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, Gwenaëlle 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 écrit : > >> De: Antonios - Constantine Thanellas <[log in to unmask]> >> Objet: [FSL] following different order on VBM analysis steps >> À: [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 _____________________________________________________________________________ Envoyez avec Yahoo! Mail. Une boite mail plus intelligente http://mail.yahoo.fr