I have trouble uploading files on the freesurfer page. I have put the files here:

http://www.wjh.harvard.edu/~mvaziri/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> 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> 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
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/

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
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/