Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well).
The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines.
Your help on this matter would be greatly appreciated.
Sal
On Sat, May 25, 2013 at 8:23 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Sal, can you post this to the list instead of me directly? thanks! doug
On 5/25/13 11:00 PM, Salil Soman wrote:
Dear Doug,
I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run.
I had run an FSSPGR for my subject using the following command:
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all
It finished without any problems.
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
(this version was with bold contrast, but I get the same error if I try t1 or t2).
The process fails and I get the following error log (below). Any suggestions on what I am doing wrong?
Thanks,
Sal
---------- Forwarded message ---------- From: Salil Soman salsoman@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu
Logfile for bbregister Sat May 25 19:51:15 PDT 2013
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range.
Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013
fslregister Done
To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig
mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up
Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9
bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf
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.
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files.
Code in question from fslregister script:
# Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF
I think this lack of fsvol being named results in the errors I am getting:
-------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman salsoman@stanford.edu wrote:
Done. Thank you for your consideration. The best I can figure so far is
- the script's attempt to make the tmp.bbregister.7392 directory fails
and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well).
The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines.
Your help on this matter would be greatly appreciated.
Sal
On Sat, May 25, 2013 at 8:23 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Sal, can you post this to the list instead of me directly? thanks! doug
On 5/25/13 11:00 PM, Salil Soman wrote:
Dear Doug,
I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run.
I had run an FSSPGR for my subject using the following command:
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all
It finished without any problems.
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
(this version was with bold contrast, but I get the same error if I try t1 or t2).
The process fails and I get the following error log (below). Any suggestions on what I am doing wrong?
Thanks,
Sal
---------- Forwarded message ---------- From: Salil Soman salsoman@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu
Logfile for bbregister Sat May 25 19:51:15 PDT 2013
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range.
Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013
fslregister Done
To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig
mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up
Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9
bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf
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.
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug
On 5/26/13 12:58 AM, Salil Soman wrote:
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files.
Code in question from fslregister script:
# Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF
I think this lack of fsvol being named results in the errors I am getting:
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu mailto:salsoman@stanford.edu> wrote:
Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote:Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: *Salil Soman* <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu <mailto:salsoman@stanford.edu> Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu <http://corn18.stanford.edu> Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surfThe 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.
Thank you Doug,
fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell).
-Sal
On Mon, May 27, 2013 at 7:16 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug
On 5/26/13 12:58 AM, Salil Soman wrote:
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files.
Code in question from fslregister script:
# Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF
I think this lack of fsvol being named results in the errors I am getting:
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman salsoman@stanford.eduwrote:
Done. Thank you for your consideration. The best I can figure so far is
- the script's attempt to make the tmp.bbregister.7392 directory fails
and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well).
The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines.
Your help on this matter would be greatly appreciated.
Sal
On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Sal, can you post this to the list instead of me directly? thanks! doug
On 5/25/13 11:00 PM, Salil Soman wrote:
Dear Doug,
I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run.
I had run an FSSPGR for my subject using the following command:
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all
It finished without any problems.
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
(this version was with bold contrast, but I get the same error if I try t1 or t2).
The process fails and I get the following error log (below). Any suggestions on what I am doing wrong?
Thanks,
Sal
---------- Forwarded message ---------- From: Salil Soman salsoman@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu
Logfile for bbregister Sat May 25 19:51:15 PDT 2013
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range.
Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013
fslregister Done
To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig
mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up
Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9
bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf
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.
which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 5/27/13 10:32 PM, Salil Soman wrote:
Thank you Doug,
fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell).
-Sal
On Mon, May 27, 2013 at 7:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote:Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF I think this lack of fsvol being named results in the errors I am getting: -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote:Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: *Salil Soman* <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu <mailto:salsoman@stanford.edu> Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu <http://corn18.stanford.edu> Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surfThe 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.
I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again.
Thank you,
Sal
On Mon, May 27, 2013 at 7:43 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 5/27/13 10:32 PM, Salil Soman wrote:
Thank you Doug,
fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell).
-Sal
On Mon, May 27, 2013 at 7:16 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug
On 5/26/13 12:58 AM, Salil Soman wrote:
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files.
Code in question from fslregister script:
# Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF
I think this lack of fsvol being named results in the errors I am getting:
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman salsoman@stanford.eduwrote:
Done. Thank you for your consideration. The best I can figure so far is
- the script's attempt to make the tmp.bbregister.7392 directory fails
and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well).
The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines.
Your help on this matter would be greatly appreciated.
Sal
On Sat, May 25, 2013 at 8:23 PM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Sal, can you post this to the list instead of me directly? thanks! doug
On 5/25/13 11:00 PM, Salil Soman wrote:
Dear Doug,
I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run.
I had run an FSSPGR for my subject using the following command:
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all
It finished without any problems.
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
(this version was with bold contrast, but I get the same error if I try t1 or t2).
The process fails and I get the following error log (below). Any suggestions on what I am doing wrong?
Thanks,
Sal
---------- Forwarded message ---------- From: Salil Soman salsoman@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu
Logfile for bbregister Sat May 25 19:51:15 PDT 2013
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range.
Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013
fslregister Done
To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig
mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up
Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9
bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf
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.
Can you send me your original version of fslregister and bregister?
On 5/27/13 10:53 PM, Salil Soman wrote:
I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again.
Thank you,
Sal
On Mon, May 27, 2013 at 7:43 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/27/13 10:32 PM, Salil Soman wrote:Thank you Doug, fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell). -Sal On Mon, May 27, 2013 at 7:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote:Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF I think this lack of fsvol being named results in the errors I am getting: -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote:Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: *Salil Soman* <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu <mailto:salsoman@stanford.edu> Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu <http://corn18.stanford.edu> Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surfThe 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.
It was attached to my earlier email (included again here). The only chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo "FSVOL $fsvol").
-S
On Mon, May 27, 2013 at 9:14 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Can you send me your original version of fslregister and bregister?
On 5/27/13 10:53 PM, Salil Soman wrote:
I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again.
Thank you,
Sal
On Mon, May 27, 2013 at 7:43 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 5/27/13 10:32 PM, Salil Soman wrote:
Thank you Doug,
fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell).
-Sal
On Mon, May 27, 2013 at 7:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug
On 5/26/13 12:58 AM, Salil Soman wrote:
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files.
Code in question from fslregister script:
# Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF
I think this lack of fsvol being named results in the errors I am getting:
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman salsoman@stanford.eduwrote:
Done. Thank you for your consideration. The best I can figure so far is
- the script's attempt to make the tmp.bbregister.7392 directory fails
and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well).
The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines.
Your help on this matter would be greatly appreciated.
Sal
On Sat, May 25, 2013 at 8:23 PM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Sal, can you post this to the list instead of me directly? thanks! doug
On 5/25/13 11:00 PM, Salil Soman wrote:
Dear Doug,
I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run.
I had run an FSSPGR for my subject using the following command:
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all
It finished without any problems.
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
(this version was with bold contrast, but I get the same error if I try t1 or t2).
The process fails and I get the following error log (below). Any suggestions on what I am doing wrong?
Thanks,
Sal
---------- Forwarded message ---------- From: Salil Soman salsoman@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu
Logfile for bbregister Sat May 25 19:51:15 PDT 2013
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range.
Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013
fslregister Done
To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig
mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up
Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9
bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf
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.
and bbregister?
On 05/28/2013 02:03 AM, Salil Soman wrote:
It was attached to my earlier email (included again here). The only chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo "FSVOL $fsvol").
-S
On Mon, May 27, 2013 at 9:14 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send me your original version of fslregister and bregister? On 5/27/13 10:53 PM, Salil Soman wrote:I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again. Thank you, Sal On Mon, May 27, 2013 at 7:43 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/27/13 10:32 PM, Salil Soman wrote:Thank you Doug, fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell). -Sal On Mon, May 27, 2013 at 7:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote:Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF I think this lack of fsvol being named results in the errors I am getting: -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote:Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: *Salil Soman* <salsoman@stanford.edu <mailto:salsoman@stanford.edu>> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu <mailto:salsoman@stanford.edu> Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu <http://corn18.stanford.edu> Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surfThe 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.
I did not make any changes to bbregister.
Thank you for all your help.
Sal On May 28, 2013 6:57 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
and bbregister?
On 05/28/2013 02:03 AM, Salil Soman wrote:
It was attached to my earlier email (included again here). The only chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo "FSVOL $fsvol").
-S
On Mon, May 27, 2013 at 9:14 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
Can you send me your original version of fslregister and bregister? On 5/27/13 10:53 PM, Salil Soman wrote:I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again. Thank you, Sal On Mon, May 27, 2013 at 7:43 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote:
which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/bbregisterftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug On 5/27/13 10:32 PM, Salil Soman wrote:Thank you Doug, fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell). -Sal On Mon, May 27, 2013 at 7:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>wrote:
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote:Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$**fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/**orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/**rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/**brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF I think this lack of fsvol being named results in the errors I am getting: ------------------------------**-------- /mnt/glusterfs/salsoman/**output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/**output/FS/WMR3T_0015z_FS/mri/**ERROR: ./tmp.bbregister.756/**fslregister/refvol.** fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/**output/FS/WMR3T_0015z_FS/mri/** ERROR: ./tmp.bbregister.756/**fslregister/refvol.** fslregister.nii
mri_convert: extra arguments ("not" and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu <mailto:salsoman@stanford.edu>**> wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote:
Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote:Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: *Salil Soman* <salsoman@stanford.edu <mailto:salsoman@stanford.edu>**> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu <mailto:salsoman@stanford.edu> Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/**output/FS cd /mnt/glusterfs/salsoman/**output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/** freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/**freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/**template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/**template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/** template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/**template.nii --reg ./tmp.bbregister.26724/reg.**init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/**fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.26724/reg.**init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/**template.nii --reg ./tmp.bbregister.26724/reg.**init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/**fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu <http://corn18.stanford.edu> Linux corn18.stanford.edu <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 ------------------------------**-------- /mnt/glusterfs/salsoman/**output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/** output/FS/WMR3T_0015z_FS/mri/**ERROR: ./tmp.bbregister.26724/**fslregister/refvol.** fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/** output/FS/WMR3T_0015z_FS/mri/**ERROR: ./tmp.bbregister.26724/**fslregister/refvol.** fslregister.nii
mri_convert: extra arguments ("not" and following) type mri_convert -u for usage ------------------------------**-------- /mnt/glusterfs/salsoman/**output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/**template.nii ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/**template.nii ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/**template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/** output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii --reg ./tmp.bbregister.26724/** fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.**init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/**freesurfer/tktools/** tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii reg file ./tmp.bbregister.26724/** fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/** output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; ------------------------------**--------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/** output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/**fslregister/refvol.** fslregister.nii -in ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/** fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/** etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.** init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/**fslregister/refvol.** fslregister' ** ERROR: nifti_image_open(./tmp.** bbregister.26724/fslregister/**refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/** fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/** fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/**fslregister/refvol.** fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/** output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/**fslregister/refvol.** fslregister.nii -in ./tmp.bbregister.26724/**fslregister/movvol.** fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.**init.dat.fsl.mat -init ./tmp.bbregister.26724/** fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/**freesurfer/bin/flirt.** newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/**fslregister/refvol.** fslregister' ** ERROR: nifti_image_open(./tmp.** bbregister.26724/fslregister/**refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/** fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/** fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/**fslregister/refvol.** fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/**template.nii --reg ./tmp.bbregister.26724/reg.**init.dat --fslreg ./tmp.bbregister.26724/reg.**init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/**freesurfer/tktools/** tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.**init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.**init.dat: No such file or directory tmp: Subscript out of range.
Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/**template.nii --reg ./tmp.bbregister.26724/reg.**init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/**template.nii --init-reg ./tmp.bbregister.26724/reg.**init.dat --out-reg ./tmp.bbregister.26724/bbr.**pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.**init.dat mri_segreg --mov ./tmp.bbregister.26724/**template.nii --init-reg ./tmp.bbregister.26724/bbr.**pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.**curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.**pass1.dat Cleaning up
Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surfThe 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<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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
I know, but I want to see what version of bbregister you are using On 05/28/2013 10:29 AM, Salil Soman wrote:
I did not make any changes to bbregister.
Thank you for all your help.
Sal
On May 28, 2013 6:57 AM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
and bbregister? On 05/28/2013 02:03 AM, Salil Soman wrote: It was attached to my earlier email (included again here). The only chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo "FSVOL $fsvol"). -S On Mon, May 27, 2013 at 9:14 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Can you send me your original version of fslregister and bregister? On 5/27/13 10:53 PM, Salil Soman wrote: I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again. Thank you, Sal On Mon, May 27, 2013 at 7:43 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/27/13 10:32 PM, Salil Soman wrote: Thank you Doug, fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed "ERROR". Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell). -Sal On Mon, May 27, 2013 at 7:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote: Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd |& tee -a $LF $cmd |& tee -a $LF I think this lack of fsvol being named results in the errors I am getting: -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu <mailto:salsoman@stanford.edu> <mailto:salsoman@stanford.edu <mailto:salsoman@stanford.edu>>> wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote: Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: *Salil Soman* <salsoman@stanford.edu <mailto:salsoman@stanford.edu> <mailto:salsoman@stanford.edu <mailto:salsoman@stanford.edu>>> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman@stanford.edu <mailto:salsoman@stanford.edu> <mailto:salsoman@stanford.edu <mailto:salsoman@stanford.edu>> Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu <http://corn18.stanford.edu> <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu <http://corn18.stanford.edu> <http://corn18.stanford.edu> Linux corn18.stanford.edu <http://corn18.stanford.edu> <http://corn18.stanford.edu> 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.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 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/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 ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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/
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Salil Soman