Hi, yes in this case the recommended approach is to do the initial
warp to get the subject into standard space and then use invwarp to
invert this warp.
Cheers
On 28 Oct 2008, at 06:39, Anthony Ang wrote:
> Hi Steve,
>
> To clarify, I wish to register a MNI image (or more accurately a
> lobe-based mask e.g. temporal lobe mask) into subject space. My
> question is whether flirt and fnirt can be carried out with
> ref=subject image and input=MNI-image (lobe-based mask)?
>
> Thanks.
>
> Best regards
> Anthony
>
>
> On Tue, Oct 28, 2008 at 5:24 PM, Steve Smith <[log in to unmask]>
> wrote:
> Hi - in general if you are just wanting to register a subject into
> standard space then no you don't need to run invwarp to generate the
> inverse warp. You only need that if you _also_ want to apply the
> inverse warp to bring a standard space image back into subject space.
>
> Cheers.
>
>
>
>
> On 27 Oct 2008, at 22:59, Anthony Ang wrote:
>
> Hi,
>
> FSL4.1.1 was reinstalled on the computer. fnirt now takes 76 min and
> invwarp is finally working! It takes 8.05 h.
> The MNI152 image is registered well to the subject image. Also fnirt
> -iout image is the same as applywarp output (with MNI152 image as
> the ref).
>
> However, I could not view (under fslview) -iout image initially. The
> min intensity is 3000 and max intensity is 8000. It is only after I
> have changed the intensity range to 0-100 that I could view the -
> iout image. I didn't get this output with the previous FSL version.
> Why is this so?
>
> Hence, the problem is indeed due to the use of Analyze rather than
> NIFTI output files. Mark and Jesper, thank you very much for your
> help!
>
> Now, I am doing:
> flirt (subject to MNI152 linear transform)
> fnirt (subject to MNI152 nonlinear transform)
> invwarp (MNI152 to subject)
> applwarp (MNI152 to subject)
>
> The question is why is the invwarp step necessary? Why can't I do
> the following directly?: -
> flirt (MNI152 to subject linear transform)
> fnirt (MNI152 to subject nonlinear transform) and using the --iout
> file directly
>
> I'm trying this out to see what's the result? Mark and Jesper, what
> are the reasons for doing the 4 steps instead of the 2 steps directly?
>
> Thank you very much.
>
> Best regards
> Anthony
>
>
>
> On Fri, Oct 24, 2008 at 11:00 AM, Anthony Ang <[log in to unmask]>
> wrote:
> Hi Mark,
>
> My IT Manager said that FSL was previously installed in /usr/local.
> But the latest version was installed in in /usr/share
> Both local and share appear to point to /usr/lib. He suspect when
> the new version was installed, some old files may not be overwritten
> so although these files read as FSL4.1, they may have been older
> versions.
>
> He would clear this computer of all previous FSL version and
> reinstall FSL4.1
>
> He said that FSL was downloaded as a binary version from the German
> mirror site and installed as according to the instructions provided.
> Is it better to download the binary version or to compile from source?
>
> I have copied him into this email. Thanks.
>
> Best regards
> Anthony
>
>
>
> On Fri, Oct 24, 2008 at 10:17 AM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Hi,
>
> The use of Analyze does explain the problem on your machine, as it is
> incorrectly reading the warp file (being in Analyze format) and so
> has to do
> a lot more filing of blank area and correcting for problems due to
> poorly
> constrained Jacobians.
>
> The puzzling thing is that you can get Analyze output from FSL4.1 as
> this
> should not be possible. Setting my FSLOUTPUTTYPE variable to ANALYZE
> (which is what yours is set to) gives me an error of the form:
> ERROR:: Unrecognised value (ANALYZE) of environment variable
> FSLOUTPUTTYPE
> Legal values are: NIFTI, NIFTI_PAIR, NIFTI_GZ, NIFTI_PAIR_GZ
>
> If you are not getting this error it makes me think that you are not
> using
> FSL4.1. I notice that in your PATH you have both /usr/share/fsl/bin
> and /usr/lib/fsl.
> I would check what version you are really using. See what you get
> with
> "which invwarp" to see where it is finding the files.
>
> As for your supercomputer - invwarp will not be run in parallel, so
> it is
> only using one node of your system, and each node seems to be a 1.5GHz
> processor, which may not be so fast. Hence 10 hours, although long,
> doesn't
> seem unreasonable. However, your setup problems here (I don't know
> what
> your fslinit file is or why it is needed) also makes me wonder if
> you have
> the right version of FSL installed and are using that one.
>
> We really, really strongly recommend using NIFTI for your output
> format
> (in FSL4.1 you just cannot have ANALYZE for output) and for FNIRT it
> is
> essential. It is the warp fields - particular the coeff fields -
> which must use
> the nifti format and so you cannot use any tools that deal with
> these (including
> applywarp and invwarp) with ANALYZE. I would change your
> FSLOUTPUTTYPE
> to NIFTI_GZ, check that you are using FSL4.1 (and install it if
> necessary) and
> then try running the sequence of commands again on your machine and
> see
> if that fixes the problem.
>
> All the best,
> Mark
>
>
>
> On 24 Oct 2008, at 00:00, Anthony Ang wrote:
>
> Hi Jesper,
>
> Attached is the angs_set.txt file for our lab computer. Yes, I
> notice that Analyze output files are produced.
> I also notice that the supercomputer that I used produces NIFTI
> files and when I compared the fnirt --iout file and Applywarp file
> generated by the supercomputer, they are identical.
>
> My subject images (1000024 and so on) are in Analyze format. Do I
> need to convert them to NIFTI in order for flirt, fnirt, invertwarp,
> applywarp to work correctly? Does the use of Analyze files also
> affect other FSL tools such as bet and fast?
>
> However, the difference in the file format still does not explain
> the >10 hours taken by the supercomputer to complete invwarp.
> I remembered when I was using invwarp on the supercomputer, it
> doesn't recognize the invwarp command. A fellow colleague helped and
> found an fslinit file somewhere; copied and pasted one of the lines
> (I think it is module load fsl ....) into the terminal and execute
> it. Then the invwarp is working. We have no control over the
> supercomputer. Could this have explained the long time taken even
> for this supercomputer to carry out invwarp, although it uses NIFTI
> files?
>
> Thanks.
>
> Best regards
> Anthony
>
>
>
> On Thu, Oct 23, 2008 at 8:44 PM, Jesper Andersson <[log in to unmask]
> > wrote:
> Hi again Antony,
>
> the files you sent us are in analyze format. I am not really sure
> how that happened. As of FSL 4.0, there shouldn't really be any
> (simple) way of producing analyze files as output.
>
> This also explains the problems you are having. When fnirt produce
> coefficient files (--cout) it uses a number of fields in the nifti
> header to encode various bits of information that is needed for the
> other applications to later decode them. Not all of those fields are
> present in the analyze format, and the files do not get interpreted
> correctly by either applywarp (which explains that mismatch) or
> invwarp.
>
> As a first step, could you please do
>
> set > angs_set.txt
>
> and then email us angs_set.txt?
>
> Best regards Jesper
>
>
> On 23 Oct 2008, at 08:19, Anthony Ang wrote:
>
> Hi Mark,
>
> The ref no is 470181
> Thanks.
>
> Best regards
> Anthony
>
>
> ---------- Forwarded message ----------
> From: Jesper Andersson <[log in to unmask]>
> Date: Thu, Oct 23, 2008 at 5:38 PM
> Subject: Re: [FSL] Problem with invwarp
> To: [log in to unmask]
> Cc: Mark Jenkinson <[log in to unmask]>, [log in to unmask]
>
>
> Hi Antony,
>
> >
> > fslroi x1000024_resize x1000024_roi 29 182 0 186 41 176
> > fslroi x1000024_n3ed x1000024_roi_n3ed 29 182 0 186 41 176
> >
> > flirt -v -ref MNI152_T1_2mm_brain -in x1000024_roi_n3ed -omat
> > flirted_x1000024_reducedFOV.mat -out
> flirted_x1000024_reducedFOV.hdr >
> > flirt_output
> >
> > fnirt -v --in=x1000024_roi --aff=flirted_x1000024_reducedFOV.mat
> > --cout=fnirted_x1000024_cout --iout=fnirted_x1000024_iout
> > --config=T1_2_MNI152_2mm > fnirt_output
> > *
> > applywarp -v --ref=MNI152_T1_2mm --in=x1000024_roi
> > --warp=fnirted_x1000024_cout --out=warped_x1000024 >
> applywarp_output
>
> the fnirted_x1000024_iout and warped_x1000024 files should
> definitely be
> identical. Could you please tar fnirted_x1000024_iout,
> warped_x1000024 and
> nirted_x1000024_cout and then go to
>
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>
> and follow the instructions there to upload the file? When you have
> done
> that please email me and Mark with the six-digit code that you are
> given.
>
> Best regards Jesper
>
>
>
>
>
>
> <angs_set.txt>
>
>
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
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