Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

RE: [Freesurfer] reg-feat2anat failed
by Wang, Xin 13 Jan '09

13 Jan '09

Hello, Freesurfer group, I registered the example_func.nii.gz to brain.mgz in tkregister2 using FS/anat2exf.register.dat, and --fslregout fsl.feat/reg/example_func2highres.mat. I have a couple of questions. 1) could anybody confirm that using--fslregout does apply .mat file for registration based on the following information on the screen? surfname set to orig target volume PT01/mri/brain.mgz movable volume Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz reg file Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.995 -0.028 0.093 4.032; -0.091 0.069 0.994 1.194; -0.035 -0.997 0.066 0.264; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target PT01/mri/brain.mgz INFO: changing target type to float 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 Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 3.000 -60.000; 0.000 -3.438 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.995 -0.028 0.093 4.032; -0.091 0.069 0.994 1.194; -0.035 -0.997 0.066 0.264; 0.000 0.000 0.000 1.000; subject = PT01 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window PT01 NVIDIA: could not open the device file /dev/nvidiactl (Permission denied). NVIDIA: Direct rendering failed; attempting indirect rendering. Setting scale Tagging mov volume tkregister2: interface: /net/dysthymia/freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} % 2) The results are quite the same (and good) in the tkregister2 with a slightly difference as shown below. Could anyone please tell me what these numbers mean? with .bat file Screen: 256 257 (113,113,113), inorm = 1, mov_frame = 0 Anat: (128 126 127) ( 0.0 -1.0 2.0) 25.0000 32.7 Func: ( 31 32 21) ( 4.2 3.1 1.4) 756.0000 112.5 with .mat file Screen: 257 257 (175,175,175), inorm = 1, mov_frame = 0 Anat: (128 126 127) ( 0.0 -1.0 2.0) 25.0000 28.3 Func: ( 31 32 21) ( 4.2 3.1 1.4) 756.0000 106.2 Thanks, Xin -----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/12/2009 4:02 PM To: Wang, Xin Cc: analysis-bugs(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg-feat2anat failed reg-feat2anat calls fslregister, so they should produce the same result. There is no need for an "intermediate" volume since you are registering from the subject's EPI to the subject's structure. Does the registration not look good? Wang, Xin wrote: > Thank you, Dr. Greve. It seems work ok. what is the difference between > reg-feat2anat and fslregister? although both commands are working for > me, I don't think either of them serve my propose. Freesurfer does not > use initial_highres to improve the reg of example_func to highres, but > FSL/FEAT uses this inter-mediate step. I try to use registration.mat > files of FSL/FEAT step-wise registrations to improve the > reg. I think flag --fsl allow me to use a fsl.mat file as reg > file. How to make it work in the way I need? > > Thank you again, > > Xin > > ------------------------------------------------------------------------ > *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > *Sent:* Mon 1/12/2009 3:29 PM > *To:* Wang, Xin > *Cc:* analysis-bugs(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] reg-feat2anat failed > > when you say everything looked ok, do you mean that the orientation was > correct? If so, try running this: > > fslregister --s subject --mov example_func.nii.gz --reg newreg.dat > > then > > tkregister2 --mov example_func.nii.gz --reg newreg.dat --surfs > > > > > Wang, Xin wrote: > > Sorry, Dr. Greve. I copied addtional parts after I killed the > > tkmedit. The following is on the screen when I saw the image. > > > > []$ tkmedit -f > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > Reading /net/dysthymia/freesurfer/lib/tcl/tkm_common.tcl > > Reading /net/dysthymia/freesurfer/lib/tcl/tkm_wrappers.tcl > > Reading /net/dysthymia/freesurfer/lib/tcl/fsgdfPlot.tcl > > Reading /net/dysthymia/freesurfer/lib/tcl/tkUtils.tcl > > % > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > > *Sent:* Mon 1/12/2009 3:10 PM > > *To:* Wang, Xin > > *Cc:* analysis-bugs(a)nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] reg-feat2anat failed > > > > I don't understand. If it segfaulted how did you look at the images? > > > > > > Wang, Xin wrote: > > > Thank you, Dr. Greve. > > > This time tkmedit read the image, and the image looks ok to me. But > > > following information appeared. > > > > > > []$ tkmedit -f > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > Reading /net/dysthymia/freesurfer/lib/tcl/tkm_common.tcl > > > Reading /net/dysthymia/freesurfer/lib/tcl/tkm_wrappers.tcl > > > Reading /net/dysthymia/freesurfer/lib/tcl/fsgdfPlot.tcl > > > Reading /net/dysthymia/freesurfer/lib/tcl/tkUtils.tcl > > > % Killed > > > > > > =================================== > > > ERROR: A segfault has occurred. This is not your fault, > > > : but is most likely an unrecoverable error and has > > > : made the program unstable. > > > : > > > : Please send the contents of the file .xdebug_tkmedit > > > : that should be in this directory to > > > analysis-bugs(a)nmr.mgh.harvard.edu > > > <mailto:analysis-bugs@nmr.mgh.harvard.edu> > > > : > > > : Now exiting... > > > : > > > []$ cat .xdebug_tkmedit > > > tkmedit started: Mon Jan 12 15:14:52 2009 > > > tkmedit.bin -f > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > $Id: tkmedit.c,v 1.320.2.5 2008/03/10 14:02:35 nicks Exp $ $Name: > > > stable4 $ > > > Set user home dir to /net/data4/CCMB08/PTSD/Thickness > > > Set subject home dir to > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > Using interface file /net/dysthymia/freesurfer/lib/tcl/tkmedit.tcl > > > Tcl: Successfully parsed tkmedit.tcl > > > Tcl: Successfully parsed tkm_functional.tcl > > > Segfault > > > Entering main loop > > > xDebug stack (length: 2) > > > 01: main() > > > 01: Entering main loop > > > 00: > > > 00: > > > > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > > > *Sent:* Mon 1/12/2009 2:55 PM > > > *To:* Wang, Xin > > > *Cc:* analysis-bugs(a)nmr.mgh.harvard.edu > > > *Subject:* Re: [Freesurfer] reg-feat2anat failed > > > > > > what is your tkmedit cmd? > > > > > > It should be > > > > > > tkmedit -f example_func.nii.gz > > > > > > Wang, Xin wrote: > > > > Hello, Dr. Greve, > > > > tkmedit can not open the example_func.nii.gzI attached the header of > > > > example_func.nii.gz (after mri_convert), and the contents of > > > > .xdebug_tkmedit file > > > > > > > > []$ fslhd > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > filename > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > sizeof_hdr 348 > > > > data_type FLOAT32 > > > > dim0 3 > > > > dim1 64 > > > > dim2 64 > > > > dim3 40 > > > > dim4 1 > > > > dim5 1 > > > > dim6 1 > > > > dim7 1 > > > > vox_units mm > > > > time_units s > > > > datatype 16 > > > > nbyper 4 > > > > bitpix 32 > > > > pixdim0 0.0000000000 > > > > pixdim1 3.4375000000 > > > > pixdim2 3.4375000000 > > > > pixdim3 3.0000000000 > > > > pixdim4 1.0000000000 > > > > pixdim5 1.0000000000 > > > > pixdim6 1.0000000000 > > > > pixdim7 1.0000000000 > > > > vox_offset 352 > > > > cal_max 0.0000 > > > > cal_min 0.0000 > > > > scl_slope 0.000000 > > > > scl_inter 0.000000 > > > > phase_dim 0 > > > > freq_dim 0 > > > > slice_dim 0 > > > > slice_name Unknown > > > > slice_code 0 > > > > slice_start 0 > > > > slice_end 0 > > > > slice_duration 0.000000 > > > > time_offset 0.000000 > > > > intent Unknown > > > > intent_code 0 > > > > intent_name > > > > intent_p1 0.000000 > > > > intent_p2 0.000000 > > > > intent_p3 0.000000 > > > > qform_name Scanner Anat > > > > qform_code 1 > > > > qto_xyz:1 -3.437500 0.000000 -0.000000 220.000000 > > > > qto_xyz:2 0.000000 3.437500 -0.000000 0.000000 > > > > qto_xyz:3 0.000000 0.000000 3.000000 0.000000 > > > > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > > > > qform_xorient Right-to-Left > > > > qform_yorient Posterior-to-Anterior > > > > qform_zorient Inferior-to-Superior > > > > sform_name Scanner Anat > > > > sform_code 1 > > > > sto_xyz:1 -3.437500 0.000000 0.000000 220.000000 > > > > sto_xyz:2 0.000000 3.437500 0.000000 0.000000 > > > > sto_xyz:3 0.000000 0.000000 3.000000 0.000000 > > > > sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > > > > sform_xorient Right-to-Left > > > > sform_yorient Posterior-to-Anterior > > > > sform_zorient Inferior-to-Superior > > > > file_type NIFTI-1+ > > > > file_code 1 > > > > descrip FreeSurfer Jun 14 2008 > > > > aux_file > > > > .xdebug_tkmedit > > > > tkmedit started: Mon Jan 12 15:05:46 2009 > > > > tkmedit.bin > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > $Id: tkmedit.c,v 1.320.2.5 2008/03/10 14:02:35 nicks Exp $ $Name: > > > > stable4 $ > > > > Set user home dir to /net/data4/CCMB08/PTSD/Thickness > > > > ERROR: Parsing arguments > > > > Subject and image not declared > > > > Fatal error in parsing command line args. > > > > Segfault > > > > Copying argv[1] > > > > xDebug stack (length: 3) > > > > 02: ParseCmdLineArgs( argc=2, argv=tkmedit.bin ) > > > > 02: Copying argv[1] > > > > 01: main() > > > > 01: Parsing command line arguments > > > > 00: > > > > 00: > > > > > > > > > > ------------------------------------------------------------------------ > > > > *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > > > > *Sent:* Mon 1/12/2009 2:38 PM > > > > *To:* Wang, Xin > > > > *Cc:* analysis-bugs(a)nmr.mgh.harvard.edu > > > > *Subject:* Re: [Freesurfer] reg-feat2anat failed > > > > > > > > > > > > If the orientation of the example func in tkmedit is wrong, then the > > > > reg-feat2anat is destined to fail. tkmedit (usually) reads the nifti > > > > header correctly. How do you know the header is right? > > > > > > > > > > > > Wang, Xin wrote: > > > > > > > > > > My problem about tkregister2 is that the flag -fsl > > > > > example_func2highres.mat does not work properly. The tkregister2 > > > > > catastrophically failed to register two brains. > > > > > I submit the bugreport of tkregister2 (please see the COMMAND > > 3). The > > > > > two early steps (mri_convert and reg-feat2anat) are included for > > your > > > > > references. > > > > > > > > > > Thanks, > > > > > > > > > > Xin > > > > > > > > > > > > --------------------------------------------------------------------- > > > > > > > > > > FREESURFER_HOME: /net/dysthymia/freesurfer > > > > > > > > > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 > > > > > > > > > > RedHat release: Red Hat Enterprise Linux Client release 5.2 > > (Tikanga) > > > > > > > > > > Kernel info: Linux 2.6.18-92.1.1.el5 x86_64 > > > > > > > > > > > > --------------------------------------------------------------------- > > > > > Subject name: PT01 > > > > > > > > > > COMMAND 1: > > > > > []$ mri_convert > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > mri_convert > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > > > > > reading from > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz... > > > > > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > i_ras = (-1, 0, 0) > > > > > j_ras = (0, 1, 0) > > > > > k_ras = (0, 0, 1) > > > > > writing to > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz... > > > > > > > > > > COMMAND 2: > > > > > []$ reg-feat2anat --feat > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat > > > > > --subject PT01 > > > > > FeatDir is Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat > > > > > template volume is > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > log file is > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/reg-feat2anat.log > > > > > Mon Jan 12 14:08:56 CST 2009 > > > > > /net/data4/CCMB08/PTSD/Thickness > > > > > /net/dysthymia/freesurfer/bin/reg-feat2anat > > > > > --feat Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat --subject PT01 > > > > > Linux schizo.psych.med.umich.edu 2.6.18-92.1.1.el5 #1 SMP Thu > May 22 > > > > > 09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux > > > > > example_func ras_good_flag 1 > > > > > ------------------------------------------------------- > > > > > Initializing exf2anat with header > > > > > tkregister2_cmdl --targ > > > > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz --mov > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat.init > > > > > --fslregout > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.init.fsl.mat > > > > > --regheader --noedit > > > > > target volume > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz > > > > > movable volume > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > reg file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat.init > > > > > LoadVol 0 > > > > > ZeroCRAS 0 > > > > > $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ > > > > > Diagnostic Level -1 > > > > > INFO: loading target > > > > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.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 > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > Tmov: -------------------- > > > > > -3.438 0.000 0.000 110.000; > > > > > 0.000 0.000 3.000 -60.000; > > > > > 0.000 -3.438 0.000 110.000; > > > > > 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 -110.507; > > > > > 0.000 0.000 1.000 -41.354; > > > > > 0.000 -1.000 0.000 93.531; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > ---- Input registration matrix -------- > > > > > 1.000 0.000 0.000 -110.507; > > > > > 0.000 0.000 1.000 -41.354; > > > > > 0.000 -1.000 0.000 93.531; > > > > > 0.000 0.000 0.000 1.000; > > > > > subject = subject-unknown > > > > > RegMat --------------------------- > > > > > 1.000 0.000 0.000 -110.507; > > > > > 0.000 0.000 1.000 -41.354; > > > > > 0.000 -1.000 0.000 93.531; > > > > > 0.000 0.000 0.000 1.000; > > > > > register: file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat.init > > > > > written > > > > > FSLOUTPUTTYPE NIFTI_GZ > > > > > tkreg2FSL: mov det = -35.4492, ref det = -1 > > > > > fslregister --s PT01 --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > --mov > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > --dof 6 --bins 256 --cost corratio --fslmat > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > --fsvol brainmask --maxangle 90 --initfslmat > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.init.fsl.mat > > > > > --tmp > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp > > > > > --out > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz > > > > > > > > > > Log file is > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat.fslregister.log > > > > > > > > > > Mon Jan 12 14:08:56 CST 2009 > > > > > --s PT01 --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > --mov > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > --dof 6 --bins 256 --cost corratio --fslmat > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > --fsvol brainmask --maxangle 90 --initfslmat > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.init.fsl.mat > > > > > --tmp > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp > > > > > --out > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz > > > > > $Id: fslregister,v 1.16 2007/07/26 16:52:54 greve Exp $ > > > > > schizo.psych.med.umich.edu > > > > > Linux schizo.psych.med.umich.edu 2.6.18-92.1.1.el5 #1 SMP Thu > May 22 > > > > > 09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux > > > > > -------------------------------------- > > > > > /net/data4/CCMB08/PTSD/Thickness > > > > > mri_convert > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/refvol.fslregister.nii > > > > > mri_convert > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/refvol.fslregister.nii > > > > > $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > > > > > reading from > > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz... > > > > > TR=12.27, TE=5.21, TI=650.00, flip angle=9.00 > > > > > i_ras = (-1, 0, 0) > > > > > j_ras = (0, 0, -1) > > > > > k_ras = (0, 1, 0) > > > > > writing to > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/refvol.fslregister.nii... > > > > > -------------------------------------- > > > > > /net/data4/CCMB08/PTSD/Thickness > > > > > mri_convert > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/movvol.fslregister.nii > > > > > --frame 0 > > > > > mri_convert > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/movvol.fslregister.nii > > > > > --frame 0 > > > > > $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > > > > > reading from > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz... > > > > > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > i_ras = (-1, 0, 0) > > > > > j_ras = (0, 1, 0) > > > > > k_ras = (0, 0, 1) > > > > > keeping frame 0 > > > > > writing to > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/movvol.fslregister.nii... > > > > > Mon Jan 12 14:09:00 CST 2009 > > > > > /net/data4/CCMB08/PTSD/Thickness > > > > > bet > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/movvol.fslregister.nii > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/movvol.fslregister.nii > > > > > -f 0.1 > > > > > Mon Jan 12 14:09:04 CST 2009 > > > > > /net/data4/CCMB08/PTSD/Thickness > > > > > flirt -ref > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/refvol.fslregister.nii > > > > > -in > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/movvol.fslregister.nii > > > > > -omat > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 > > -searchrz -90 > > > > > 90 -init > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.init.fsl.mat > > > > > -o > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/outvol.fslregister.nii > > > > > Mon Jan 12 14:09:20 CST 2009 > > > > > /net/data4/CCMB08/PTSD/Thickness > > > > > mri_convert > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/outvol.fslregister.nii > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz > > > > > mri_convert > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/outvol.fslregister.nii > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz > > > > > $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > > > > > reading from > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/outvol.fslregister.nii... > > > > > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > i_ras = (-1, 0, 0) > > > > > j_ras = (0, 0, -1) > > > > > k_ras = (0, 1, 0) > > > > > writing to > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz... > > > > > tkregister2_cmdl --s PT01 --mov > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > --fslreg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > --noedit > > > > > ---- FSL registration matrix -------- > > > > > 0.995 -0.035 0.091 20.763; > > > > > 0.093 0.066 -0.994 171.738; > > > > > 0.028 0.997 0.069 11.368; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > > > > target volume orig > > > > > movable volume > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > reg file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > LoadVol 0 > > > > > ZeroCRAS 0 > > > > > $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ > > > > > Diagnostic Level -1 > > > > > INFO: loading target > > > /net/data4/CCMB08/PTSD/Thickness/PT01/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 > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > Tmov: -------------------- > > > > > -3.438 0.000 0.000 110.000; > > > > > 0.000 0.000 3.000 -60.000; > > > > > 0.000 -3.438 0.000 110.000; > > > > > 0.000 0.000 0.000 1.000; > > > > > mkheaderreg = 0, float2int = 0 > > > > > FSLOUTPUTTYPE NIFTI > > > > > fsl2TkReg: mov det = -35.4492, ref det = -1 > > > > > ---- Input registration matrix (computed) -------- > > > > > 0.995 -0.028 0.093 4.032; > > > > > -0.091 0.069 0.994 1.194; > > > > > -0.035 -0.997 0.066 0.264; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > ---- Input registration matrix -------- > > > > > 0.995 -0.028 0.093 4.032; > > > > > -0.091 0.069 0.994 1.194; > > > > > -0.035 -0.997 0.066 0.264; > > > > > 0.000 0.000 0.000 1.000; > > > > > subject = PT01 > > > > > RegMat --------------------------- > > > > > 0.995 -0.028 0.093 4.032; > > > > > -0.091 0.069 0.994 1.194; > > > > > -0.035 -0.997 0.066 0.264; > > > > > 0.000 0.000 0.000 1.000; > > > > > register: file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > written > > > > > (standard_in) 1: illegal character: P > > > > > (standard_in) 1: illegal character: T > > > > > > > > > > Started at Mon Jan 12 14:08:57 CST 2009 > > > > > Ended at Mon Jan 12 14:09:24 CST 2009 > > > > > > > > > > fslregister Done > > > > > > > > > > To check results, run: > > > > > tkregister2 --mov > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > --surf orig > > > > > > > > > > tkregister2_cmdl --targ > > > > > /net/misc/fsl/etc/standard/avg152T1_brain.nii.gz --mov > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > --fslreg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/example_func2standard.mat > > > > > --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/std2exf.register.dat > > > > > --noedit > > > > > ---- FSL registration matrix -------- > > > > > 1.122 0.029 0.006 -34.123; > > > > > -0.061 1.041 0.128 -3.403; > > > > > -0.010 -0.119 1.224 25.844; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > target volume /net/misc/fsl/etc/standard/avg152T1_brain.nii.gz > > > > > movable volume > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > reg file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/std2exf.register.dat > > > > > LoadVol 0 > > > > > ZeroCRAS 0 > > > > > $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ > > > > > Diagnostic Level -1 > > > > > INFO: loading target > > /net/misc/fsl/etc/standard/avg152T1_brain.nii.gz > > > > > INFO: target does not conform to COR format, so I'm going to > > > > > reslice to COR. This will not affect the final registration. > > > > > 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 > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > Tmov: -------------------- > > > > > -3.438 0.000 0.000 110.000; > > > > > 0.000 0.000 3.000 -60.000; > > > > > 0.000 -3.438 0.000 110.000; > > > > > 0.000 0.000 0.000 1.000; > > > > > mkheaderreg = 0, float2int = 0 > > > > > FSLOUTPUTTYPE NIFTI_GZ > > > > > fsl2TkReg: mov det = -35.4492, ref det = -8 > > > > > ---- Input registration matrix (computed) -------- > > > > > 0.890 0.025 0.002 1.505; > > > > > -0.013 0.092 0.807 4.483; > > > > > 0.051 -0.947 0.099 3.604; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > ---- Input registration matrix -------- > > > > > 0.890 0.025 0.002 1.505; > > > > > -0.013 0.092 0.807 4.483; > > > > > 0.051 -0.947 0.099 3.604; > > > > > 0.000 0.000 0.000 1.000; > > > > > subject = subject-unknown > > > > > RegMat --------------------------- > > > > > 0.890 0.002 -0.025 1.505; > > > > > -0.013 0.807 -0.092 4.483; > > > > > 0.051 0.099 0.947 3.604; > > > > > 0.000 0.000 0.000 1.000; > > > > > register: file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/std2exf.register.dat > > > > > written > > > > > mri_matrix_multiply -fsl -im > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > -iim > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/example_func2standard.mat > > > > > -om > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/std2anat.fsl.mat > > > > > ------------------------------------------------------- > > > > > tkregister2_cmdl --s PT01 --targ > > > > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz --mov > > > > > /net/misc/fsl/etc/standard/avg152T1_brain.nii.gz --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2std.register.dat > > > > > --fslreg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/std2anat.fsl.mat > > > > > --noedit > > > > > ---- FSL registration matrix -------- > > > > > 0.885 -0.049 0.075 48.869; > > > > > 0.074 -0.031 -0.809 195.041; > > > > > 0.077 0.950 -0.044 18.348; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > target volume > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.mgz > > > > > movable volume /net/misc/fsl/etc/standard/avg152T1_brain.nii.gz > > > > > reg file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2std.register.dat > > > > > LoadVol 0 > > > > > ZeroCRAS 0 > > > > > $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ > > > > > Diagnostic Level -1 > > > > > INFO: loading target > > > > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/brainmask.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 > > /net/misc/fsl/etc/standard/avg152T1_brain.nii.gz > > > > > Tmov: -------------------- > > > > > -2.000 0.000 0.000 91.000; > > > > > 0.000 0.000 2.000 -91.000; > > > > > 0.000 -2.000 0.000 109.000; > > > > > 0.000 0.000 0.000 1.000; > > > > > mkheaderreg = 0, float2int = 0 > > > > > FSLOUTPUTTYPE NIFTI_GZ > > > > > fsl2TkReg: mov det = -8, ref det = -1 > > > > > ---- Input registration matrix (computed) -------- > > > > > 1.116 -0.061 0.100 2.757; > > > > > -0.105 -0.035 1.225 -4.398; > > > > > -0.085 -1.046 -0.064 -3.213; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > ---- Input registration matrix -------- > > > > > 1.116 -0.061 0.100 2.757; > > > > > -0.105 -0.035 1.225 -4.398; > > > > > -0.085 -1.046 -0.064 -3.213; > > > > > 0.000 0.000 0.000 1.000; > > > > > subject = PT01 > > > > > RegMat --------------------------- > > > > > 1.116 -0.061 0.100 2.757; > > > > > -0.105 -0.035 1.225 -4.398; > > > > > -0.085 -1.046 -0.064 -3.213; > > > > > 0.000 0.000 0.000 1.000; > > > > > register: file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2std.register.dat > > > > > written > > > > > > > > > > To visually check your results, run: > > > > > tkregister2_cmdl --s PT01 --mov > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > --reg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > --fslreg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > --surf orig --tag > > > > > > > > > > > > > > > Mon Jan 12 14:09:25 CST 2009 > > > > > reg-feat2anat done > > > > > > > > > > COMMAND 3: > > > > > []$ tkregister2 --s PT01 --mov > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > --reg > > > > > > > > > > > > > > > call/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > --fslreg > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/exf2anat.fsl.mat > > > > > --surf orig --tag --fsl > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/example_func2highres.mat > > > > > ---- FSL registration matrix -------- > > > > > 0.995 -0.035 0.091 20.763; > > > > > 0.093 0.066 -0.994 171.738; > > > > > 0.028 0.997 0.069 11.368; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > surfname set to orig > > > > > ---- FSL registration matrix -------- > > > > > 1.043 -0.038 0.042 18.354; > > > > > 0.020 1.036 0.060 9.413; > > > > > -0.046 -0.068 1.128 70.358; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > > > > target volume orig > > > > > movable volume > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > reg file > > > > > > > > > > > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat > > > > > LoadVol 1 > > > > > ZeroCRAS 0 > > > > > $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ > > > > > Diagnostic Level -1 > > > > > INFO: loading target > > > /net/data4/CCMB08/PTSD/Thickness/PT01/mri/orig.mgz > > > > > INFO: changing target type to float > > > > > 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 > > > > > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz > > > > > Tmov: -------------------- > > > > > -3.438 0.000 0.000 110.000; > > > > > 0.000 0.000 3.000 -60.000; > > > > > 0.000 -3.438 0.000 110.000; > > > > > 0.000 0.000 0.000 1.000; > > > > > mkheaderreg = 0, float2int = 0 > > > > > FSLOUTPUTTYPE NIFTI_GZ > > > > > fsl2TkReg: mov det = -35.4492, ref det = -1 > > > > > ---- Input registration matrix (computed) -------- > > > > > 0.956 0.037 0.032 3.452; > > > > > -0.038 0.882 -0.059 1.969; > > > > > -0.021 0.050 0.961 1.159; > > > > > 0.000 0.000 0.000 1.000; > > > > > --------------------------------------- > > > > > ---- Input registration matrix -------- > > > > > 0.956 0.037 0.032 3.452; > > > > > -0.038 0.882 -0.059 1.969; > > > > > -0.021 0.050 0.961 1.159; > > > > > 0.000 0.000 0.000 1.000; > > > > > subject = PT01 > > > > > Reading lh surface orig > > > > > Done reading surface > > > > > Reading rh surface orig > > > > > Done reading surface > > > > > Zoom Factor = 2 > > > > > FOV = 256 > > > > > Opening window PT01 > > > > > Setting scale > > > > > Tagging mov volume > > > > > tkregister2: interface: > > > > /net/dysthymia/freesurfer/lib/tcl/tkregister2.tcl > > > > > tkregister.tcl: startup done > > > > > tkregister.tcl: default macro interface (to change: > > macro,mini,micro) > > > > > tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} > > > > > % > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > > > > Sent: Tue 1/6/2009 12:30 PM > > > > > To: Wang, Xin > > > > > Cc: freesurfer > > > > > Subject: Re: [Freesurfer] reg-feat2anat failed > > > > > > > > > > Hi Xin, I'm not sure what's going wrong here, I think I need more > > > info. > > > > > Can you follow the steps in > > > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting? > > > > > > > > > > doug > > > > > > > > > > > > > > > Wang, Xin wrote: > > > > > > > > > > > hello, Freesurfer group, > > > > > > > > > > > > I try to use registration.mat files of FSL/FEAT routines, > > instead of > > > > > > anat2example_func.bat, to register the orig.mgz and > > > > > > example_func.nii.gz with the thinking that using > > initial_highres in > > > > > > FEAT may improve the reg. However, tkregister2 catastrophically > > > failed > > > > > > to register two brains when I use --fsl flag. Modifying > header of > > > > > > example_func with mri_convert does not solve the problem. I will > > > > > > appreciate any suggestion on using .mat file for registration. > > > > > > > > > > > > second question: what is the best registration of > example_func and > > > > > > orig.mgz? In another word, what should I check besides things > > in the > > > > > > FS tutorial when I check/modify the registration in > > tkregister2? Is > > > > > > there golden reference points I can use? > > > > > > > > > > > > Thank you in advance for any suggestion. > > > > > > > > > > > > Xin wang > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > > > > > Sent: Mon 12/15/2008 1:26 PM > > > > > > To: Wang, Xin > > > > > > Cc: freesurfer > > > > > > Subject: Re: [Freesurfer] reg-feat2anat failed > > > > > > > > > > > > There is a flag in the nifti header saying whether the qform or > > > sform > > > > > > are valid, and it looks like your scripts do not set this flag. > > > > You can > > > > > > use mri_convert (the freesurfer program). This will create valid > > > files > > > > > > that can be read into any program. > > > > > > > > > > > > doug > > > > > > > > > > > > Wang, Xin wrote: > > > > > > > > > > > > > Thank you very much for your quick reply, Dr. Greve. I > asked our > > > > > > > institutional MRI center for correct information on qform and > > > sform > > > > > > > since the header of nifti files are created by their scripts. > > > > But I do > > > > > > > not know what they can do to fix this problem. I will > > > appreciate if > > > > > > > you have any further suggestion on how to do the registration > > > > without > > > > > > > the information on qform and sform in case I can not get them. > > > Does > > > > > > > convert to ANALYZE format or manually correct in tkregister2 > > work? > > > > > > > > > > > > > > Thank you again, > > > > > > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > > > > > > Sent: Mon 12/15/2008 1:09 PM > > > > > > > To: Wang, Xin > > > > > > > Cc: freesurfer > > > > > > > Subject: Re: [Freesurfer] reg-feat2anat failed > > > > > > > > > > > > > > Hi Xin, the problem is that neither the sform nor the > qform are > > > > valid. > > > > > > > Did the message below not appear when you ran tkmedit? > > > > > > > > > > > > > > WARNING: neither NIfTI-1 qform or sform are valid > > > > > > > WARNING: your volume will probably be incorrectly oriented > > > > > > > > > > > > > > Fix that, and everything will work fine. > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > Wang, Xin wrote: > > > > > > > > > > > > > > > Hello, Freesurfer group, > > > > > > > > I am registering the fMRI results to surface using > > > > reg-feat2anat (v > > > > > > > > 1.26.2.1 2007/08/15) and tkregister2. The automatic > > registration > > > > > > > > catastrophically failed in the subject space, but worked > fine > > > > in the > > > > > > > > standard space. The orientations of example_func.nii.gz > in the > > > > > subject > > > > > > > > space are flipped in any view. I use the tkmedit to view the > > > > > > > > example_func, and found the orientation is wrong. It seems > > > > > Freesurfer > > > > > > > > can not read nifti header correctly. I attach the > > > > reg-feat2anat log > > > > > > > > file and an example_func.nii.gz. > > > > > > > > I found the following message from Freesurfer email list. > > > > > > > > > > > > > > > > > > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html > > > > > > > > Does Freesurfer have a solution for this type of problems by > > > now? > > > > > > > > > > > > > > > > Thank you in advance, > > > > > > > > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >------------------------------------------------------------------------ > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > >Freesurfer mailing list > > > > > > > >Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Douglas N. Greve, Ph.D. > > > > > > > MGH-NMR Center > > > > > > > greve(a)nmr.mgh.harvard.edu > > > > > > > Phone Number: 617-724-2358 > > > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > In order to help us help you, please follow the steps in: > > > > > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Douglas N. Greve, Ph.D. > > > > > > MGH-NMR Center > > > > > > greve(a)nmr.mgh.harvard.edu > > > > > > Phone Number: 617-724-2358 > > > > > > Fax: 617-726-7422 > > > > > > > > > > > > In order to help us help you, please follow the steps in: > > > > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > In order to help us help you, please follow the steps in: > > > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >

2 5

Freesurfer 4.0.5 Leopard
by Ming Hsu 13 Jan '09

13 Jan '09

Hi, is FS v4.0.5 for Leopard still available? I upgraded from Tiger and would like to keep the same version for my analyses, but cannot find the previous version on the ftp site. Thanks, Ming Hsu

2 1

Dent in Inflated Brain
by Vina Goghari 13 Jan '09

13 Jan '09

Hi guys, Many of inflated brains have a little dent on the side. I looked at the white/grey segmentations and they look good to my eye. Since you have looked at way more of these brains I wanted to consult - is this something I need to be concerned about that is more subtle and I need to fix? Thanks, Vina

2 1

Dent in Inflated Brain
by Vina Goghari 13 Jan '09

13 Jan '09

1 0

3D graphics card and blade systems
by Anderson Winkler 13 Jan '09

13 Jan '09

4 6

Segmentation fault - mris_make_surfaces
by Adrian Williams 13 Jan '09

13 Jan '09

Dear all Came across a segmentation fault while running recon-all, specifically during mris_make_surfaces... Output pasted below... Any ideas/help greatly appreciated! Adrian. -- Adrian L. Williams, PhD Centre for Cognition & Neuroimaging Brunel University Uxbridge Middlesex UB8 3PH #-------------------------------------------- #@# Make Final Surf rh Sun Jan 11 09:11:39 GMT 2009 /Volumes/DataDisk/freesurf/adrian/scripts \n mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs adrian rh \n not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ $Id: mrisurf.c,v 1.557.2.15 2008/07/30 17:54:19 greve Exp $ reading volume /Volumes/DataDisk/freesurf/adrian/mri/filled.mgz... reading volume /Volumes/DataDisk/freesurf/adrian/mri/brain.finalsurfs.mgz... reading volume /Volumes/DataDisk/freesurf/adrian/mri/wm.mgz... 19879 bright wm thresholded. 4 bright non-wm voxels segmented. reading original surface position from /Volumes/DataDisk/freesurf/adrian/surf/rh.orig... computing class statistics... border white: 277588 voxels (1.65%) border gray 287750 voxels (1.72%) WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] GM (88.0) : 86.5 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 75.9 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 66.8 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 80.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 57.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->6.25) (max @ vno 57593 --> 140123) face area 0.28 +- 0.12 (0.00-->4.95) mean absolute distance = 0.84 +- 1.11 3662 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=85 using class modes intead of means.... mean inside = 100.7, mean outside = 89.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=92.7, 106 (106) missing vertices, mean dist 0.2 [0.8 (%36.9)->0.8 (%63.1))] %59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ALW-A, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.90 +- 0.24 (0.10-->7.73) (max @ vno 57593 --> 140123) face area 0.28 +- 0.12 (0.00-->4.09) vertex spacing 0.91 +- 0.25 (0.08-->8.87) (max @ vno 57593 --> 140123) face area 0.28 +- 0.13 (0.00-->4.04) smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.06-->8.92) (max @ vno 57593 --> 140123) face area 0.28 +- 0.13 (0.00-->4.04) mean absolute distance = 0.46 +- 0.83 3512 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3631140.5, rms=6.62 001: dt: 0.5000, sse=4303983.5, rms=4.71 002: dt: 0.5000, sse=4324421.5, rms=3.47 003: dt: 0.5000, sse=4337002.0, rms=2.68 004: dt: 0.5000, sse=4291947.5, rms=2.21 005: dt: 0.5000, sse=4263108.5, rms=1.94 006: dt: 0.5000, sse=4212978.0, rms=1.80 007: dt: 0.5000, sse=4200574.0, rms=1.72 rms = 1.68, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4191339.5, rms=1.68 009: dt: 0.2500, sse=3181011.8, rms=1.44 rms = 1.42, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3087899.5, rms=1.42 rms = 1.41, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3061586.0, rms=1.41 positioning took 75.5 minutes inhibiting deformation at non-cortical midline structures... mean border=94.2, 141 (49) missing vertices, mean dist -0.2 [0.6 (%61.8)->0.3 (%38.2))] %65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ALW-A, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.90 +- 0.24 (0.03-->9.51) (max @ vno 57593 --> 140123) face area 0.34 +- 0.16 (0.00-->5.05) smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.24 (0.07-->9.67) (max @ vno 57593 --> 140123) face area 0.34 +- 0.16 (0.00-->5.09) mean absolute distance = 0.39 +- 0.57 4028 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3383843.2, rms=3.03 012: dt: 0.5000, sse=3668512.5, rms=2.02 013: dt: 0.5000, sse=3762432.5, rms=1.65 014: dt: 0.5000, sse=3746829.0, rms=1.49 015: dt: 0.5000, sse=3832901.5, rms=1.41 rms = 1.41, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=3843775.0, rms=1.41 017: dt: 0.2500, sse=3401710.2, rms=1.27 rms = 1.26, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3332062.8, rms=1.26 rms = 1.26, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3308422.0, rms=1.26 positioning took 36.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=95.9, 155 (28) missing vertices, mean dist -0.2 [0.5 (%68.6)->0.2 (%31.4))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ALW-A, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.89 +- 0.24 (0.06-->9.72) (max @ vno 57593 --> 140123) face area 0.34 +- 0.16 (0.00-->5.02) Segmentation fault Darwin ALW-Apple-G5.local 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Sun Jan 11 11:29:52 GMT 2009

3 5

Gray matter question
by Martin Ystad 13 Jan '09

13 Jan '09

Hi all, I have a question relating to some quite poor data I have been analyzing. It seems that not all of the gray matter is included in the segmentation, especially in the lower part of the left temporal lobes (see attached image). It looks like the white matter has been correctly segmented in the area (i have also included 3 wm-images from the slices around the problematic area). I am not sure however, whether the tissue seen outside the pial surface is in fact gray matter. I have had some problems during scull stripping on these subjects. I would appreciate any opinions and tips on this. Regards, Martin Ystad

1 0

segementation
by GaBbo Go. Es. 13 Jan '09

13 Jan '09

hello i'm asking about a the cerebellum segmentation,i'm sending someimages, wich are exacly the same slice, but in two views(coronal and sagital)in those slices y show how looks the cerebellum together with cortex, and how i separated them. Thanks Gabriel. _________________________________________________________________ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx

1 0

Res: [Freesurfer] Segmentation
by Kelly Silva 13 Jan '09

13 Jan '09

Hi, Bruce I´m sending some pictures of aseg.mgz. Is this well done? Is there any objective and specific criteria to separate the cerebelum from the cortex? Is really necessary to do the manual segmentation on that area? Thanks, Kelly ________________________________ De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Para: Kelly Silva <kcasilva(a)yahoo.com.br> Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Enviadas: Segunda-feira, 12 de Janeiro de 2009 15:40:34 Assunto: Re: [Freesurfer] Segmentation Hi Kelly, did you check the aseg.mgz? Did it separate them properly? cheers, Bruce On Mon, 12 Jan 2009, Kelly Silva wrote: > Hello, > I´m sending an image and I want to know how is the best way to separate cerebelum from the cortex with the preservation of the both structures. > Thanks! > Best regards, > Kelly > > > Veja quais são os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

1 0

Cortical thickness in WM disease - experience
by Martin Kavec 13 Jan '09

13 Jan '09

Hi, I have been running quite a few clinical subjects (close to 300) through FS pipeline and comparing cortical thickness from parcellated cortex for each individual subject to its agematched controls. The subject clinical symptoms are not specific, ranging from amnesia, reduced ability to generate words, confusion, ... Every now and that I see that the cortical thickness is suspiciously higher than STD of the controls even if there are no leftovers after brain extraction (I specifically verify it, and if necessary do the corrections). In the vast majority of these cases I also find lower total white matter volume. I am speculating, if possible subcortical WM disease (as detected by reduced total volume of the WM) may come into the play. If subcortical WM gets darker, near the intensity of the GM, the cortical thickness may be overestimated. Could anybody comment on this idea? I suppose there is no way of correcting this. At the same time I wonder, whether cortical atrophy in MS assessed by the FS is accurate. The cortical atrophy reported in MS by FS methods (Sailer2003) was highly focal, and I am wondering if such atrophy can reflect the wide range of disables and clinical symptoms. I would appreciate any comments to my thought. Best, Martin

2 2

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Freesurfer January 2009