Dear Gwenaelle,
This time it worked the template 4D_GM image was created, i might have made some mistake previously which i am not able to find out. Anyhow i will stick your guidelines.
Sorry to bother you i would like to clarify the following, there is a file named "control_003_struc_brain_pve_0" in this file i see ventricles having PV value of 1 but there is another file which i noticed this time namely "control_003_struc_GM" where only the GM structures have PVs and the PV value is 0 in ventricles what is the difference between these two files.
Under the processing step "D Processing the native GM images: fslvbm_3_proc" a warning: By default fslvbm_3_proc concatenates the images in alphabetical order (following the names that they started with); make sure this matches the subject ordering assumed in your design.mat model. For instance my files are named as Control_003......Control_012, then my patients as demen_003.........demen 027. I have designed my design matrix based on this ordering will the concatenation step also follow this ordering or will it be different.
One last question TFCE is recommended i would like to see voxelwise results instead of clusters how can i do this.
Thanks in advance.
venkateswaran
________________________________
From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Wed 9/16/2009 12:05 PM
To: [log in to unmask]
Subject: Re: [FSL] Re : [FSL] FSL-VBM GM template creation problem
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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> P Please consider the environment before printing this
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> Cleveland Clinic is ranked one of the top hospitals
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> a complete listing of our services, staff and
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P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals
in America by U.S. News & World Report (2008).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.
Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If
you have received this communication in error, please
contact the sender immediately and destroy the material in
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