Re: [Freesurfer] BBR Register failing

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

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