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 > <[email protected] <mailto:[email protected]>> 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 >> <[email protected] <mailto:[email protected]>> 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 >>> <[email protected] >>> <mailto:[email protected]>> 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 >>>> <[email protected] <mailto:[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] >>>> <mailto:[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] >>>>> <mailto:[email protected]>> >>>>> Date: Sat, May 25, 2013 at 7:54 PM >>>>> Subject: bbregister fail log >>>>> To: [email protected] >>>>> <mailto:[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 >>>>> <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 [email protected] 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/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
