Thanks a lot, Wolf, for chiming in!
Best,
Jochen
On 4/6/2010 2:47 AM, wolf zinke wrote:
> Hi Jochen,
>
> I had the same problem that in genral the segementation was doing fine,
> but in part, especially in occipital regions, the results haven't been
> convincing. I manually added missing brains voxel with the Segmentation
> Volume Editor ('Turn Voxels on') in the *GraphErroCorrected file.
>
> Another Different step in my procedure was a proper brain extraction
> prior segmentation. Here, automatic methods such as FSL's Bet might
> help, but again do not give satisfying results on macaque data. So The
> extraction was done again manually, making sure to remove voxels
> belonging to the dura and surface blood vessels (especially the central
> sinus).
>
> In the end I got results I could live with, but it was a time consuming
> work.
>
> I hope this helps,
> wolf
>
>
> On 04/05/2010 11:28 PM, Jochen Ditterich wrote:
>> 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
>>>> [email protected]
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
>>> _______________________________________________
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>
>
>
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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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