Hi Guang,
I cc'd the freesuefer list as this is where the expert are... :). I do not think that I fully understand what you want to achieve here, so bear with me as my response might be really really daft. In that case I really recommend to bring this onto the experts on the freesurfer list... I guess my first question is: How did you get the niftii files in the first place? It looks like the tool you used there did have some differences in say the origin. Now, I am no expert, but I would go and register and reslice the volumes, taking your niftii as target (otherwise switch arguments), make sure the volumes are in the current directory or adjust the pathes:
tkregister2 --targ nu_C1NC0.mgz --mov nu_fs.mgz --regheader --reg nu_fs_2_nu_C1NC0.register.dat and then reslice:
mri_vol2vol --mov nu_fs.mgz --targ nu_fs.mgz --o nu_fs_C1NC0space.mgz --reg nu_fs_2_nu_C1NC0.register.dat
that should give you the freesurfer NU in C1NC0 space. If you want the whole surface recon in freesurfer in C1NC0 space you probably should do this registration with the initial volume you feed into freesurfer so that all following steps are already in the correct space.
I hope that helps Sebastian
On Aug 27, 2009, at 7:52 AM, Guang Zeng wrote:
Hello, Sebastian,
I hope I explained my question clearly, I attached the mri_info of these two mgz files. I noticed that there are few differences such as c_r, c_a and c_s. But why there are different? Oh maybe I need ask how could I make them the same?
Sorry, ask you so many questions.
Guang Zeng
//////// Converted from DICOM ///////// Volume information for nu_fs.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.40 msec, TE: 4.09 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5.0421 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 6.3413 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -10.1429
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 133.0421 0.0000 0.0000 1.0000 -121.6587 0.0000 -1.0000 0.0000 117.8571 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 133.0421 -0.0000 -0.0000 -1.0000 117.8571 -0.0000 1.0000 -0.0000 121.6587 0.0000 0.0000 0.0000 1.0000
//////// Converted from NIfTI ///////// Volume information for nu_C1NC0.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.8830 : x_a = -0.0000, y_a = -0.0000, z_a = 1.0000, c_a = -6.1862 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 2.6867
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 127.1170 -0.0000 -0.0000 1.0000 -134.1862 0.0000 -1.0000 0.0000 130.6867 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 -0.0000 127.1170 -0.0000 0.0000 -1.0000 130.6867 -0.0000 1.0000 0.0000 134.1862 0.0000 0.0000 0.0000 1.0000 From: freesurfer_zg@hotmail.com To: moeller@caltech.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9 Date: Thu, 27 Aug 2009 09:28:17 -0500
Hello, Sebastian,
Sorry to bother you again, I got a question about mri_convert now,
I have a subject in dicom format, I convert it to NIfTI format. Then I convert both of them to mgz format, using mri_convert -- conform.
I thought they should look as the same, but actually they are not at all. Do you meet this kind of problem before? Does mri_convert treat dicom and NIfTI differently?
Thanks a lot!
Guang Zeng
From: moeller@caltech.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9 Date: Tue, 25 Aug 2009 09:07:40 -0700
Hi Guang,
always happy to help :)...
On Aug 25, 2009, at 7:04 AM, Guang Zeng wrote:
Hello, Sebastian,
Thanks a lot for your help yesterday about that "redraw fails" problem, it works on my machine now. However, I also noticed that although the tksurfer is working well now, that "redraw fails, no gl window open" message is still there.
Well, I have no real idea, except I recall that I saw these messages as well but always ignored them if tksurfer worked. Oh make sure you have "export doublebufferflag=1" in your bashrc, that often
convinces
tksurfer to use doublebuffering even if tksurfer thinks your
computer
can not do this.
Anyway, I am very glad that I can use tksurfer now, it bothers me for two weeks.
Glad I could help...
ahoi & regards Sebastian
Guang
From: moeller@caltech.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9 Date: Mon, 24 Aug 2009 09:01:28 -0700
hi Guang,
Have a look at this:
ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored.
I guess there is a missing a "/" in the LD_PRELOAD line. Try:
setenv LD_PRELOAD ${FREESURFER_HOME}/bin/libGL.so.1 NOTE the extra "/" between ${FREESURFER_HOME} and bin. That
should
fix
this part of the problem, but whetheer it fixes tksurfer I do
not
know...
hope this helps Sebastian
On Aug 24, 2009, at 8:55 AM, Guang Zeng wrote:
Hi, Sebastian,
Thanks a lot for forwarding the files. I tried to use your method, but it does not work, and give
me some
errors as:
ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. surfer: current subjects dir: /home/m047599/freesurfer-
install/
freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599/freesurfer-install/freesurfer ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. surfer: Reading header info from /home/m047599/freesurfer-
install/
freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/home/m047599/freesurfer-install/
freesurferbin/
libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. Loading /home/m047599/freesurfer-install/freesurfer/
surface_labels.txt
surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/
freesurfer/
lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ tkUtils.tcl Successfully parsed tksurfer.tcl
Do you have some ideas about this?
Thanks a lot!
Guang
From: moeller@caltech.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9 Date: Mon, 24 Aug 2009 08:18:00 -0700
Hi Guang,
let me send you the attachement again. This contains redhat
server 4
GL libraries that have to be unpacked in $FREESURFER_HOME/
bin.
The
system we use it on only has a lowly ATI card without
proper 3D
support, so I think MESA is installed there and we use
nomachine's
NX
client to access the server over the network, which works
nicely and
displays the full surfaces. Unfortunately since I
responded to
your
post other people tried my proposed solution and failed,
so I am
unsure whether it will help in your case...
good luck Sebastian
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-- Sebastian Moeller
telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
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-- Sebastian Moeller
telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
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