[caret-users] Problem segmenting macaque brain

Jochen Ditterich jd at shadlen.org
Mon Apr 5 16:28:53 CDT 2010


Thank you, Donna!

I have uploaded a bias-corrected version named 
"freckles_bias_corrected.zip" (using BrainSuite's BFC algorithm). After 
adjusting the peaks, the segmentation runs through, but the 
posteriormost parts of the cortex are always missing. I have tried a 
manual correction of the segmentation volume, but, while I am able to 
remove unwanted parts from the fiducial surface, I am apparently unable 
to add missing parts. Is this possible? If so, is there a special step 
involved other than selecting "Segmentation Volume Post Processing" and 
the manually corrected segmentation volume?

In case it is not possible to add missing parts using a manual 
correction of the segmentation volume, is there anything else I can do? 
Shifting the grey matter peak in the appropriate direction for including 
the missing voxels makes the segmentation process fail.

Best,

Jochen

On 4/5/2010 8:12 AM, Donna Dierker wrote:
> Hi Jochen,
>
> I think your biggest problem was that your peaks were set too low.
>
> The MRI quality is not the best, and perhaps some nonuniformity
> correction (e.g., FSL's fast) might improve your result further. But
> your GM peak was set way too low. You histogram is somewhat misleading
> (capture attached). If you set it at the peaks, the way you did, the
> GMpeak will be way too low. See
> http://brainvis.wustl.edu/help/peak_tweaking for more help on peaks.
>
> Try GMpeak=190, WMpeak=230 and see how you do. My results looked
> reasonable (reasonable.jpg). In my case, though, the graph error
> correction method cut off a lateral slab. Turning it off should restore
> sanity (if not a few pesky handles).
>
> There were two issues with stereotactical_coord_AC_R.hdr:
>
> * The name suggests right hem, but the hem appeared to be a left hem
> (left-right flipped?).
>
> * It was not centered near the AC, so the origin would need to be re-set
> before you could hope to get any decent segmentation.
>
> Donna
>
> On 04/02/2010 01:20 PM, Jochen Ditterich wrote:
>> Hi Donna and John,
>>
>> I am trying to segment a macaque brain and to flatten the cortex, but
>> I haven't been able to make it through the segmentation process
>> without error messages. I am not sure whether this is due to quality
>> issues with the MRI or whether it has something to do with the
>> implanted recording chambers. I have uploaded a file named
>> "freckles.zip" that contains both the uncropped volume as well as the
>> cropped volumes for the two hemispheres. Any feedback would be
>> appreciated. Does anybody have experience segmenting MRIs taken from
>> animals with implants?
>>
>> Thanks a lot,
>>
>> Jochen
>>
>> -------------------------
>>
>> Jochen Ditterich, Ph.D.
>> Assistant Professor
>> Center for Neuroscience
>> University of California
>> 1544 Newton Court
>> Davis, CA 95618
>> USA
>>
>> office: +1 (530) 754-5084
>> lab: +1 (530) 754-6987
>> fax: +1 (530) 757-8827
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
>
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-- 

-------------------------

Jochen Ditterich, Ph.D.
Assistant Professor
Center for Neuroscience
University of California
1544 Newton Court
Davis, CA 95618
USA

office: +1 (530) 754-5084
lab:    +1 (530) 754-6987
fax:    +1 (530) 757-8827



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