DTI to MNI. But I have a puzzle here. The standard MNI reference is the MNI152_T1_1mm_brain.nii.gz or the FMRIB58_FA_1mm.nii.gz. And Do I have to bet the individual FA data? Or I should use the procedures in TBSS.
Finally, I want to register the JHU-ICBM-tracts atlas to individual DTI space and then test each tracts between groups. So I am not sure which warpfield to be used for this register， the MNI152 to individual b0 one, or the FMRIB58_FA to individual FA one.
I know there are so many questions here. Maybe some are so stupid. Any suggestions and helps will be appreciated！ Thanks in advance！
the script that used to register are like the follows:
fslmaths 3d_brain highres
fslmaths ${FSL_DIR}/data/standard/MNI152_T1_2mm_brain standard
fslmaths ${FSL_DIR}/data/standard/MNI152_T1_2mm standard_head
fslmaths 3d highres_head
fslmaths ${FSL_DIR}/data/standard/MNI152_T1_2mm_brain_mask_dil standard_mask
fslmaths ../nodif_brain nodif_brain
fslmaths ../../DTI/nodif nodif
flirt -ref highres -in nodif_brain -out nodif2highres -omat nodif2highres.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
convert_xfm -inverse -omat highres2nodif.mat nodif2highres.mat
flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
fnirt --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2standard_jac --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --warpres=10,10,10
convertwarp -o nodif2standard_warp -r standard -m nodif2highres.mat -w highres2standard_warp
convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
convert_xfm -omat nodif2standard.mat -concat highres2standard.mat nodif2highres.mat
applywarp --ref=standard --in=nodif --out=nodif2standard --warp=highres2standard_warp --premat=nodif2highres.mat
invwarp --ref=nodif_brain --warp=nodif2standard_warp --out=standard2nodif_warp
invwarp --ref=highres --warp=highres2standard_warp --out=standard2highres_warp
convert_xfm -inverse -omat standard2nodif.mat nodif2standard.mat
On Thu, Dec 2, 2010 at 6:27 PM, xuemei lei <[log in to unmask]> wrote:
Hi， this is the picture attached.The DTI data are with few slice lack on the top. After registered, the image showed some tines in the place with few top slices lack.
Xuemei Lei
<http://psychbrain.bnu.edu.cn/> National Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China. 100875
Tel: +86-13269171259
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