Hi Steve ,
two more questions:
1. please correct me if I am wrong: if my t1_stdmask_pve1.nii.gz
looks fine but the t1_stdmask_pve_1_segperiph has some cortical
omissions ( seen also in t1_periph_render) this means that the
segmentation is correct and cannot be improved further ( with Fast),
but there is a masking problem when we pass from grey to peripheral
grey to get the cortical volume only?
2. the output of Sienax called t1_stdmask_segvent and
t1_stdmask_segperiph come out as completely empty. Does this
indicate any error of some kind?
thanks a lot for all the help,
Paul
At 01:01 AM 10/23/2006, you wrote:
>You can certainly tune the FAST options - if you put these after -S
>at the end of the sienax command then when SIENAX calls FAST these
>get passed on.
>
>To get the FAST options type
>fast -h
>
>Cheers, Steve.
>
>
>On 22 Oct 2006, at 22:24, Paul Geha wrote:
>
>>thank you Steve,
>>
>>so yes the question is : can I use FAST to improve the output of
>>Sienax?
>>
>>Paul
>>
>>
>>==============Original message text===============
>>On Sun, 22 Oct 2006 1:32:24 am CST Steve Smith wrote:
>>
>>Hi - I'm not sure if you're saying that you'd like to improve the
>>segmentation output by FAST or the effect of the cortical masking
>>carried out by affine-transforming a simple cortical standard space
>>mask onto the data - it sounds like it may be the latter, in which
>>case you might want to use your own version of $FSLDIR/etc/standard/
>>avg152T1_strucseg_periph - or it may simply be that your subject is
>>too different from the MNI152 for a purely affine transformation to
>>give you a good match of the mask, in which case SIENAX can't help
>>you there!
>>
>>Hope this helps - cheers, Steve.
>>
>>
>>On 21 Oct 2006, at 17:57, Paul Geha wrote:
>>
>>>Hello,
>>>
>>>I am trying to do a cortical volume quantification using Sienax on
>>>t1 images. When I run it I get
>>>the output called t1_periph_render. This one shows that there are
>>>some small areas in the
>>>fusiform gyrus, and the orbito-frontal cortex. I tried to
>>>increase the number of iteration with
>>>the S option (to 15) in Sienax to improve this but this did not
>>>work. However, if I run FAST on
>>>the t1 image with the "use a priori probability maps for
>>>initialising" I get a better peripheral
>>>gray matter mask in t1_brain_seg1 image with no omissions, but
>>>this one includes the sub-cortical
>>>structures and the cerebellum, which I want to exclude.
>>>
>>>Can I improve Sienax segmentation in anyway? Please advise.
>>>
>>>thanks a lot,
>>>
>>>Paul
>>>
>>>Paul Geha M.D.
>>>Northwestern University
>>>The Feinberg School of Medicine
>>>Department of Physiology M211
>>>303 E. Chicago Ave.
>>>Chicago, IL 60611
>>>Tel:312-503 2886
>>>Fax: 312-503-5101
>>
>>
>>---------------------------------------------------------------------- --
>>---
>>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---------------------------------------------------------------- --------
>>---
>>
>>===========End of original message text===========
>>
>>
>>
>>Paul Geha M.D.
>>Northwestern University
>>The Feinberg School of Medicine
>>Department of Physiology M211
>>303 E. Chicago Ave.
>>Chicago, IL 60611
>>Tel:312-503 2886
>>Fax: 312-503-5101
>
>
>------------------------------------------------------------------------ ---
>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
>------------------------------------------------------------------------ ---
Paul Geha M.D.
Northwestern University
The Feinberg School of Medicine
Department of Physiology M211
303 E. Chicago Ave.
Chicago, IL 60611
Tel:312-503 2886
Fax: 312-503-5101
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