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SPM  August 2011

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Subject:

Re: Inverse Normalization error - parameter files problem?

From:

Barbara Vogt <[log in to unmask]>

Reply-To:

Barbara Vogt <[log in to unmask]>

Date:

Fri, 5 Aug 2011 20:07:45 +0200

Content-Type:

text/plain

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text/plain (131 lines)

Dear Chris, 

many thanks for your help!

As far as I can see, it works when I use the "New Segment" segmentation method. However, it does not seem like I can use the deformations utility for building ^y files with sn.mat files created using the "old" segmentation method with the "Segment" button. When I do that, it causes a similar error to the one I used to get when trying normalize->write with the old sn.mat files.

Running 'Deformations'
Failed  'Deformations'
Reference to non-existent field 'VG'.
In file "/ ... /spm_defs.m" (v4194), function "get_sn2def" at line 113.
In file "/ ... /spm_defs.m" (v4194), function "get_job" at line 63.
In file "/ ... /spm_defs.m" (v4194), function "get_comp" at line 29.
In file "/ ... /spm_defs.m" (v4194), function "spm_defs" at line 16.

The following modules did not run:
Failed: Deformations


Is that so? Is it not possible?
Or do you know if I might have done something wrong?


Regards, 
Barbara



***********************************************

Barbara Vogt, PhD student
Max Planck Research Group 'Body & Self'
Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig
Stephanstr. 1a, D-04103 Leipzig, Germany
Phone:  ++49 (0)341 9940-2669
Fax: ++49 (0)341 9940-2204



----- Original Message -----
From: Christian Lambert <[log in to unmask]>
To: Barbara Vogt <[log in to unmask]>
Cc: [log in to unmask]
Sent: Fri, 05 Aug 2011 15:27:46 +0200 (CEST)
Subject: Re: [SPM] Inverse Normalization error - parameter files problem?

Select the forward and inverse deformation field option at the bottom of SPM
new segment - That will give you your ^y files. Then in deformations-select
new deformation and input the corresponding files (forward or inverse
depending where your going). You can also use the sn.mat files in the
deformations tool box, and to inverse, use the "new inverse" followed by
"new imported sn.mat", and select individual subject space as your target.

Hope that helps.

- Chris

On Fri, Aug 5, 2011 at 2:04 PM, Barbara Vogt <[log in to unmask]> wrote:

> Dear Mr. Ashburner, dear SPM list.
>
> Last year (Thu, 28 Oct 2010) there was an email conversation mentioning
> problems with the normalization parameter files written by an SPM "New
> Segment" toolbox (as it was seemingly called then).
>
> I am having trouble using the normalization parameter files (and inverse
> parameter files) created using the "normal", integrated segmentation
> approach, with the versions SPM 8.3684 and 8.4290, getting practically the
> same error message as the person did back then.
>
> Namely
>
>
> Running 'Normalise: Write'
> Failed  'Normalise: Write'
> Reference to non-existent field 'VG'.
> In file "/afs/cbs.mpg.de/software/spm/8.3684/7.11/2.7/spm_write_sn.m"
> (v2534), function "get_xyzmat" at line 430.
> In file "/afs/cbs.mpg.de/software/spm/8.3684/7.11/2.7/spm_write_sn.m"
> (v2534), function "spm_write_sn" at line 96.
> In file "/afs/
> cbs.mpg.de/software/spm/8.3684/7.11/2.7/config/spm_run_normalise_write.m"
> (v2312), function "spm_run_normalise_write" at line 25.
>
> The following modules did not run:
> Failed: Normalise: Write
>
>
>
> Last year, Mr. Ashburner answered to the person having this problem:
>
> "...The new segmentation does generate deformation fields,
> but not in a form that is easy to use via the Normalise->Write option.
>  You would need to use the Deformations Utility (with the y_*.nii file
> that is optionally generated), which is not so straightforward.
>
> I will eventually get around to streamlining this procedure. ..."
>
>
> Could it be, that the segmentation approach in SPM 8.3684 and 8.4290 still
> has this same problem...?
>
> Since I really need to use the inverse normalization parameter files, in
> order to bring functionally defined ROIs back into the subjects' own space,
> I would like to ask for help.
>
> I would use the Deformations Utility, but if it is not very
> straightforward, I would be extremely glad for any help on how to start, and
> information on what the problem with the deformation fields is and what we
> need to do to solve it (and what the y_*.nii file is, and how to obtain it).
>
> Otherwise, could someone tell me how far I would have to go back into old
> SPM versions, to find one where the parameters are still given in a way that
> the normalize->write function can handle?
>
>
> Sincere thanks,
> Barbara
>
>
>
>
> ***********************************************
>
> Barbara Vogt, PhD student
> Max Planck Research Group 'Body & Self'
> Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig
> Stephanstr. 1a, D-04103 Leipzig, Germany
> Phone:  ++49 (0)341 9940-2669
> Fax: ++49 (0)341 9940-2204
>

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