Hello, Dr. Greve,
I used brain.mgz of freesurfer after mri_converted it to nii.gz as
highres in feat registration with the thinking that the brain.mgz is
the final product of freesurfer pre-processing. Using scalp-striped
brain.mgz should be more comparable between fsl and FS than using
T1.mgz or orig.mgz as I guess. Correct me if I am wrong.
Xin
-----Original Message-----
From: Douglas N Greve [mailto:[email protected]]
Sent: Tue 1/13/2009 11:27 AM
To: Wang, Xin
Cc: [email protected]; freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed
what did you use as the highres volume in feat? If you want that reg to
work, it has to be a "freesurfer anatomical volume", meaning 256^3, 1mm3
doug
Wang, Xin wrote:
>
> 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:[email protected]]
> Sent: Mon 1/12/2009 4:02 PM
> To: Wang, Xin
> Cc: [email protected]
> 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:[email protected]]
> > *Sent:* Mon 1/12/2009 3:29 PM
> > *To:* Wang, Xin
> > *Cc:* [email protected]
> > *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:[email protected]]
> > > *Sent:* Mon 1/12/2009 3:10 PM
> > > *To:* Wang, Xin
> > > *Cc:* [email protected]
> > > *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
> > > > [email protected]
> > > > <mailto:[email protected]>
> > > > :
> > > > : 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:[email protected]]
> > > > *Sent:* Mon 1/12/2009 2:55 PM
> > > > *To:* Wang, Xin
> > > > *Cc:* [email protected]
> > > > *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:[email protected]]
> > > > > *Sent:* Mon 1/12/2009 2:38 PM
> > > > > *To:* Wang, Xin
> > > > > *Cc:* [email protected]
> > > > > *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:[email protected]]
> > > > > > 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:[email protected]]
> > > > > > > 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:[email protected]]
> > > > > > > > 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/[email protected]/msg05573.html
> > > > > > > > > Does Freesurfer have a solution for this type of
> problems by
> > > > now?
> > > > > > > > >
> > > > > > > > > Thank you in advance,
> > > > > > > > >
> > > > > > > > > Xin
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
>------------------------------------------------------------------------
> > > > > > > > >
> > > > > > > > >_______________________________________________
> > > > > > > > >Freesurfer mailing list
> > > > > > > > >[email protected]
> > > > > > > >
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > Douglas N. Greve, Ph.D.
> > > > > > > > MGH-NMR Center
> > > > > > > > [email protected]
> > > > > > > > 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
> > > > > > > [email protected]
> > > > > > > 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
> > > > > > [email protected]
> > > > > > 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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
>
>
