Re: [caret-users] Question about converting a metric file to RGB paint

[Dierker, Donna]

Hi Heather,

You probably already saw John Harwell’s response off-list:

> I do not know why this option is not working for you.  Did you try Metric to 
> RGB paint without any thresholds?
> 
> There is also an item titled “Copy Current Coloring to RGB Paint" near the 
> bottom of the Attributes Menu that you may want to try.
> 
> I will also add that Caret5 is “deprecated software” and it has been may 
> years since its last and final update.  You are welcome to continue using 
> Caret5 and we still try to provide support for Caret5.  Our software 
> development focuses on Connectome Workbench 
> (https://www.humanconnectome.org/software/connectome-workbench.html).

You are using Attributes: Metric: Convert Metric to RGB Paint, right?
With no minimum, as John asked?
The only other explanations I can come up with for how you got the second 
capture from the first capture are:

* You have the wrong column(s) selected in the Metric to RGB paint channels 
(red, green, blue).
* You have the wrong RGB paint output column selected in the D/C 
overlay/underlay when taking the second capture.

I was able to get that feature to work as expected on some of my metric files.
Puzzling!

Donna


> On May 5, 2017, at 3:31 AM, Heather Iriye  wrote:
> 
> Hi there,
> 
> I'm running into a problem trying to convert a metric file to RGB paint. When 
> I display the metric file before conversion, I get the first picture attached 
> (Right_lateral.jpg). However, when I convert to RGB paint and display the 
> positive activations I get the second picture attached, which fails to match 
> the metric file. I've tried adjusting the threshold settings both in the 
> Metrics to RGB paint window and RGB Paint Settings in the Display Control, 
> but this doesn't seem to help the problem. Do you have an idea of what may be 
> going on? 
> 
> Best wishes,
> 
> Heather Iriye 
> Psychology PhD Student
> University of Sussex
> Pevensey Building 1, 2D6
> Brighton, UK
> BN1 9QH
> 
> 
> Memory for Events Lab
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Re: [caret-users] SumsDB website can't be reached

[Dierker, Donna]

Quick!  Thanks to Ben & Chip, sumsdb.wustl.edu is up -- at least for the moment.

This system is quite dated and would need considerable effort to make it 
sustainable, so we are in the process of extracting as many archives as 
possible from it and making them available elsewhere.  We are still figuring 
out how they will be delivered. but for now the process of extracting them from 
sumsdb is going well.  Still, I can't promise that every archive will be 
extracted, so if you need something, now would be a good time to get it.

We hope it will be available for at least another couple of weeks, but keeping 
it working has been an increasingly uphill battle.

I have harvested several F99-related archives here:

http://brainmap.wustl.edu/pub/donna/ATLASES/SUMSDB/ROOT/MacaqueZip/
login pub
password download

Let me know if you need something specific and have trouble finding it.


On Jun 29, 2016, at 3:03 PM, Donna Dierker  wrote:

> I think you will need to follow instructions that more resemble the tutorials 
> here:
> 
> Caret 5.5 Tutorial - Segmentation, Flattening, and Registration
> http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf
> 
> But I'd still read the FS-to-99 document below, because certain sections 
> (e.g., delineating the medial wall) will still be useful when you follow the 
> older tutorial.  Also, I think the atlas target dataset in the FS-to-F99 
> could probably still work with the older Caret 5.5 tutorial.  There's a very 
> good chance David made improvements to the parcellations in the later 
> dataset, and at the very least, the FS-to-F99 is on the 73730 standard mesh, 
> which has advantages.
> 
> One gotcha using SureFit-generated segmentations is when you do finally get a 
> patched hemisphere with no handles that you want to prepare for flattening, 
> you probably have to convert it to NIFTI and make sure it the correct 
> voxdims.  It's been years since I've done this, but as I recall, we used 
> monkey T1's with voxdims in the 0.5-0.8mm range, but the volume header didn't 
> necessarily reflect that.  Just make sure when you do the Prepare for 
> Flattening step, the segmentation volume's header accurately reflects the 
> voxdims, so that the coordinates in the resulting vtk/coord files are 
> accurate.
> 
> 
> On Jun 29, 2016, at 1:12 PM, Cody Sarrazin 
> wrote:
> 
>> I do not have Freesurfer since I only have access to PCs right now. I am 
>> also having difficulty finding the tutorials and this is my first experience 
>> with caret.
>> 
>> Cody
>> 
>> On Tue, Jun 28, 2016 at 1:57 PM, Ting-Yu Chang  
>> wrote:
>> Hi Donna,
>> 
>> Thanks for your reply and help. I segmented our macaque volume data using 
>> SureFit, not using FreeSurfer. Can I do registration by these datasets? or 
>> if not, could you or anyone please upload the datasets which can register 
>> individual SureFit segmentation with F99 atlas?
>> 
>> Thanks very much,
>> TingYu
>> 
>> On Tue, Jun 28, 2016 at 1:25 PM, Donna Dierker  
>> wrote:
>> It sure would be nice if sumsdb were working right now, but it's not, and I 
>> have no quick-fix for getting it to work (though we are discussing ideas).
>> 
>> Meanwhile, I'd like to narrow down which F99 individual to F99 registration 
>> dataset you were looking for.  If you segmented your monkey's brain using 
>> Freesurfer, then maybe archives in this directory might be helpful:
>> 
>> http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/
>> login pub
>> password download
>> 
>> There was this document:
>> 
>> http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/FS-to-F99_Tutorial_Sept10.doc
>> (same login/password)
>> 
>> I had these in my download directory, though there is no guarantee they are 
>> the latest/greatest:
>> 
>> -rw--- 1 donna velab 10272560 Feb  7  2014 FS-to-F99_Aug10.zip
>> -rw-r--r-- 1 donna velab 10114922 Apr  3  2014 
>> Figs-8-10_architectonic_compare.74k_f99.zip
>> -rw-r--r-- 1 donna velab  7797951 Apr  3  2014 
>> Figs-3_4_register-F99-with-Chip.R.74k_f99.zip
>> -rw-r--r-- 1 donna velab  4729026 Apr  3  2014 
>> Fig-1A_C_register-F99-with-Chip.R.74k_f99.zip
>> 
>> I'm cc'ing Chad Donahue, who is a grad student in our lab who does primate 
>> registration, among other things.
>> 
>> I believe these datasets were the ones cited in this paper:
>> 
>> Van Essen, D.C., Glasser, M.F., Dierker, D. and Harwell, J. (2011) Cortical 
>> parcellations of the Macaque monkey analyzed on surface-based atlases. 
>> Cerebral Cortex doi: 10.1093/cercor/bhr290.
>> 
>> Ting-Gu and Cody:  Confirm you have Freesurfer segmentations for your 
>> monkeys.
>> 
>> Chad:  Comment on any later/greater docs/datasets/methods for registering 
>> monkeys, if they're ready for public use.
>> 
>> Everyone else:  Speak up if you have versions of these datasets you 
>> downloaded from sumsdb.  I'm not 100% certain mine are final, but