[caret-users] Does "?" mean a broken font in the identify window?
Yune S. Lee
yune-sang.lee at dartmouth.edu
Mon Apr 13 10:56:49 CDT 2009
Thanks a lot for your great help, Donna!!
Your answer is very helpful. :-)
Have a good week,
YSL
Donna Dierker wrote:
> Hi YSL,
>
> Unfortunately, the bold font weight doesn't display in my email reply,
> because I've got my email client set to text only, rather than HTML.
> (And I'm not going to change it -- not even for you, YSL.;-)
>
> But here is what I meant by BOLD:
>
> http://brainmap.wustl.edu/pub/donna/ETC/bold_not_bold.html
> login pub
> password download
>
> The bold font just has heavier weighting; it is thicker.
>
> If you want to pinpoint the anatomic region of activation, then there
> are many ways to do this. Some use AAL in MRIcron. Some use the
> Harvard Oxford Atlas in FSL or Freesurfer. And some use PALS, as you
> are trying to do. Here are the paint/parcellation/label columns in the
> Human.PALS_B12.BOTH.COMPOSITE_Areas_Functional_WS.73730.paint paint file:
>
> Lobes (PALS atlas)
> Geography - Colin RIGHT on PALS-B12
> AVERAGE-MED-WALL B1-12 RIGHT
> AVERAGE-MED-WALL B1-12 LEFT
> Visuotopic - BOTH (from colin RIGHT) - PALS-B12
> Brodmann - BOTH (from colin RIGHT) - PALS-B12
> OrbitoFrontal BOTH - PALS-B12 (from case Fb LEFT)
> Visuotopic + OrbitoFrontal - RIGHT - PALS-B12
> Modalities - RIGHT - PALS-B12
> Modalities - LEFT - PALS-B12
> Clusters - Left-right depth asymmetries (Cases B1-24, paired
> Williams Syndrome folding abnormalities (RIGHT) - PALS-B12
> Williams Syndrome folding abnormalities (LEFT) - PALS-B12
> Sulcal ID - Colin RIGHT on PALS-B12
> Geography - Colin LEFT on PALS-B12
> Sulcal ID - Colin LEFT on PALS-B12
>
> Both the Brodmann and Sulcal ID colums are good general use columns.
> But if your activation is in the visuotopic or orbitofrontal regions,
> then those columns are likely to give you greater specificity.
>
> For some regions, there are probabilistic atlases for the anatomical
> regions mapped by the Amunts/Zilles et. al. See
> PALS_B12.BOTH-HEMS.DEMO.73730.spec, scene 10. There are many different
> columns in the probabilistic atlas metric file loaded in that scene.
>
> Finally, if you are getting overwhelmed by too many columns in a paint
> or metric file, then you can try:
>
> Toolbar: spec: paint: open desired paint file
> select "Erase all existing columns"
> press Set All Columns to Do Not Load
> For the single column or two of interest, change Do Not Load to Create
> New Column
>
> This will load just the column of interest, and thereby cut way back the
> amount of output you get when you click on nodes.
>
> Donna
>
> On 04/13/2009 09:16 AM, Yune S. Lee wrote:
>
>> Hello Donna,
>> Many thanks for your answer and it did help me understanding on the
>> previous question.
>> But below are the parts that I wasn't clear.
>>
>> Paint: LOBE.PARIETAL GYRUS ??? ???????? ??? Brodmann.4 ??? ???
>> COGNITIVE COGNITIVE minus_cluster_area_424.611_nodes_569 ??? ??? ???
>> GYRUS ???
>>
>> The paint name associated with the currently selected paint column is
>> printed in BOLD, while the paint names associated with all other columns
>> are not in bold.
>> -> what do you mean by 'BOLD'? you mean the words with captial such as
>> LOBE.PARIETAL GYRUS?
>> it would be great what BOLD / non-bold is about again.
>>
>> Basically, I'm trying to figure out the anatomy region of the
>> activation. Should it be the only way to click areas one by one
>> and see the results of the identify window or is there any better way
>> something like AAL map in the MRIcron.
>> Your help would be again greatly appreciated.
>>
>> Thanks,
>> YSL
>>
>>
>>
>> Donna Dierker wrote:
>>
>>> On 04/13/2009 08:23 AM, Yune S. Lee wrote:
>>>
>>>
>>>> I see. Glad to hear that it has nothing to do with any font failure.
>>>> By the way, I went to the paint selection page to see what was mapped
>>>> for the particular column, but I couldn't find it.
>>>> As is shown in the attached, Average-MED-Wall B1-12 was selected
>>>> (assume it was the default or automatically selected when I opened up
>>>> the left template), but I didn't notice any change when I tried some
>>>> other views (e.g., Modalities-LEFT-PALS-B12).
>>>>
>>>>
>>> When Average-MED-Wall B1-12 column is selected, then only the nodes
>>> inside the medial wall will have a paint name associated with them. All
>>> other nodes will have paint name "?????", which in this context means
>>> "not inside the medial wall".
>>>
>>> The Modalities paint column should have a real paint name for almost
>>> every node.
>>>
>>> I think I know what is confusing you, though: When you click on a node
>>> with the composite paint file loaded, you get a BUNCH of output like this:
>>>
>>>
>>>
>>>
>>>
>>> They are printed in the same sequence as the columns
>>> are listed in the D/C paint selection menu (or the Overlay/Underlay -
>>> Surface paint dropdown menu). You will get some ??? output for almost
>>> every node, since many of the parcellation schemes apply to a restricted
>>> area (e.g., visuotopic or frontal). All nodes outside those areas will
>>> get ???? for that column.
>>>
>>>
>>>
>>>> It would be appreciated to help me understand your tip.
>>>>
>>>> Thanks,
>>>> YSL
>>>>
>>>>
>>>>
>>>> David Van Essen wrote:
>>>>
>>>>
>>>>> YSL,
>>>>>
>>>>> Basically, '???' means that there was no specific assignment for that
>>>>> node in that column of the paint file. Use Display Control: Page
>>>>> Selection: Paint Selection to see what was mapped for that particular
>>>>> column (e.g., the 4th column is probably visuotopic areas, which only
>>>>> cover a small fraction of the cortical surface and therefore have
>>>>> lots of '???' entries.
>>>>>
>>>>> DVE
>>>>>
>>>>> On Apr 12, 2009, at 4:30 PM, Yune S. Lee wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hello Caret users,
>>>>>>
>>>>>> I'm wondering if a string of '?' means the broken font in the
>>>>>> paint of the identify window or something meaningless
>>>>>> For instance, for the node 71770, the identify window shows as below:
>>>>>>
>>>>>> *paint: LOBE.PARIETAL SUL ??? ?????????? ??? Broadmann.43 ??? ???
>>>>>> SOMATOSENSORY AUDITORY ???
>>>>>>
>>>>>> * I don't have other language package installed any more, but wonder
>>>>>> if this has something to do with character issue.
>>>>>> Any help would be appreciated.
>>>>>>
>>>>>> Thanks,
>>>>>> YSL
>>>>>>
>>>>>>
>>>>>> *
>>>>>>
>>>>>> *
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>>>>>>
>>>>>>
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