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FSL  July 2008

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Subject:

Re: Re : [FSL] following different order on VBM analysis steps

From:

Antonios - Constantine Thanellas <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 29 Jul 2008 13:33:29 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (108 lines) , text_files.tar.gz (108 lines)

Hi Gwenaelle,

I've followed exactly the description that you've proposed.

During the next step of vbm analysis i encountered the following errors and
i don't know where do they come from.

More specific i run fslvbm_2_template -a in a folder containing the
design.mat, design.con, template_list and the folders FAi and origdata. FAi
folder contains the folder slicesdir and the files 
        controls_XXX_FAi.hdr (0 bytes hdr. doc)
        controls_XXX_FAi.img(0 bytes plain text doc)
        controls_XXX_FAi_brain.hdr
        controls_XXX_FAi_brain.img
              .....
        patients_XXX_FAi.hdr (0 bytes hdr. doc)
        patients_XXX_FAi.img(0 bytes plain text doc)
        patients_XXX_FAi_brain.hdr
        patients_XXX_FAi_brain.img
             .....

After the fslvbm_2_template -a scipt run i had the following outputs:

        controls_XXX_FAi.hdr (0 bytes hdr. doc)
        controls_XXX_FAi.img(0 bytes plain text doc)
        controls_XXX_FAi_brain.hdr
        controls_XXX_FAi_brain.img
        controls_XXX_FAi_brain_pve_0.hdr
        controls_XXX_FAi_brain_pve_0.img
        controls_XXX_FAi_brain_pve_1.hdr
        controls_XXX_FAi_brain_pve_1.img
        controls_XXX_FAi_brain_pve_2.hdr
        controls_XXX_FAi_brain_pve_2.img
        controls_XXX_FAi_brain_seg.hdr
        controls_XXX_FAi_brain_seg.img
        controls_XXX_FAi_GM.hdr
        controls_XXX_FAi_GM.img
        controls_XXX_FAi_GM_xflipped.hdr
        controls_XXX_FAi_GM_xflipped.img
              .....
        same for the patients group

 a T.hdr and T.img files and finally the following text files that i've
attached in this e-mail .
No other file was created (for instance template_4D_GM.nii.gz etc) during
this step's analysis.

Can you help me on what went wrong here?
Thank you once more
Antonios-Konstantinos Thanellas



On Mon, 21 Jul 2008 14:20:23 +0000, GwenaŽlle DOUAUD
<[log in to unmask]> wrote:

>Hi Antonios,
>
>absolutely. The only thing that is required is to present the data as if
they'd been processed in the right order...
>
>If, say, you've named your various brain extracted exams:
exam00X_brain.nii.gz, then after running tbss_1_preproc, you'll have in your
FAi/ directory all your images called exam00X_brain_FAi.hdr and .img.
>
>So you then just need to rename them exam00X_FAi_brain.hdr and .img.
>
>One additional requirement (for nomenclature purposes) is that you need to
have in your FAi/ directory corresponding files *without* the _brain suffix,
 so in this case: exam00X_FAi.hdr and .img (no matter what they are, so for
you, empty files would just be fine: touch exam00X_FAi.hdr and .img).
>
>Hope this makes sense,
>Gwenaelle
>
>
>--- En date de : Lun 21.7.08, Antonios - Constantine Thanellas
<[log in to unmask]> a ťcrit :
>
>> De: Antonios - Constantine Thanellas <[log in to unmask]>
>> Objet: [FSL] following different order on VBM analysis steps
>> ņ: [log in to unmask]
>> Date: Lundi 21 Juillet 2008, 12h23
>> Dear fsl users,
>> 
>> I want to analyse my data (controls-patients) using
>> fsl's VBM.
>> 
>> All my data (whole heads) have been brain extracted with
>> BET beforehand in
>> another analysis part.
>> 
>> So instead of "beting" my data again (2nd step of
>> VBM analysis) can i just
>> modify the already extracted brains with tbss_1_preproc
>> (1st step of VBM
>> analysis) and omit the second step?
>> 
>> Thank you in advance
>> Antonios-Konstantinos Thanellas


     
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