Hi,
Seems like you have file naming problems....did your input files have
strange names, with .nii (etc) in the middle of them? What do you
get if you type "ls -lrt" in the "struc" directory?
Cheers.
On 14 May 2009, at 17:50, Veena Nair wrote:
> Hi All.
> I have just started using fsl vbm on a small dataset. I got through
> steps A
> and B properly and now I am trying "step C - Creating the template:
> fslvbm_2_template" from the fsl-vbm page. At the end of the step it
> doesn't
> create the "template_4D_GM" file? although it does give the remark,
> creating
> template, once finished, check using fslview etc. I looked through the
> archives and saw some related posts but could not figure out a
> solution? I
> do have a fslvbm2a txt file in the struc folder which has lines such
> as
> below (sample for 1 subject, CON_AA):
>
> "/usr/share/fsl/bin/fast -R 0.3 -H 0.1 CON_AA.nii_struc.nii_brain ;
> /usr/share/fsl/bin/immv CON_AA.nii_struc.nii_brain_pve_1
> CON_AA.nii_struc.nii_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_brain_mixeltype.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_brain_mixeltype.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_brain_mixeltype.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_brain.nii.gz_brain ; /usr/share/fsl/
> bin/immv
> CON_AA.nii_struc.nii_brain.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_brain.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_brain_pve_0.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_brain_pve_0.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_brain_pve_0.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_brain_pve_2.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_brain_pve_2.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_brain_pve_2.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_brain_pveseg.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_brain_pveseg.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_brain_pveseg.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_brain_seg.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_brain_seg.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_brain_seg.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_cut.nii.gz_brain
> ; /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_cut.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_cut.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_GM.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_GM.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_GM.nii.gz_GM
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1
> CON_AA.nii_struc.nii_GM_to_T.nii.gz_brain ;
> /usr/share/fsl/bin/immv
> CON_AA.nii_struc.nii_GM_to_T.nii.gz_brain_pve_1
> CON_AA.nii_struc.nii_GM_to_T.nii.gz_GM"
>
> Thanks much.
>
> Veena.
>
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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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