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.
|