Mellanie,
It may have had trouble finding your SEGMENTATION/*RadialPositionMap*mnc
file.
Try starting SureFit like this:
SureFit >& session.txt
Load your volumes and try running error correction. After it finishes
(but doesn't append '_corr' to the filename), then exit SureFit (to
close the session.txt file for output). Then upload session.txt here:
http://brainvis.wustl.edu/cgi-bin/upload.cgi
It will tell me whether that was the problem. If this is the problem,
then make sure you have a file named like *RadialPositionMap*mnc in the
same directory as your segmentation.
Donna
On 07/22/2004 02:34 PM, Marc Malloy wrote:
>Hi Donna,
>
>I reran the error correction with the segmented volume loaded in Volume 2.
>There are still 9 cavities and 1 segmentation object and the 1 remaining
>error was not corrected. In fact, the automatic error correction did not
>appear to correct any errors since '_corr' was not appended to the
file name
>and even the object list remained the same. Why didn't error correction
>occur?
>
>Also, what is the difference between a cavity and a handle? Which of
these
>errors is worse?
>
>-Mellanie
>
>----- Original Message -----
>From: "Donna Hanlon" <[EMAIL PROTECTED]>
>To: "Caret, SureFit, and SuMS software users"
><[EMAIL PROTECTED]>
>Sent: Tuesday, July 20, 2004 2:26 PM
>Subject: Re: [caret-users] (no subject)
>
>
>
>
>>Hi Mellanie,
>>
>>Your segmentation has nine cavities and after moving the crosshairs well
>>within the red part of the segmentation and floodfilling, update handle
>>count reports 4 handles.
>>
>>So, I'd recommend re-running automatic error correction in your case.
>> It may fill the cavities and will definitely make sure you don't have
>>multiple segmentation objects. It might even fix some handles
>>introduced by patching. At the very least, you'll get an updated Locate
>>Objects listing.
>>
>>One other thing I forgot to mention the last time around: The -x
>>checkbox on the cropping tab should not have been checked. These volume
>>are named like "*_pad*", which means padding has been added along the
>>cut face. Cropping the contralateral hemisphere isn't considered a cut
>>face; full hemispheres (like this one) should have no cut face boxes
>>checked.
>>
>>I'm not sure what trouble this might cause in caret, but SureFit
>>probably won't copy border files to your SURFACES directory. This is
>>less important now that caret5 has template borders of its own.
>>
>>Donna
>>
>>On 07/20/2004 01:10 PM, [EMAIL PROTECTED] wrote:
>>
>>
>>
>>>Hi Donna,
>>>
>>>I have uploaded the segmentation file:
>>>
>>>nov16_2002A.R.full.segment_pad_vent_corr.patchtest17.mnc
>>>
>>>The sMRI.mnc file has not changed.
>>>
>>>Thanks,
>>>
>>>Mellanie
>>>
>>>
>>>
>>>Quoting Donna Hanlon <[EMAIL PROTECTED]>:
>>>
>>>
>>>
>>>
>>>
>>>>Hi Mellanie,
>>>>
>>>>Great news, and I sure needed right now (lots of system problems this
>>>>week).
>>>>
>>>>Go ahead and upload your segmentation volume here:
>>>>
>>>>http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>>
>>>>If your sMRI.mnc or .params changed from before, also upload those
>>>>
>>>>
>volumes.
>
>
>>>>It isn't unusual to have a handle so tiny you can't see it on the
>>>>surface and can't see any crossovers when you bring it into caret.
>>>>Handles like that almost never cause trouble during flattening or
>>>>registration. But I'll make sure this handle falls into that category.
>>>>
>>>>Donna
>>>>
>>>>On 07/20/2004 12:14 PM, [EMAIL PROTECTED] wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Hi Donna,
>>>>>
>>>>>Thanks to your great advice there is only 1 handle left on the
surface.
>>>>>However, I am having some difficulty finding where the error lies.
>>>>>
>>>>>
>Would
>
>
>>>>>
>>>>>
>>>>you
>>>>
>>>>
>>>>
>>>>
>>>>>be able to please take a look at the image to see whether you can
>>>>>
>>>>>
>provide me
>
>
>>>>>with some clues about the location of the offending voxels?
>>>>>
>>>>>Thanks,
>>>>>
>>>>>Mellanie
>>>>>_______________________________________________
>>>>>caret-users mailing list
>>>>>[EMAIL PROTECTED]
>>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>_______________________________________________
>>>>caret-users mailing list
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>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>
>>>>
>>>>
>>>>
>>>>
>>>_______________________________________________
>>>caret-users mailing list
>>>[EMAIL PROTECTED]
>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
>>>
>>>
>>>
>>_______________________________________________
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>>
>>
>>
>>
>
>
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