25 Mar
2013
25 Mar
'13
5:02 p.m.
I ran it in 5.2, and it works, but it does crash with the same error using 5.1. I have an explanation for what is happening, but it is not very satisfying:). There is a part of the FSL code that is inverting a matrix. If the matrix does not have certain properties, then it cannot be inverted. FreeSurfer creates the matrix that FSL is trying to invert. This matrix is very slightly different in 5.1 vs 5.2 (by slight, I mean one of the values is 239.199 instead of 239.198). This appears to be enough to push the matrix over the edge and make it non-invertible. I'm not sure what to tell you to do. For this subject, you can use -init-spm instead.
doug
On 03/25/2013 03:12 PM, Maryam Vaziri Pashkam wrote:
I have trouble uploading files on the freesurfer page. I have put the files here:
http://www.wjh.harvard.edu/~mvaziri/preproctest.tar http://www.wjh.harvard.edu/%7Emvaziri/preproctest.tar
I was initially running the analysis on harvard ncf network on one of the workstations. The fsl version there is fsl-4.1.7 and the freesurfer version is freesurfer 5.1. I ran the preprocessing on this run separately and got the same error. However when I transferred the files to my macintosh computer (iMAC) and ran the analysis on my computer which has the same version of freesurfer I did not get any errors and the preprocessing completed successfully. This is very puzzling as it seems to be specific to the harvard network. Any idea where the problem might be?
Maryam
On Mon, Mar 25, 2013 at 12:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 <greve@nmr.mgh.harvard.edu <mailto:greve@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> <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> <http://ncfws08.rc.fas.harvard.edu> Linux ncfws08.rc.fas.harvard.edu <http://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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/