Re: [caret-users] thresholding issues in Caret
Thanks for the reply--this is an interesting suggestion, and it does seem like one way to accomplish what I am trying to do. However, it also seems like a fairly time-consuming solution, especially given that we're just trying to get a good visualization of data that we've already analyzed elsewhere. So, I'm just curious to see whether you (or anybody else on the list) might have insight into the original questions that I had asked? Barring any additional guidance, I think we may just use the interpolated voxel algorithm on the cluster-thresholded FSL data, without any additional thresholding in Caret. But I just would like to make sure that this is a reasonable approach--since if there's a setting or two that we should tweak to get an image that more accurately represents the data, it would be great to know that before we submit these figures for publication. Thanks, Michael ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] thresholding issues in Caret
If I understand you, my inclination would be to map the unthresholded volume with interpolated voxel. Then map the thresholded volume with enclosing voxel. Then use Surface: ROI to select metric >=mythresh and draw an areal border around the resulting cluster. Then render that border over your unthresholded metric, to delimit the significant from not. On 10/24/2013 11:27 AM, Michael Cohen wrote: Hi, I was wondering if you might be able to help clarify some uncertainty that I've had with thresholding images in Caret. I am using thresholded volumetric images from FSL, and mapping them into Caret. I did see in an old post from the mailing list that this is a common approach, which was good to see. But there are still a few things that I'm uncertain about: -- Is it OK to use the interpolated voxel algorithm with pre-thresholded images? It seems to me that this could be problematic, since it's averaging zeros in with the data. But if I use the unthresholded images, I'd have to apply cluster correction in Caret, rather than having FSL do it...which introduces other complications. -- Given that the interpolation yields a number of areas in which the actual z score in Caret is less than our original z threshold, is it advisable to re-threshold the image using Caret display options (under Metric Settings) to eliminate all activations under our original threshold (in this case, z = 2.3)? That seems to show much less activity on the brain, which could be good or bad, I guess, but the more important question is whether it's a more or less faithful rendering of the original volumetric image, which I'm not sure about. -- Is there some "trick" to setting a volume threshold when you import data to Caret using the "Map volume to surface" option? I tried enabling the volume threshold, and entered a number to use as a threshold that was higher than the original threshold used on the image file. But when it imported the image, that option didn't seem to do anything at all. Is there something else that I need to do? Thanks, Michael -- Michael S. Cohen, M.S., C. Phil Ph.D. Candidate Department of Psychology University of California, Los Angeles Los Angeles, CA 90095 ___ 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] ribbon generation
Subject: Re: [caret-users] ribbon generation > I think we may have intended workbench-related things to go on hcp-users, > but I'm not sure. > > I know, but this is actually more caret related. caret is the software I'll use for the myelin mapping. workbench might play an ancillary role but doesn't need to exist for this present task. > At any rate, -create-signed-distance-volume and -volume-math will allow > you to do something like what you want. The first creates the signed > distance function in whatever voxel grid you tell it to, as it takes a > template volume to get the voxel grid. Make this for both white and pial > surfaces, and then use -volume-math to threshold and "and" the results (via > multiplication, like "(x > 0) * (y < 0)"). > > If you want voxels to be included/excluded by their centers, use a > threshold of 0, or you can use something like half the voxel diagonal to > exclude any voxel that could possibly have even a corner outside the ribbon > (though that could exclude some voxels that are entirely inside the ribbon, > as it doesn't actually do voxel/surface intersection, it just calculates > signed distance at voxel centers). I think Matt has done this, but I don't > recall what threshold he used. > > that's very helpful I'll experiment with that. That could be very handy indeed for lots of things. > Tim > > > Subject: Re: [caret-users] ribbon generation > > You dont need to create a conform volume. You can select the x y z size > for volume in mris_fill. Also you can apply or use mris_vol2vol to > regenerate the volume according the header that you want. > Hope it helps > Rouhi > Yes that helps a very great deal that's the answer I need in this case. Many thanks indeed. Colin ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] thresholding issues in Caret
Hi, I was wondering if you might be able to help clarify some uncertainty that I've had with thresholding images in Caret. I am using thresholded volumetric images from FSL, and mapping them into Caret. I did see in an old post from the mailing list that this is a common approach, which was good to see. But there are still a few things that I'm uncertain about: -- Is it OK to use the interpolated voxel algorithm with pre-thresholded images? It seems to me that this could be problematic, since it's averaging zeros in with the data. But if I use the unthresholded images, I'd have to apply cluster correction in Caret, rather than having FSL do it...which introduces other complications. -- Given that the interpolation yields a number of areas in which the actual z score in Caret is less than our original z threshold, is it advisable to re-threshold the image using Caret display options (under Metric Settings) to eliminate all activations under our original threshold (in this case, z = 2.3)? That seems to show much less activity on the brain, which could be good or bad, I guess, but the more important question is whether it's a more or less faithful rendering of the original volumetric image, which I'm not sure about. -- Is there some "trick" to setting a volume threshold when you import data to Caret using the "Map volume to surface" option? I tried enabling the volume threshold, and entered a number to use as a threshold that was higher than the original threshold used on the image file. But when it imported the image, that option didn't seem to do anything at all. Is there something else that I need to do? Thanks, Michael -- Michael S. Cohen, M.S., C. Phil Ph.D. Candidate Department of Psychology University of California, Los Angeles Los Angeles, CA 90095___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
