When you run (without --noedit) do the two volumes look to be in register?
tkregister2 --mov ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.mgz --targ ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.finalsurfs.mgz --s sub_100307_T1 --regheader --reg ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat On 01/09/2015 03:48 AM, LiuKai wrote: > Dear FS expert, > > I got into a trouble when used the command of mri_vol2surf. I planned > to project a volume file (merged_diff2fs.nii.gz) onto the surface(lh) > of the same subject. While i got nothing (value=0 for nearly all the > vertexes except for a few valued vertexes on the medial surface, see > attached fig1.jpg). However, i tried to project this volume (with > value in lh) file onto the surface of rh, some vertexes were valued, > but the dimension seems wrong (see attached fig2.jpg). > > I guess there may be something wrong with the coordinate system of > this volume file. This volume file was initially generated from the > command of mri_surf2vol as a mask (which can be projected to the > surface correctly), and i assigned some values to this mask volume > then generated this problematic volume file (as attached). So where is > the problem? > > Thank you so much for any help!!! > > > > --------------------------------------------------------------------- > > FREESURFER_HOME: /home/fsl/Program/freesurfer > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > RedHat release: CentOS release 6.3 (Final) > > Kernel info: Linux 2.6.32-279.5.2.el6.x86_64 x86_64 > > --------------------------------------------------------------------- > > 1)subject name: fs_HCP_40unrelated > > 2)the entire command line: > FREESURFER_HOME='/home/fsl/Program/freesurfer' > export FREESURFER_HOME > source $FREESURFER_HOME/SetUpFreeSurfer.sh > SUBJECTS_DIR='/home/fsl/Desktop/SCD/fs_HCP_40unrelated' > > cd '/home/fsl/Desktop/SCD' > > mri_convert --in_type nii --out_type mgz --input_volume > '/home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.nii.gz' > > '/home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz' > > tkregister2 --mov ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.mgz > --targ ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.finalsurfs.mgz > --noedit --s sub_100307_T1 --regheader --reg > ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat > > mri_vol2surf --src > ./fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz --srcreg > ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat --hemi lh > --out ./fs_HCP_40unrelated/sub_100307_T1/lh.merged_vol2surf.mgh > --cortex --noreshape > > mri_vol2surf --src > ./fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz --srcreg > ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat --hemi rh > --out ./fs_HCP_40unrelated/sub_100307_T1/rh.merged_vol2surf.mgh > --cortex --noreshape > > 3)the error message: (actually no error reported, but the results were > not corrected as shown in tksurfer, as attached figures, the full > script as following listed) > mri_convert --in_type nii --out_type mgz --input_volume > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.nii.gz > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz... > tkregister_tcl /home/fsl/Program/freesurfer/tktools/tkregister2.tcl > target volume ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.finalsurfs.mgz > movable volume ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.mgz > reg file ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat > LoadVol 0 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > Diagnostic Level -1 > INFO: loading target > ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.finalsurfs.mgz > 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 ./fs_HCP_40unrelated/sub_100307_T1/mri/brain.mgz > Tmov: -------------------- > -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; > mkheaderreg = 1, float2int = 0 > Computing reg from header (and possibly input matrix) > ---- Input registration matrix (computed) -------- > 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; > --------------------------------------- > ---- 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; > Determinant 1 > subject = sub_100307_T1 > 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; > srcvol = ./fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz > srcreg = ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > Done loading volume > Loading label > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/lh.cortex.label > Reading surface > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/surf/lh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 79833 > Masking with > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/lh.cortex.label > Writing to ./fs_HCP_40unrelated/sub_100307_T1/lh.merged_vol2surf.mgh > Dim: 128476 1 1 > srcvol = ./fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz > srcreg = ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = rh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > Done loading volume > Loading label > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/rh.cortex.label > Reading surface > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/surf/rh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 79447 > Masking with > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/rh.cortex.label > Writing to ./fs_HCP_40unrelated/sub_100307_T1/rh.merged_vol2surf.mgh > Dim: 126700 1 1 > > 4)recon-all.log: not attached > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu 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.
