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 <[email protected]> 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
> <[email protected]>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 <[email protected]>
>> Date: Sat, May 25, 2013 at 7:54 PM
>> Subject: bbregister fail log
>> To: [email protected]
>>
>>
>> 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
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>>
>
>
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