Hi Donna,
I've uploaded my preborder script onto the link you provided me.
I do have the lines in my preborder script:
# Sync source border names with target
sed 's/Medial/Med/g' $BORDERPROJ_IN > $BORDERPROJ_IN.rev
mv $BORDERPROJ_IN.rev $BORDERPROJ_IN
Regards
Kwliu
________________________________________
From: [email protected]
[[email protected]] on behalf of Donna Dierker
[[email protected]]
Sent: 10 August 2010 20:25
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Postborder.sh problem
Kwliu,
I figured out what is causing the problem. Your borderproj has these
landmarks:
10 62 LANDMARK.MedialWall.DORSAL 25.000000 1.000000 0.000000 0.000000
11 39 LANDMARK.MedialWall.VENTRAL 25.000000 1.000000 0.000000 0.000000
But the target borders are named LANDMARK.MedWall.DORSAL and
LANDMARK.MedWall.VENTRAL. There is a step in the preborder.sh script,
in the loop that does the border variability, that fixes this inconsistency:
# Sync source border names with target
sed 's/Medial/Med/g' $BORDERPROJ_IN > $BORDERPROJ_IN.rev
mv $BORDERPROJ_IN.rev $BORDERPROJ_IN
Does your preborder.sh script have those lines in it? I'm wondering if
you are using an older version of preborder.sh, or if you somehow had
the border variability loop disabled.
Dpmma
On 08/10/2010 11:00 AM, Donna Dierker wrote:
> Hmmm. Then I have a hunch what might have happened. Please upload
> your postborder.sh script here:
>
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> Do *not* email it.
>
> On 08/10/2010 10:22 AM, Kuk Wai Liu wrote:
>> Hi Donna,
>>
>> Sorry i was mistaken about there not being a LANDMARK.MedWall.VENTRAL
>> that was missing from the Human.003.L.LANDMARKS.updated.borderproj.
>> I've just taken another look inside the
>> Human.003.L.LANDMARKS.updated.borderproj file and there is a
>> LANDMARK.MedWall.VENTRAL border.
>>
>> I've attached the file with this email.
>>
>> I apologise for my earlier email and for the time you spent analysing
>> it.
>>
>> Regards
>>
>> Kwliu
>> ________________________________________
>> From: Kuk Wai Liu
>> Sent: 10 August 2010 16:15
>> To: Caret, SureFit, and SuMS software users
>> Subject: RE: [caret-users] Postborder.sh problem
>>
>> ________________________________________
>> From: [email protected]
>> [[email protected]] on behalf of Donna Dierker
>> [[email protected]]
>> Sent: 10 August 2010 15:20
>> To: Caret, SureFit, and SuMS software users
>> Subject: Re: [caret-users] Postborder.sh problem
>>
>> So, we know that Human.003.L.LANDMARKS.borderproj did have a medial wall
>> ventral border, but Human.003.L.LANDMARKS.updated.borderproj, for some
>> reason, did not. (The difference in the filenames is the string
>> "updated." preceding borderproj.)
>>
>> Here is a relevant excerpt from the README.txt:
>>
>>
>>> If any borders do need correction, use Caret's Layers: Border: Border
>>> Update. When the borders are good, use File: Save Data File:
>>> borderproj and
>>> overwrite the borderproj named like *.updated.borderproj. (The
>>> auto-landmarks routine copies Human.SAIS_001.L.LANDMARKS.borderproj to
>>> Human.SAIS_001.L.LANDMARKS.updated.borderproj, so until the borders
>>> are updated, these files are identical. The postborder.sh script uses
>>> the *.updated.borderproj files for registration.)
>>>
>>
>> This suggests that somehow the medial wall ventral border got deleted
>> during the manual border update process.
>>
>> You can cd 003/surf and launch Caret, opening the left hem spec file and
>> loading scenes.
>>
>> Redo the tweaks, taking care not to delete the medial wall ventral
>> border. Save as Human.003.L.LANDMARKS.updated.borderproj.
>>
>> Re-run postborder.sh on just that subject (i.e., edit subject list to
>> include just 003).
>>
>> I can't think of a more straightforward way of doing it.
>>
>> If you spent a ton of time tweaking the borders in
>> Human.003.L.LANDMARKS.updated.borderproj, and don't want to have to
>> repeat those edits, then there are ways of salvaging them. But I'm
>> guessing that is not likely.
>>
>> On 08/10/2010 06:29 AM, Kuk Wai Liu wrote:
>>
>>> Hi Donna,
>>>
>>> It appears that you are correct about the LANDMARK.MedWall.VENTRAL
>>> that is missing from the Human.003.L.LANDMARKS.updated.borderproj.
>>> What would i need to do to generate one?
>>>
>>> There does appear to be a medial wall ventral border capture in the
>>> html directory.
>>>
>>> I've attached the images i've obtained for one subject (including
>>> both left and right hemispheres) after running the preborder script.
>>>
>>> Regards
>>>
>>> Kwliu
>>> ________________________________________
>>> From: [email protected]
>>> [[email protected]] on behalf of Donna Dierker
>>> [[email protected]]
>>> Sent: 09 August 2010 16:48
>>> To: Caret, SureFit, and SuMS software users
>>> Subject: Re: [caret-users] Postborder.sh problem
>>>
>>> Kwliu,
>>>
>>> It appears that Human.003.L.LANDMARKS.updated.borderproj is missing
>>> LANDMARK.MedWall.VENTRAL, which causes all the downstream trouble.
>>>
>>> It is possible that the auto-landmark algorithm had trouble
>>> identifying this landmark (although in our experience this is
>>> rare). Or it is possible that it got deleted during tweaking.
>>>
>>> Or redrawn using the border name ATLAS_LANDMARK.MedWall.VENTRAL
>>> instead of just LANDMARK.MedWall.VENTRAL. (All borders named like
>>> "ATLAS_*" get deleted by the postborder.sh script. They are useful
>>> for showing where the target borders lie, though.)
>>>
>>> Did the captures generated by preborder.sh (in the HTMLDIR) show a
>>> medial wall ventral border?
>>>
>>> Donna
>>>
>>>
>>> On 08/09/2010 06:18 AM, Kuk Wai Liu wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> Thanks for your help on the preborder.sh problem. Having run the
>>>> preborder.sh command successfully without errors, i've now got errors
>>>> in the postborder.sh command, could you help me out please? My output
>>>> is attached with this email.
>>>>
>>>> Regards
>>>>
>>>> Kwliu
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