Thank you Doug, that seems to solve the issue!
Try this instead
mri_vol2vol --inv --targ M4_LH_orig.mgz --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
On 07/14/2014 02:07 PM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer,
I am attempting to take label files generated in fsaverage surface space and transform them into MNI152 volume space.
Using the commands below, I am able to view the final output image with fslview in the the same space as the MNI brain. However, the registration is very off. Additionally, tkregister2 also displays the image in the same incorrect location.
Any help identifying what may be going wrong with the registration/the transformation matrix would be greatly appreciated!
Thank you for the help and or suggestions, Jacob
- mri_label2vol --label M4_LH.label --subject fsaverage --temp
/autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/fsaverage/mri/orig.mgz --o M4_LH_orig.mgz --identity
Terminal output: orig.mgz --identity INFO: subject not needed, igorning. Number of labels: 1 M4_LH.label Annot File: (null) Template Volume: /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/fsaverage/mri/orig.mgz Outut Volume: M4_LH_orig.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; nlabels = 1 Allocating Hit Volume (16777216) voxels Loading M4_LH.label
PVF (null) Thesholding hit volume. mri_label2vol done
- mri_vol2vol --mov M4_LH_orig.mgz --targ
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
Terminal output: Matrix from regfile: 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000;
movvol M4_LH_orig.mgz targvol /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz outvol M4_LH_orig_MNI152.nii.gz regfile /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1406309355
Final tkRAS-to-tkRAS Matrix is: 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000;
Vox2Vox Matrix is: 1.995 0.035 0.015 33.682; -0.029 0.005 2.002 56.525; 0.026 -1.994 -0.019 218.527; 0.000 0.000 0.000 1.000;
Resampling Output registration matrix is identity INFO: writing registration to M4_LH_orig_MNI152.nii.gz.lta transformed matrix: 1.000 -0.000 -0.000 -1.000; -0.000 -0.000 -1.000 -17.000; -0.000 1.000 -0.000 19.000; 0.000 0.000 0.000 1.000; transformed matrix: 0.500 0.000 0.000 -18.500; 0.000 0.500 0.000 -9.500; 0.000 0.000 0.500 -18.500; 0.000 0.000 0.000 1.000; INFO: writing registration matrix to M4_LH_orig_MNI152.nii.gz.reg To check registration, run:
tkregister2 --mov M4_LH_orig_MNI152.nii.gz --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg M4_LH_orig_MNI152.nii.gz.reg
mri_vol2vol done
- tkregister2 --mov M4_LH_orig_MNI152.nii.gz --targ
/usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg M4_LH_orig_MNI152.nii.gz.reg
Terminal output: tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl target volume /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz movable volume M4_LH_orig_MNI152.nii.gz reg file M4_LH_orig_MNI152.nii.gz.reg LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; float2int = 0
INFO: loading target /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable M4_LH_orig_MNI152.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = fsaverage Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window fsaverage Opening fsaverage, xnum = 256, xdim = 512 Setting scale tkregister2: interface: /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
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