[caret-users] problem with border file

Wed Jun 11 10:11:02 CDT 2008

Hi Donna

I've just uploaded the directory with my data.
The name of the zipped directory is "SofiaCrespi_BorderProblem_forDonna.zip"
I'll wait fur further suggestions tomorrow
thank you

Sofia

----- Original Message ----- 
From: "Donna Dierker" <donna at brainvis.wustl.edu>
To: "Caret, SureFit, and SuMS software users" 
<caret-users at brainvis.wustl.edu>
Sent: Wednesday, June 11, 2008 3:06 PM
Subject: Re: [caret-users] problem with border file

> Hi Sofia,
>
> See inline replies below.
>
> Donna
>
> On 06/11/2008 06:45 AM, Sofia Crespi wrote:
>> Dear Donna
>> unfortunately the  borders  checkbox is selected on the D/C:
>> Overlay/Underlay -
>> Surface menu .
>>
> So much for the quick fix....
>> When I select the Border Page on the D/C I can see tha name of the new
>> borders in the color section but not in the name section..
>> I guess this is the problem.....
>>
> This is informative:  It suggests that the border colors are fine
> (unless the color is transparent, which I doubt), but that the border
> didn't load or was empty.
>
> If you saved your border, relative to the FLAT map (i.e., with the FLAT
> map in the main window or the FLAT map selected in the Save Data File:
> Border surface file dialog), then this should not happen with you
> relaunch Caret and select this border file.
>
> Can you upload your data directory (if less than a Gigabyte zipped) here:
>
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> I want to look at the border file in particular, but other files might 
> also offer clues.
>
>> the next time I'll try to design the border and save the resulting
>>  borderproj files but what you mean with "we project borders after 
>> drawing
>> them ?"
>>
> More recent Caret versions have the radio button "Auto Project" (no by
> default); we usually change this to Yes, because then then the border
> will automatically project as soon as you draw it.  If Auto Project is
> set to No, you can manually project by selecting Layers: Borders:
> Project Borders (or Project Fiducial Borders on older versions).
>
> The "projection" process takes each border point and attaches it to the
> closest surface tile.  This is why you can view projected borders on
> multiple surface configurations (fiducial, flat, inflated).  When you
> save a borderproj file, you're saving the border as attached to the
> nearest tile; when you save as border, there is no surface allegiance;
> the points are floating in 2D or 3D space -- perhaps close to the
> surface, perhaps not (kind of like foci in that respect).
>
> I don't think your trouble with the border saving/reloading is due to
> your not projecting; the cause remains elusive.
>> thank you
>> Sofia
>>
>> ----- Original Message ----- 
>> From: "Donna Dierker" <donna at brainvis.wustl.edu>
>> To: "Caret, SureFit, and SuMS software users"
>> <caret-users at brainvis.wustl.edu>
>> Sent: Tuesday, June 10, 2008 2:55 PM
>> Subject: Re: [caret-users] problem with border file
>>
>>
>>
>>> Hi Sofia,
>>>
>>> See inline replies below.
>>>
>>> Donna
>>>
>>> On 06/10/2008 06:18 AM, Sofia Crespi wrote:
>>>
>>>> Hi I have a question.
>>>> I've designed some closed border on my flat surface in order to use
>>>> them for surface region of interest operation.
>>>> More precisely I've daone these operations:
>>>> 1.Layers---->Borders---->draw Borders
>>>> 2. I've selected a new name, closed boundaries and 2D,
>>>>     in the closed border assignement frame-----> Voxels I've selected
>>>> Assign voxels within closed borders and +/-1 for the thickness.
>>>> 3. I've choosed a color and designed my border on the flat map.
>>>> 4.Then I saved the file with a new name as: border file Surface,
>>>> border file Volume, Border color file.
>>>>
>>>> Now I'm able to see the border and if I select the Border Page in the
>>>> Dispaly control dialog I can find the name and the color of my new
>>>> border. Now I close caret.
>>>> If I open caret again and load my spec file, loading also the new
>>>> border file already created I cannot display the new border on the
>>>> flat map...
>>>> why?
>>>>
>>> If both the border file Surface and border color files that you saved in
>>> step 4 above were selected when you loaded the spec file, then the only
>>> other reason I can imagine that you don't see the border on your flat
>>> map is that borders are not selected on the D/C: Overlay/Underlay -
>>> Surface menu (scroll all the way to the bottom, until you see a borders
>>> checkbox); see attached capture, which shows the Borders checkbox
>>> toggled on at the bottom of the D/C: Overlay/Underlay - Surface page.
>>>
>>> Depending on which Caret version you have, this checkbox may or may not
>>> be on by default when you load a spec with borders selected.
>>>
>>>> I opened the border file Surface just created....
>>>> all the other border file come out as *appended* (why since are
>>>> different file????) the last one is not appended and I cannot see that
>>>> border....
>>>>
>>> This is not clear to me.  Perhaps if you uploaded your dataset, I could
>>> decipher what you mean.
>>>
>>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>
>>> It sounds like one or more of the following possibilities might
>>> contribute to the confusion:
>>>
>>> 1. You have multiple border files loaded, which may have borders that
>>> intersect/duplicate with one another.
>>> 2. When you couldn't see the border upon opening, you tried loading
>>> again, resulting in the same borders being loaded twice.
>>>
>>> I hope this is just a case of the borders not being turned on when you
>>> relaunch Caret.
>>>
>>>> Please have a look to the doc fiel attached:
>>>>
>>> No doc file was attached.
>>>
>>>> in yellow I've underlined all the attached file...:
>>>> *1* *why the same file "V6 border color " is appended more than 1 
>>>> time?*
>>>>
>>> Something similar to possibilities 1 and 2 occurred wth the bordercolor
>>> file.
>>>
>>>> *2. the appended file LO-MST-MT is refereed to 3 border That I'm not
>>>> able to disply any more..*
>>>>
>>> I don't understand this question, but I hope the display problem is
>>> resolved by the D/C checkbox.
>>>
>>>> *3 the new border V6NEW does not result as appended ??*
>>>>
>>> Perhaps it was added after the last save?  I can't think of another
>>> plausible explanation.
>>>
>>>> where is my error?
>>>>
>>> Let's hope the D/C checkbox resolves 90% of your issues.
>>>
>>>> can you help me?
>>>>
>>> Typically, we project borders after drawing them and save the resulting
>>> borderproj files.  This allows you to view the borders on multiple
>>> surfaces (e.g., fiducial, inflated).  There are definitely contexts in
>>> which border files have distinct advantages, however (e.g., when viewing
>>> on surfaces of different mesh / number of nodes than the drawing
>>> substrate; when using the 2D/3D coordinates for an outside application).
>>>
>>> But you clearly state above you are trying to view your borders on the
>>> flat map, which is the same surface used for the drawing substrate.
>>> Thus, I conclude that this is probably a D/C checkbox not selected 
>>> issue.
>>>
>>>> Thank you in advance
>>>>
>>>> Sofia Crespi
>>>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>>
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
>>
>>
>>
>> ********************************************************************
>> Sostieni la ricerca del San Raffaele con il 5permille!
>> E' SEMPLICE E NON COSTA NULLA.
>> Basta indicare nell'apposito riquadro della dichiarazione dei
>> redditi ("Finanziamento agli enti della ricerca sanitaria")
>> il codice fiscale della
>> Fondazione Centro S. Raffaele del Monte Tabor:
>> 03 06 42 80 153 e ricordarsi di firmare.
>> Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
>> www.5xmille.org
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users 

********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Finanziamento agli enti della ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
www.5xmille.org