Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

[Donna Dierker]

On Oct 29, 2014, at 10:56 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu 
wrote:

 
 Dear all,
 
 I have an averaged T1-image and co-registered volumetric atlas of the macaque 
 brain (which has been digitized by a collaborator) and want to derive from it 
 a surface-based
 atlas. Subsequently, I would like to use this atlas to get a parcellation of 
 the cortical surface of an individual macaque brain). How should I approach 
 this problem?
 
 I have extracted the cortical surface from the averaged T1-weigthed scan.  
 Should I now
 just label each cortical vertex by determining to which ROI it belongs? And 
 what if some vertices fall outside all ROI's? Also, the result does not look 
 so smooth as existing atlases.

It sounds like you need to map the volume(s) onto the surface.  It also sounds 
like these are discrete parcellations (ROI/label/paint) as opposed to 
probabilistic atlases, since it sounds like it is an individual monkey's data, 
rather than group data.  It would be helpful to clarify this.

Assuming it is ROI/label (i.e., each intensity value -- e.g., 1, 2, 3, … -- 
corresponds to a region -- e.g., cingulate, arcuate, …), then I would map it as 
a paint volume.  I believe doing so constrains the mapping algorithms, but I am 
not certain.

If you load your anatomical T1 with your surfaces and toggle on the surface 
contours (Volume Surface Outline, on the D/C page selection), then you can 
overlay the volumetric atlas over these two anatomical underlays (T1+surface 
contours) to look for regions where the surface does not intersect the atlas.  
I see three choices:

* fix the volumetric atlas data
* fix the surfaces, so the intersection is improved
* accept the fact that there are real holes in your data

You will be better equipped to make that choice when you are looking at 
T1+surface contours+volumetric-atlas.

 And to parcellate an individual macaque brain, can I register both the 
 surfaces (that is, the template surface and the individual surface) 
 spherically?

Registering an individual monkey brain to a monkey atlas (e.g., F99) isn't 
really parcellating it, but there are parcellations already on the F99 atlas, 
so if you use spherical registration to register your monkey to F99, then you 
could look at the F99 parcellations overlaid on your monkey's surface.  But 
it's not a quick or easy process.  You need to draw registration borders.  
(Though there are other registration algorithms out there that use sulcal maps 
and/or other data to automatically derive the deformation.  I encourage others 
to chime in if they ones they have used and found not too hard.)  How would you 
be using the registered surface?

(Sorry for the delayed reply, but it wasn't a quick one. ;-)

 Thanks a lot,
 Rikkert
 
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://brainvis.wustl.edu/mailman/listinfo/caret-users

Re: [caret-users] threshold of metric file

[Donna Dierker]

I'm sorry I don't know the answer to the Freesurfer question, but someone else 
might know.  And I confess I don't understand the rationale for thresholding at 
that value, possibly because I am unfamiliiar with the contents of those files.

So I'm keeping the responsibility for ensuring a reasonable threshold on you. 
;-)  But If it's each subject, then it's probably worth scripting it using 
these caret_command tools:

  caret_command -surface-region-of-interest-selection  
 [-metric  metric-file-name  column  min  max SEL-TYPE]

  caret_command -surface-roi-statistical-report  

And you can use each subject's surface/topo for that surface area calculation.  
Your min is your threshold and max something like 999.  Your report will 
include the area of the suprathreshold regions, and you can grep that line from 
the resulting report file.


On Oct 29, 2014, at 11:30 PM, wangzhiwei3233 wangzhiwei3...@126.com wrote:

 Hi, Donna,
 
 My purpose is counting activated area size on each subject.
 
 I did do significance test using Freesurfer on individual level. The results 
 contained many files,for example, sig.nii.gz and Fsig.nii.gz 
 corresponding to result of t and f test respectively. Is that right?
 But I do not know how to determine tha suprathreshold on subject level as you 
 mentioned. 
 
 For display and counting area size, I converted the results file(sig.nii.gz) 
 to Caret. Then I count area size on Caret. When I counted area size, I 
 selected a uniform threshold 1.3, i.e.-log10(0.05) for each subject. So I set 
 the scale to 1.3 ~ maxminum on Caret. Is this right?
 
 So I could draw a border around the  suprathreshold region and generated a 
 paint file. I  got the area size of the region using the paint file.
 
 Is there any step wrong?
 
 Thanks!
 Zhiwei
 
 
 
 At 2014-10-30 00:27:14, Donna Dierker do...@brainvis.wustl.edu wrote:
 Hi wangzhiwei,
 
 I'm a little confused by the question.  There mention of area size and 
 scales hints that there might be a confusion between tools used for 
 quantification / significance testing and those used for display purposes.
 
 Freesurfer has its own tools for significance testing, so you could use 
 those.  We often use threshold-free cluster enhancement for that purpose, 
 which finds the significance threshold.  Suprathreshold area can be computed 
 once this threshold has been determined.
 
 But usually when I make a figure, I generate border around the 
 suprathreshold regions and display these bordersover the real t- or f-map, 
 using a scale that corresponds to my alpha (e.g., .05) divided by two (since 
 I usually do both right and left hem tests).  I compute this t or f-stat 
 using my n / degrees of freedom.
 
 So the significance testing and display steps are separate, the way I do it.
 
 Now you might not be going as far as significance testing.  Sometimes you 
 just want to look at some preliminary data -- particularly for a single 
 subject.  A good start might be to understand if this is a single subject, 
 group results, what kind of statistic.
 
 And certainly not everyone does this the way I do, so it would be helpful 
 for others to weigh in with their viewpoints/conventions.
 
 Donna
 
 
 On Oct 28, 2014, at 9:53 PM, wangzhiwei3233 wangzhiwei3...@126.com wrote:
 
  Hi, experts,
  I converted fMRI results derived from freesurfer to caret, and not I want 
  to count activation areas on caret. So there is a problem of threshold and 
  scale.
  
  Auto scale range is 0~60. I found that the area size was different when 
  using scale 1.3~4 from when using scale 1.3~60. And the latter one was 
  smaller. However , in the latter case(1.3~60),  the value of a point that 
  was next to the border of activation area but in non-activation area was a 
  little bit lager than the threshold 1.3. 
  
  How to set the scale to guarantee the activation accurate?
  
  Best!
  
  
  ___
  caret-users mailing list
  caret-users@brainvis.wustl.edu
  http://brainvis.wustl.edu/mailman/listinfo/caret-users
 
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users
 
 
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://brainvis.wustl.edu/mailman/listinfo/caret-users