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(a)hotmail.com
> To: moeller(a)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(a)caltech.edu
> > To: freesurfer_zg(a)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(a)caltech.edu
> > > > To: freesurfer_zg(a)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(a)caltech.edu
> > > > > > To: freesurfer_zg(a)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
> > > > > >
> > > > >
> > > > > Hotmail® is up to 70% faster. Now good news travels really
> fast.
> > > Try
> > > > > it now.
> > > >
> > > >
> > > > --
> > > > Sebastian Moeller
> > > >
> > > > telephone: 626-395-6713
> > > > German GSM: 0 15 77 - 1 90 31 41
> > > > moeller(a)caltech.edu
> > > >
> > > > Division of Biology
> > > > MC 114-96
> > > > California Institute of Technology
> > > > 1200 East California Boulevard
> > > > CA 91125, Pasadena
> > > > USA
> > > >
> > >
> > > Windows Live: Make it easier for your friends to see what you’re
> up
> > > to on Facebook. Find out more.
> >
> >
> > --
> > Sebastian Moeller
> >
> > telephone: 626-395-6713
> > German GSM: 0 15 77 - 1 90 31 41
> > moeller(a)caltech.edu
> >
> > Division of Biology
> > MC 114-96
> > California Institute of Technology
> > 1200 East California Boulevard
> > CA 91125, Pasadena
> > USA
> >
>
> With Windows Live, you can organize, edit, and share your photos.
> Click here.
> Windows Live: Make it easier for your friends to see what you’re up
> to on Facebook. Find out more.
