Hi again,
no problem!
let me know how it goes...
Cheers,
Gwenaelle
--- En date de : Mer 16.9.09, Rajagopalan, Venkateswaran <[log in to unmask]> a écrit :
> De: Rajagopalan, Venkateswaran <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] FSL-VBM GM template creation problem
> À: [log in to unmask]
> Date: Mercredi 16 Septembre 2009, 16h46
> Dear Gwenaelle,
>
> I am sorry for the confusion. Yesterday i ran template
> creation step once again in a subsample of subjects after
> carefully noting down your suggestions and it worked, so i
> decided to try again making sure that i followed all your
> instructions correctly so i was rerunning it (it is still
> running), so when i you asked me yesterday to list the files
> in struc directory just at that time i deleted all the files
> from my struc directory w prepared my struc directory for
> the rerun. I will get back to you after this rerun. I am
> sorry.
>
> I tried to recover "fslvbm2a.e and fslvbm2a.o" from trash.
> There is nothing inside those files error reports or
> anything like that. I am attaching them for you to take a
> look at them. I am very sorry again to confuse you.
>
> Thanks a lot for your patience and kind help.
>
> venkateswaran
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of
> Gwenaëlle DOUAUD
> Sent: Wed 9/16/2009 9:19 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Re : [FSL] FSL-VBM GM template creation
> problem
>
> Hi Venkateswaran,
>
> I am confused. You said the fslvbm2a.e* was empty? From the
> look of your struc directory, it is however obvious that the
> GM segmentation images using fast were not created. Now you
> also say that you have some GM maps as you found a value of
> 1 in the ventricles, but I don't see any of them in your
> struc directory...
> Where are your *_struc_GM.nii.gz?
> Can you copy/paste the contents of the fslvbm2a.e and
> fslvbm2a.o?
>
> Cheers,
> Gwenaelle
>
> --- En date de : Mar 15.9.09, Rajagopalan, Venkateswaran
> <[log in to unmask]>
> a écrit :
>
> > De: Rajagopalan, Venkateswaran <[log in to unmask]>
> > Objet: Re: [FSL] Re : [FSL] FSL-VBM GM template
> creation problem
> > À: [log in to unmask]
> > Date: Mardi 15 Septembre 2009, 19h02
> > Hi,
> >
> > Thanks again
> >
> > template list
> >
> > control_003.nii.gz
> > control_004.nii.gz
> > control_005.nii.gz
> > control_006.nii.gz
> > control_008.nii.gz
> > control_009.nii.gz
> > control_010.nii.gz
> > control_011.nii.gz
> > control_012.nii.gz
> > demen_001.nii.gz
> > demen_003.nii.gz
> > demen_006.nii.gz
> > demen_007.nii.gz
> > demen_009.nii.gz
> > demen_017.nii.gz
> > demen_020.nii.gz
> > demen_022.nii.gz
> > demen_027.nii.gz
> >
> >
> > ls of struc directory
> >
> > control_003_struc_brain.nii.gz
> > demen_008_struc.nii.gz
> > control_003_struc.nii.gz
>
> > demen_009_struc_brain.nii.gz
> > control_004_struc_brain.nii.gz
> > demen_009_struc.nii.gz
> > control_004_struc.nii.gz
>
> > demen_010_struc_brain.nii.gz
> > control_005_struc_brain.nii.gz
> > demen_010_struc.nii..gz
> > control_005_struc.nii.gz
>
> > demen_013_struc_brain.nii.gz
> > control_006_struc_brain.nii.gz
> > demen_013_struc.nii.gz
> > control_006_struc.nii.gz
>
> > demen_014_struc_brain.nii.gz
> > control_008_struc_brain.nii.gz
> > demen_014_struc.nii.gz
> > control_008_struc.nii.gz
>
> > demen_015_struc_brain.nii.gz
> > control_009_struc_brain.nii.gz
> > demen_015_struc.nii.gz
> > control_009_struc.nii.gz
>
> > demen_016_struc_brain.nii.gz
> > control_010_struc_brain.nii.gz
> > demen_016_struc.nii.gz
> > control_010_struc.nii.gz
>
> > demen_017_struc_brain.nii.gz
> > control_011_struc_brain.nii.gz
> > demen_017_struc.nii.gz
> > control_011_struc.nii.gz
>
> > demen_020_struc_brain.nii.gz
> > control_012_struc_brain.nii.gz
> > demen_020_struc.nii.gz
> > control_012_struc.nii.gz
>
> > demen_022_struc_brain.nii.gz
> > demen_001_struc_brain.nii.gz
> > demen_022_struc.nii.gz
> > demen_001_struc.nii.gz
>
> > demen_024_struc_brain.nii.gz
> > demen_003_struc_brain.nii.gz
> > demen_024_struc.nii.gz
> > demen_003_struc.nii.gz
>
> > demen_025_struc_brain.nii..gz
> > demen_005_struc_brain.nii.gz
> > demen_025_struc.nii.gz
> > demen_005_struc.nii.gz
>
> > demen_026_struc_brain.nii.gz
> > demen_006_struc_brain.nii.gz
> > demen_026_struc.nii.gz
> > demen_006_struc.nii.gz
>
> > demen_027_struc_brain.nii.gz
> > demen_007_struc_brain.nii.gz
> > demen_027_struc.nii.gz
> > demen_007_struc.nii.gz
>
> > demen_028_struc_brain.nii.gz
> > demen_008_struc_brain.nii.gz
> > demen_028_struc.nii.gz
> >
> >
> > I reduced the size of the image to 83 kb. If you have
> > problems please inform me. Thanks a lot.
> >
> > venkateswaran
> >
> >
> >
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library on behalf of
> > Gwenaëlle DOUAUD
> > Sent: Tue 9/15/2009 1:32 PM
> > To: [log in to unmask]
> > Subject: Re: [FSL] Re : [FSL] FSL-VBM GM template
> creation
> > problem
> >
> > Hi,
> >
> > > So do i need to change the
> > > name in my template list to
> > "control_003_struc.nii..gz"
> > > instead of "control_003.nii.gz" what i have
> right
> > now.
> >
> > No this should be fine... Could you please copy the
> result
> > of an ls in your struc directory and the content of
> your
> > template_list file?
> >
> > > I am attaching a a JPEG image of the print
> screen
> > version
> > > of GM and WM pve PLACED SIDE BY SIDE.
> >
> > There is no attachment. It might be that your jpeg is
> too
> > big, try a lower resolution...
> >
> > Cheers,
> > Gwenaelle
> >
> >
> >
> >
> >
> >
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> Cleveland Clinic is ranked one of the top hospitals
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> Visit us online at http://www.clevelandclinic.org for
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> Confidentiality Note: This message is intended for
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