Hi Maryam, I'm not sure what is wrong. Can you check the image in bold/018 to make sure that there is not something horribly wrong? Eg, it is not a localizer or only has one slice. And it is only the last run? The others are ok? doug
On 03/22/2013 03:05 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > I am running fsfast preprocessing on my data and I am getting an error > on one of the runs. > > This is the preprocessing code that I run: > > preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder > siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh > > > The error seems to happen during the fsl registration on the last run > (out of 12 runs): > > /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 > flirt.fsl -ref > bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins > 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz > -90 90 -verbose 0 -omat > bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init > bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule > /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch > terminate called after throwing an instance of 'NEWMAT::SingularException' > Abort > ERROR: flirt > > bellow is the register-sess log file. I have only included the section > for the registration of the last run. > > I have looked at the raw data of this run and it does not look > different from the other runs (all other runs are successfully > registered). I am running freesurfer 5.1. Any idea how I can fix the > error? > > Thanks, > Maryam > > > > $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ > Linux ncfws08.rc.fas.harvard.edu <http://ncfws08.rc.fas.harvard.edu> > 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 > x86_64 GNU/Linux > FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ > mri_convert bold/018/template.nii.gz > bold/018/tmp.bbregister.1228/template.nii > mri_convert bold/018/template.nii.gz > bold/018/tmp.bbregister.1228/template.nii > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from bold/018/template.nii.gz... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998239, -0.0522464, 0.0280991) > j_ras = (0.0500393, -0.995986, -0.0742193) > k_ras = (0.031864, -0.0726825, 0.996846) > writing to bold/018/tmp.bbregister.1228/template.nii... > fslregister --s blue_street_kcb --mov > bold/018/tmp.bbregister.1228/template.nii --reg > bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 > --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 > > Log file is bold/018/tmp.bbregister.1228/reg.init.dat.fslregister.log > > Fri Mar 22 14:42:18 EDT 2013 > --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii > --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle > 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 > $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ > ncfws08.rc.fas.harvard.edu <http://ncfws08.rc.fas.harvard.edu> > Linux ncfws08.rc.fas.harvard.edu <http://ncfws08.rc.fas.harvard.edu> > 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 > x86_64 GNU/Linux > nIters 1 > -------------------------------------- > /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 > mri_convert > /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz > bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii > mri_convert > /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz > bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz... > TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 > i_ras = (-1, 4.47035e-08, -4.65661e-08) > j_ras = (-5.58793e-08, -4.05125e-08, -1) > k_ras = (-5.96046e-08, 1, 1.11759e-08) > writing to > bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii... > -------------------------------------- > /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 > mri_convert bold/018/tmp.bbregister.1228/template.nii > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 > mri_convert bold/018/tmp.bbregister.1228/template.nii > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from bold/018/tmp.bbregister.1228/template.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998239, -0.0522464, 0.0280991) > j_ras = (0.0500393, -0.995986, -0.0742193) > k_ras = (0.031864, -0.0726825, 0.996846) > keeping frame 0 > writing to > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii... > Mov determinant is 35.3062 > Swapping dims for pos det > WARNING:: Flipping Left/Right orientation (as det < 0) > tkregister_tcl /ncf/apps/freesurfer-5.1.0//tktools/tkregister2.tcl > target volume > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii > movable volume bold/018/tmp.bbregister.1228/template.nii > reg file bold/018/tmp.bbregister.1228/fslregister/swapreg.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 > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii > 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 bold/018/tmp.bbregister.1228/template.nii > Tmov: -------------------- > -3.086 0.000 0.000 108.000; > 0.000 0.000 3.708 -61.182; > 0.000 -3.086 0.000 108.000; > 0.000 0.000 0.000 1.000; > mkheaderreg = 1, float2int = 0 > Computing reg from header (and possibly input matrix) > ---- Input registration matrix (computed) -------- > 0.998 0.052 -0.028 3.086; > 0.032 -0.073 0.997 -0.000; > -0.050 0.996 0.074 -0.000; > 0.000 0.000 0.000 1.000; > --------------------------------------- > ---- Input registration matrix -------- > 0.998 0.052 -0.028 3.086; > 0.032 -0.073 0.997 -0.000; > -0.050 0.996 0.074 -0.000; > 0.000 0.000 0.000 1.000; > Determinant -1 > subject = subject-unknown > RegMat --------------------------- > -1.000 0.000 0.000 3.086; > 0.000 1.000 0.000 -0.000; > -0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 > tkregister2_cmdl --mov > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --reg > bold/018/tmp.bbregister.1228/fslregister/reg0.1262.dat --regheader > --fslregout bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat0 --s > blue_street_kcb --noedit > tkregister_tcl /ncf/apps/freesurfer-5.1.0//tktools/tkregister2.tcl > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii > reg file bold/018/tmp.bbregister.1228/fslregister/reg0.1262.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 > /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/orig.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 > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii > Tmov: -------------------- > -3.086 0.000 0.000 108.000; > 0.000 0.000 3.708 -61.182; > 0.000 -3.086 0.000 108.000; > 0.000 0.000 0.000 1.000; > mkheaderreg = 1, float2int = 0 > Computing reg from header (and possibly input matrix) > ---- Input registration matrix (computed) -------- > -0.998 -0.052 0.028 3.326; > 0.032 -0.073 0.997 -29.376; > -0.050 0.996 0.074 29.949; > 0.000 0.000 0.000 1.000; > --------------------------------------- > ---- Input registration matrix -------- > -0.998 -0.052 0.028 3.326; > 0.032 -0.073 0.997 -29.376; > -0.050 0.996 0.074 29.949; > 0.000 0.000 0.000 1.000; > Determinant 1 > subject = blue_street_kcb > RegMat --------------------------- > -0.998 -0.052 0.028 3.326; > 0.032 -0.073 0.997 -29.376; > -0.050 0.996 0.074 29.949; > 0.000 0.000 0.000 1.000; > FSLOUTPUTTYPE NIFTI > tkreg2FSL: mov det = -35.3062, ref det = -1 > Fri Mar 22 14:42:22 EDT 2013 > /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 > flirt.fsl -ref > bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins > 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz > -90 90 -verbose 0 -omat > bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule > /ncf/apps/fsl-4.1.7/etc/flirtsch/xyztrans.sch -init > bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat0 > Fri Mar 22 14:42:30 EDT 2013 > /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 > flirt.fsl -ref > bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in > bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins > 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz > -90 90 -verbose 0 -omat > bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init > bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule > /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch > terminate called after throwing an instance of 'NEWMAT::SingularException' > Abort > ERROR: flirt > -- 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: 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.
