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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
