Can you tar up the subject and the last run and drop it to me on our file drop system? doug
On 03/25/2013 12:07 PM, Maryam wrote: > The raw images of the last run seems fine. And it is only the last run out of > 12. > > M > > On Mar 25, 2013, at 10:36 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> 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/ >> >> >> >> 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. >> > -- 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
