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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in America by U.S. News & World Report (2008).
Visit us online at http://www.clevelandclinic.org for
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Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed
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