I tried to use the old segmentation. It works for this image. But the new segmentation does not work.
Running 'New Segment'
Failed 'New Segment'
Error using ==> times
Matrix dimensions must agree.
In file "C:\spm8\toolbox\Seg\spm_maff8.m" (v2281), function "affreg" at line 157.
In file "C:\spm8\toolbox\Seg\spm_maff8.m" (v2281), function "spm_maff8" at line 27.
In file "C:\spm8\toolbox\Seg\spm_preproc_run.m" (v2281), function "run_job" at line 80.
In file "C:\spm8\toolbox\Seg\spm_preproc_run.m" (v2281), function "spm_preproc_run" at line 27.
The following modules did not run:
Failed: New Segment
--- On Sun, 6/21/09, Markus Gschwind <[log in to unmask]> wrote:
> From: Markus Gschwind <[log in to unmask]>
> Subject: Re: [SPM] Another problem with New Segment
> To: [log in to unmask], "cliff macnab" <[log in to unmask]>
> Date: Sunday, June 21, 2009, 8:21 PM
> Hi!
> Did you use them simultaionsly ore one after the other?
> Is there no difference between the T1 that did not work and
> the others? I cannot imagine that there is not.
> Have you had a look with Display at the resolution,
> dimensions etc.?
>
>
> cheers,
> Markus
>
> 2009/6/21 cliff macnab <[log in to unmask]>
>
>
>
>
> I have a couple of T1 nii images. Using checkreg, all of
> them look similar, in same oritation. Only one of them gave
> me trouble using the new segmentation, and all others can go
> through smoothingly without any trouble.
>
>
>
>
>
> Thanks,
>
>
>
> Cliff
>
>
>
> --- On Sun, 6/21/09, Markus Gschwind <[log in to unmask]>
> wrote:
>
>
>
> > From: Markus Gschwind <[log in to unmask]>
>
> > Subject: Re: [SPM] Another problem with New Segment
>
> > To: "cliff macnab" <[log in to unmask]>
>
> > Date: Sunday, June 21, 2009, 2:48 PM
>
> > Hi,
>
> > have you tried several different T1 from different
> subjects
>
> > or just this one? Are you sure that the problem
> persists
>
> > with other T1s?
>
> > How have you started the NewSegment? By using the
> batch?
>
> > And if so, have you deactivated the second etc
> channel?
>
> >
>
> > Cheers,
>
> > Markus
>
> >
>
> >
>
> > 2009/6/21 cliff macnab <[log in to unmask]>
>
> >
>
> >
>
> >
>
> > Thanks for your message. I tried to segment 1 T1 image
> and
>
> > its origin looks fine.
>
> >
>
> >
>
> >
>
> > --- On Sun, 6/21/09, Markus Gschwind <[log in to unmask]>
>
> > wrote:
>
> >
>
> >
>
> >
>
> > > From: Markus Gschwind <[log in to unmask]>
>
> >
>
> > > Subject: Re: [SPM] Another problem with New
> Segment
>
> >
>
> > > To: "cliff macnab" <[log in to unmask]>
>
> >
>
> > > Date: Sunday, June 21, 2009, 7:11 AM
>
> >
>
> > > Hi!
>
> >
>
> > >
>
> >
>
> > > 1.) Have you set the origin correctly in all
> images?
>
> > After
>
> >
>
> > > some dicom conversions (especially if you use
> Siemens
>
> > .ima
>
> >
>
> > > files, the origin is not correct and needs to be
>
> > placed
>
> >
>
> > > manually (Display => reorient image).
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > 2.) Have you used multiple imges per subject
> (several
>
> >
>
> > > Channels)?
>
> >
>
> > > You will need to first coregister
>
> > (estimate&reslice)
>
> >
>
> > > the mulitple images to the first one (mostly the
> T1).
>
> >
>
> > >
>
> >
>
> > > 3.) Have you used several subjects?
>
> >
>
> > >
>
> >
>
> > > Maybe the T1s are not all in the same
> orientation. You
>
> > can
>
> >
>
> > > use checkreg for controlling that.
>
> >
>
> > >
>
> >
>
> > > All the best,
>
> >
>
> > > Markus
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > 2009/6/21 cliff macnab <[log in to unmask]>
>
> >
>
> > >
>
> >
>
> > > Dear John and other experts,
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > When I tried to segment a nii image with the new
>
> >
>
> > > segmentation tool, I got following error
> message:
>
> >
>
> > >
>
> >
>
> > >
>
> >
> -----------------------------------------------------------------------
>
> >
>
> > >
>
> >
>
> > > Running job #1
>
> >
>
> > >
>
> >
>
> > >
>
> >
> -----------------------------------------------------------------------
>
> >
>
> > >
>
> >
>
> > > Running 'New Segment'
>
> >
>
> > >
>
> >
>
> > > Failed 'New Segment'
>
> >
>
> > >
>
> >
>
> > > Error using ==> times
>
> >
>
> > >
>
> >
>
> > > Matrix dimensions must agree.
>
> >
>
> > >
>
> >
>
> > > In file
> "/spm8/toolbox/Seg/spm_maff8.m"
>
> > (v2281),
>
> >
>
> > > function "affreg" at line 157.
>
> >
>
> > >
>
> >
>
> > > In file
> "/spm8/toolbox/Seg/spm_maff8.m"
>
> > (v2281),
>
> >
>
> > > function "spm_maff8" at line 27.
>
> >
>
> > >
>
> >
>
> > > In file
>
> > "/spm8/toolbox/Seg/spm_preproc_run.m"
>
> >
>
> > > (v2281), function "run_job" at line
> 80.
>
> >
>
> > >
>
> >
>
> > > In file
>
> > "/spm8/toolbox/Seg/spm_preproc_run.m"
>
> >
>
> > > (v2281), function "spm_preproc_run" at
> line
>
> > 27.
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > The following modules did not run:
>
> >
>
> > >
>
> >
>
> > > Failed: New Segment
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Any idea for fixing this problem?
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Thanks,
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Cliff
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > --- On Fri, 6/19/09, John Ashburner <[log in to unmask]>
>
> >
>
> > > wrote:
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > > From: John Ashburner <[log in to unmask]>
>
> >
>
> > >
>
> >
>
> > > > Subject: [SPM] Memory problems with New
> Segment
>
> >
>
> > >
>
> >
>
> > > > To: [log in to unmask]
>
> >
>
> > >
>
> >
>
> > > > Date: Friday, June 19, 2009, 1:37 PM
>
> >
>
> > >
>
> >
>
> > > > Dear Markus and others,
>
> >
>
> > >
>
> >
>
> > > > The attached version should be a bit more
> memory
>
> >
>
> > >
>
> >
>
> > > > efficient. Replace the
>
> >
>
> > >
>
> >
>
> > > > existing version of
>
> >
>
> > > spm8\toolbox\Seg\spm_invert_def.m
> with
>
> >
>
> > >
>
> >
>
> > > > it.
>
> >
>
> > >
>
> >
>
> > > >
>
> >
>
> > >
>
> >
>
> > > > All the best,
>
> >
>
> > >
>
> >
>
> > > > -John
>
> >
>
> > >
>
> >
>
> > > >
>
> >
>
> > >
>
> >
>
> > > > --
>
> >
>
> > >
>
> >
>
> > > > John Ashburner <[log in to unmask]>
>
> >
>
> > >
>
> >
>
> > > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > --
>
> >
>
> > > Dr. med. Markus Gschwind, M.D.
>
> >
>
> > > Laboratory for Neurology and Imaging of
> Cognition
>
> >
>
> > > Dept of Neurosciences
>
> >
>
> > > University Medical Center (CMU)
>
> >
>
> > > 1 Michel-Servet - 1211 GENEVA - CH
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Tel 0041 (0) 22 379 5324
>
> >
>
> > > Fax 0041 (0) 22 379 5402
>
> >
>
> > > email: [log in to unmask]
>
> >
>
> > > http://labnic.unige.ch
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > --
>
> > Dr. med. Markus Gschwind, M.D.
>
> > Laboratory for Neurology and Imaging of Cognition
>
> > Dept of Neurosciences
>
> > University Medical Center (CMU)
>
> > 1 Michel-Servet - 1211 GENEVA - CH
>
> >
>
> >
>
> > Tel 0041 (0) 22 379 5324
>
> > Fax 0041 (0) 22 379 5402
>
> > email: [log in to unmask]
>
> > http://labnic.unige.ch
>
> >
>
> >
>
>
>
>
>
>
>
>
>
>
> --
> Dr. med. Markus Gschwind,
> M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
>
> 1 Michel-Servet - 1211 GENEVA - CH
>
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
>
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