Hi Gwenalle,
Thanks very much
venkateswaran
________________________________
From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Fri 9/18/2009 12:45 PM
To: [log in to unmask]
Subject: Re: [FSL] Re : [FSL] FSL-VBM GM template creation problem
Hi,
you have to run it from the stats directory (and leave the design.* there).
Cheers,
Gwenaelle
--- En date de : Ven 18.9.09, 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: Vendredi 18 Septembre 2009, 15h53
> Hi Gwenaelle,
>
> Sorry to bother you again, everything so far works fine
> until the smoothing step, when i tried to run "randomise -i
> GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t
> design.con -T -n 5000 -V" it gives me the following error
>
> ERROR (nifti_image_read): failed to find header file for
> 'GM_mod_merg_s3'
> ** ERROR: nifti_image_open(GM_mod_merg_s3): bad header
> info
> Error: failed to open file GM_mod_merg_s3
> ERROR: Could not open image GM_mod_merg_s3
> ERROR: Program failed
>
> An exception has been thrown
> Failed to read volume GM_mod_merg_s3
>
> I ran the above randomise command under my_fsl_vbm
> directory as it was not mentioned in documentation page is
> this the problem as it says "failed to find header file". I
> placed my design.mat and design.con matrix under my_fsl_vbm
> directory too i hope it is correct.
>
> Thanks in advance,
>
> venkateswaran
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of
> Gwenaëlle DOUAUD
> Sent: Thu 9/17/2009 11:43 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Re : [FSL] FSL-VBM GM template creation
> problem
>
> Hi,
>
> > This time it worked the template 4D_GM image was
> created
>
> Great
>
> > 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.
>
> One is the segmented image of GM, the other the segmented
> image of the csf.
>
> > 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.
>
> The concatenation will follow the order given to you by the
> ls
>
> > One last question TFCE is recommended i would like to
> see
> > voxelwise results instead of clusters how can i do
> this.
>
> TFCE is giving voxel-wise results.
>
> Cheers,
> Gwenaelle
>
>
>
>
>
>
> ===================================
>
> 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 <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
> its entirety, whether electronic or hard copy. Thank
> you.
>
===================================
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
its entirety, whether electronic or hard copy. Thank you.
|