Hi Steve,
you were right, it is only a display range issue. Sorry for that!
thanks a lot
Paul
At 03:49 AM 10/25/2006, you wrote:
>Hi,
>
>
>On 23 Oct 2006, at 18:12, Paul Geha wrote:
>
>>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?
>
>Exactly.
>
>>
>>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?
>
>Are you sure - it may just be a display range issue in FSLView?
>
>Cheers.
>
>
>>
>>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
>
>
>------------------------------------------------------------------------ ---
>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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