I did not make any changes to bbregister.
Thank you for all your help.
Sal
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 --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
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/