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> 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:
-SalThank 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).
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:
-SalAny suggestions would be a huge help.I think this lack of fsvol being named results in the errors I am getting:Dear Freesurfer experts,
Code in question from fslregister script:
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.
# 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
--------------------------------------
/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)
On Sat, May 25, 2013 at 8:35 PM, Salil Soman <salsoman@stanford.edu> wrote:
and 2) (after I manually make this directory),Done. Thank you for your consideration. The best I can figure so far is1) the script's attempt to make the tmp.bbregister.7392 directory fails
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:
The process fails and I get the following error log (below). Any suggestions on what I am doing wrong?(this version was with bold contrast, but I get the same error if I try t1 or t2).It finished without any problems.I had run an FSSPGR for my subject using the following command: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.
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
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
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