Subject: | | Re: job description (structure) under spm 8 |
From: | | Corinna Vehlow <[log in to unmask]> |
Reply-To: | | [log in to unmask][log in to unmask]> > > wrote: > > Hi Richard, > > > > > > I think that if you define the ROI from your group analysis > > using MNI space, you can inverse warp that ROI to individual > > subject spaces using the the normalise tool and *_seg_inv_sn > > files that were created when you normalized each fucntional > > scan. > > > > > > -- > > Justin Brown > > > > > > > > On Mon, Nov 2, 2009 at 8:05 AM, Richard Binney > > <[log in to unmask]> wrote: > > Dear John et al., > > > > I have used DARTEL to normalise functional data. Given > > that DARTEL produces huge files when normalising whole > > EPI runs, I ran the GLM on unsmoothed data in the > > subject space and wapred the contrast images for the > > random effects analysis. this makes several things a > > bit trickier for rookies like myself, as I will > > explain..... > > > > I want to be able to inverse warp a single set of > > coordinates (i.e. a single voxel coordinate) from MNI > > space, back to each of the individual subject spaces > > in order to perform a functional connectivity analysis > > using an ROI derived from a peak found in the group > > analysis. > > > > Is there a way I can use the DARTEL transform to > > perform forward and backward warps of a single > > coordinate set? Using segment is was previously > > possible to do this with get_orig_coord5.m > > > > This would be VERY useful for a number of things I do. > > > > Looking forward to your repsonses > > > > Richard > > > > > > > > > > -- > > Justin E Brown > > Graduate Student, Neurosciences Program > > Stanford University, School of Medicine > > email. [log in to unmask] > > > > > > > -- > John Ashburner <[log in to unmask]> > >49_3Nov200916:38:[log in to unmask] |
Date: | | Mon, 2 Nov 2009 08:22:27 +0100 |
Content-Type: | | text/plain |
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Hi Brahim,
thanks for your answer. That sounds first of all good, but how can I
do the first step and create it manually?
Thanks for your help
Best wishes
Corinna
Zitat von Brahim HAMADICHAREF <[log in to unmask]>:
>
> Hi Corinna
>
>
>
> I would
>
>
>
> 1 - Create one example manually and then save it as MyJob.mat
>
> 2 - Load the MyJob.mat into MATLAB and expand all the fields of
>
> the structure to see the default values and specific ones of
>
> your example.
>
> 3 - Modify the job (in MATLAB script format) to your needs, for
>
> e.g. path and values can be given as parameters ...
>
> 4 - Run it as batch
>
>
> Regards
>
>
> Brahim
>
>> Date: Sun, 1 Nov 2009 22:00:58 +0100
>> From: [log in to unmask]
>> Subject: [SPM] job description (structure) under spm 8
>> To: [log in to unmask]
>>
>> Hi,
>>
>> for those who already read the mail with the subject: matlab (batch)
>> scripts with spm8, can stop here. I send the mail twice (with
>> different subjects) as I was not sure, which one fits better and will
>> bring results/answers. Sorry for that!
>>
>> I'd like to write a Matlab script that performs all the spatial
>> processing steps after each other, starting with conversion of Dicom
>> files, realignment, over coregistration, estimation of the
>> transformation warp and finally normalisation. We want to use it, to
>> transform anatomical and functional brain data into MNI space. I have
>> a script, which was written to work with spm5, but it doesn't work
>> with spm8.
>> Does anybody know how the job-descriptions (variable) has to look like
>> under spm8? So what structure should it have for the different tasks
>> (conversion from dicom to analyze, realigment, coregistration etc.)? I
>> couldn't find a documentation or anything about thsi on the spm webside.
>>
>> Hope someone can help.
>> Thanks a lot in advance.
>>
>> Best wishes
>> Corinna
>
>
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