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.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> 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


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