Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

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

13 Jan '09

Sorry for the confusion. Let me rephase my questions. question 1: I want to use the example_func2highres.mat created by fsl/FEAT registration to register example_func and orig.mgz. Can the flag --fslregout or --fsl do it? Question 2: These numbers appear in the terminal whenever I click a point in tkregister2? What do these numbers mean? 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 question 3: I can only see the middle portion of the brain in tkregister2 when I zoomed in. How can I see other parts of the target and movable pictures? Thank you, Xin Wang ________________________________ From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 1/13/2009 4:19 PM To: Wang, Xin Subject: Re: [Freesurfer] reg-feat2anat failed 1) I don't know what you mean. The fslmatout is for creating an fsl mat file from a freesurfer register.dat 2. I don't know what you mean. 3. What do you mean by "moving the two images together"?

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smoothing size
by Wang, Xin 13 Jan '09

13 Jan '09

Hello, Freesurfer group, Could you tell me the default size of smoothing extents (kernel?) of smooth1 and smooth2 in the auto-recon-all? How can I change the size with mris_smooth in the auto-recon-all flow? And why does the smoothing not affect the thickness measure? Thank you in advance, Xin Wang

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mri_convert
by Jared Price 13 Jan '09

13 Jan '09

Hi everybody, We have a set of patients who were all run using the same freesurfer version, except that some of the patients had their dicom files converted to 001.mgz with a somewhat older version of freesurfer. For example some of them went through that step with version 4.0 or 4.0.2 or 4.0.5 etc. Anyway, I was wondering, is there any reason why those 001.mgz files would not be usable?

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[All] postdoc in Harvard Psych Dept. (fwd)
by Bruce Fischl 13 Jan '09

13 Jan '09

---------- Forwarded message ---------- Date: Tue, 13 Jan 2009 12:49:20 -0500 (EST) From: jgreene(a)nmr.mgh.harvard.edu To: all(a)nmr.mgh.harvard.edu Subject: [All] postdoc in Harvard Psych Dept. Hi, All, I'm looking for a postdoc to start Summer/Fall '09 This is for fMRI and/or TMS studies of moral cognition. No prior experience with moral cognition is necessary. I'm looking for someone with good technical skills and a willingness to learn about the field. See ad: https://mcl.wjh.harvard.edu/postdoc2009.html Please send materials to Shauna Gordon-Mckeon: shaunagm(a)wjh.harvard.edu Best, jdg _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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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: Top 10 - Celebridades - Música - Esportes Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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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

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