[caret-users] problem with border file

Thu Jun 12 08:47:51 CDT 2008

Dear Donna
Thank you very very much..
I've understand and fixed all the problems!
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 5:46 PM
Subject: Re: [caret-users] problem with border file

> Hi Sofia,
>
> I looked at your dataset, and all these flat border files show borders
> on my end:
>
> Human.intsac4.LR.border_file_33.2008-04-22_V1-V2-V3-V3a.border
> Human.intsac4.LR.border_file_33.2008-04-22_V6NEW.border
> Human.intsac4.L.border_file_102.2008-02-21_LO-MT-MST.border
> Human.intsac4.L.border_file_102.2008-02-21_LIP.border
> Human.intsac4.L.border_file_102.2008-02-21_VIP.border
> Human.intsac4.L.border_file_102.2008-02-21_V6.border
> Human.intsac4.L.border_file_102.2008-02-21_VHMer.border
>
> But this one does not:
>
> Human.intsac4.L.border_file_102.2008-02-21_V6NEW.border
>
> If you cat that file, it confirms there are no border points:
>
> BeginHeader
> caret-version 5.51
> comment V6 left: -17,-83,35     V6 center: -5,-76,32    V6 right: fuoco
> alto -3,-8,23, fuoco basso -4,-85,30    selezionate su RGB,
> EmicampoIpsi-Contro, EmicampoUp-Down , Eyepos F2S0 ipsilaterale
> configuration_id VOLUME
> date mar 10. giu 12:42:40 2008
> encoding ASCII
> pubmed_id
> EndHeader
> 0
>
> The configuration_id VOLUME suggests you saved this as a VOLUME border
> file -- after first saving as a FLAT border file using the same
> filename.  (The fact that the same filename is listed in the spec file
> under both FLAT and VOLUME border files is the clue.)
>
> Per John Harwell, this won't work:  If you draw on the FLAT map, you
> have to first project the borders (in effect to convert flat 2D to 3D
> coordinates).  Even then I'm not sure saving as a VOLUME border file
> would work, but it's worth a try.
>
> Either way, use distinct filenames for FLAT and VOLUME borders, since
> those coordinates won't match.
>
> Also, if you were not already aware of it, the Surface: ROI menu allows
> you to threshold anatomical (shape) and/or functional (metric) maps and
> have Cared automatically draw a border around the resulting cluster.
> Perhaps not useful now, but in the future....
>
> Donna
>
> On 06/11/2008 10:11 AM, Sofia Crespi wrote:
>> 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
>>>>>
>>>>>
>>>>>
>>>>
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>> redditi ("Finanziamento agli enti della ricerca sanitaria")
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>> Fondazione Centro S. Raffaele del Monte Tabor:
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********************************************************************
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