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, [email protected] 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 >> >> >> 1. 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 >> >> >> 2. 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 >> >> >> 3. 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} >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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