Thanks a lot, Donna! It looks like I have to take it from there and add
the occipital lobe manually (or try another bias correction algorithm
like FSL's)...
Best,
Jochen
On 4/6/2010 11:17 AM, Donna Dierker wrote:
> Jochen,
>
> I tried segmenting the bias corrected left hem, and didn't seem to have
> trouble with the temporal lobes, although the occipital lobe seemed to
> be thresholding out. The low threshold hindbrain option didn't appear to
> help (but was worth trying).
>
> Attached are some captures:
>
> * histogram.jpg shows where I put the peaks, based on the limitations of
> the data
> * GM190_WM215.jpg shows the result at those peaks -- temporal lobes
> there, occipital lobe missing
> * run_surefit.jpg shows settings to use until peak tweaking gives decent
> segmentation
>
> There's no sense wasting CPU time patching handles on a lousy segmentation.
>
> Donna
>
> On 04/06/2010 12:41 PM, Jochen Ditterich wrote:
>> 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
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>>>>>> 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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