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 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 Linux 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