Dear Gwenaelle,
Thanks for your quick response.
It looks like it might be a discrepancy between the names in your template list file (if you've got one) and the subjects in your directory. Are you sure that control_012.nii.gz is both in your template list file and your struc directory? It would also explain why it would run on your small subsample with no manual editing (as I presume either you didn't have a template list file for this sub-analysis or you had one that is correct)...
In my template list the names appear like this "control_003.nii.gz" whereas in struc list the files i have for this same control subject are "control_003_struc.nii.gz" and "control_003_struc_brain.nii.gz". As mentioned in the documentation page i created the template first and then ran BET, after BET it created these two files in the struc directory "control_003_struc.nii.gz" and "control_003_struc_brain.nii.gz". So i just manually removed some non-brain regions and replaced the control_003_struc_brain.nii.gz. 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.
I am attaching a a JPEG image of the print screen version of GM and WM pve PLACED SIDE BY SIDE.
Thanks a lot again,
venkateswaran
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Tue 9/15/2009 12:40 PM
To: [log in to unmask]
Subject: Re: [FSL] Re : [FSL] FSL-VBM GM template creation problem
Hi again,
> Answer :There is nothing inside the the files "fslvbm2a.e"
> and "fslvbm2b.e". whereas under "fslvbm2c.e" the following
> error was reported
>
>
> ** ERROR (nifti_image_read): failed to find header file for
> 'control_012_struc_GM_to_T'
> ** ERROR: nifti_image_open(control_012_struc_GM_to_T): bad
> header info
It looks like it might be a discrepancy between the names in your template list file (if you've got one) and the subjects in your directory. Are you sure that control_012.nii.gz is both in your template list file and your struc directory? It would also explain why it would run on your small subsample with no manual editing (as I presume either you didn't have a template list file for this sub-analysis or you had one that is correct)...
> There
> are two more things which i would like to clarify, even if i
> manually edit the clearly identifiable non-brain regions, in
> some cases there are some non-brain regions which are too
> close to the brain structures which is difficult to clean
> manually, i am wondering how is this taken care of because i
> don't know whether these regions will give significant
> difference on the statistical results.
This should be fine after FAST. A bit of non-brain voxels is a far better situation than some brain voxels missing, always try to be under-conservative with bet in FSL-VBM...
> One more
> clarification when i look at the PV maps of GM after FAST
> why are the PV values in ventricles are 1.
This is really odd. Could you please send me a snapshot of one of your _struc_GM.nii.gz?
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 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.
|