Hi - we don't normally recommend downsampling/resampling data before
running segmentation - however 1mm is still pretty good so that's not
too bad. However I suspect that maybe your data was only actually
acquired at lower resolution than 0.5mm in the first place, and
upsampled on the scanner - so a much better solution would be to get
the non-resampled data from your scanner if that's the case. It would
also be a good idea to try to get more RAM and swap for your computer,
and make sure you're using a 64-bit OS and 64-bit version of FSL.
Cheers.
On 8 Sep 2009, at 14:48, Rajagopalan, Venkateswaran wrote:
> Thanks very much Dr.Steve for your kind help. One more question i
> would like to ask, i am using VBM for structural image studies, our
> MPRAGE T1-W sequence has a dimension of 512*512 and 1 mm thick
> slices, my computer has only 2GB RAM so this becomes problem in case
> of FAST (FAST runs out of memory) and once i was using FNIRT on this
> data for some other purpose and it also had memory problems. Is it
> advisable to resample my 0.5*0.5*1 mm images to lower resolution,
> will this affect tissue segmentation (FAST) and eventually the VBM
> results. Any input regarding this is greatly appreciated.
>
> Thanks again
>
> venkateswaran
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Steve Smith
> Sent: Sat 9/5/2009 2:02 AM
> To: [log in to unmask]
> Subject: Re: [FSL] template list creation in FSL VBM
>
> Hi - I guess you're not using bash or sh as your shell, so this syntax
> would be wrong?
>
> You can just create this text file by hand using any text editor, or
> even just
>
> ls -1 CON_04.nii.gz CON_08.nii.gz CON_10.nii.gz CON_13.nii.gz
> CON_19.nii.gz PAT_02.nii.gz PAT_05.nii.gz PAT_11.nii.gz PAT_18.nii.gz
> PAT_19.nii.gz > template_list
>
> Cheers
>
>
>
>
> On 4 Sep 2009, at 22:48, Rajagopalan, Venkateswaran wrote:
>
>>
>> Dear FSL Users,
>>
>> I am new to Linux OS. I tried the following
>>
>> "for g in CON_04.nii.gz CON_08.nii.gz CON_10.nii.gz CON_13.nii.gz
>> CON_19.nii.gz \
>> PAT_02.nii.gz PAT_05.nii.gz PAT_11.nii.gz PAT_18.nii.gz
>> PAT_19.nii.gz; do
>> echo $g >> template_list
>> done"
>>
>> to create a template list of my data set as described in FSL_VBM
>> documentation page. I typed this in the terminal window and it gives
>> me the following error "g undefined variable "for" command not
>> found. I don't have much programming experience too. Can you pleas
>> tell me the mistake i am making here.
>>
>> Thanks
>>
>> venkat
>>
>>
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>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
> ===================================
>
> 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
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> its entirety, whether electronic or hard copy. Thank you.
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---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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