Hi,
check out this:
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html
hth,
andreas
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Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matt Glasser [[log in to unmask]]
Gesendet: Dienstag, 12. Juli 2011 23:33
An: [log in to unmask]
Betreff: Re: [FSL] functional ROIs for probtrackx
Yes, FreeSurfer can do it, though I am not sure how, as I use Caret for these sort of things. If one activation is larger than the other, wouldn’t you wan the seed masks to reflect that? You can still normalize the results by the seed mask size if you want to.
Peace,
Matt.
________________________________
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Sarina Iwabuchi
Sent: Tuesday, July 12, 2011 4:17 PM
To: [log in to unmask]
Subject: Re: [FSL] functional ROIs for probtrackx
Hi Matt,
Thanks very much for your suggestions, I will try this. I'm assuming the WM layer can be extracted from Freesurfer and somehow "superimposed" onto the SPMT map to find voxels present in both (sorry, I haven't used Freesurfer yet). Also, do you think this method would still be valid to make interhemispheric comparisons given that the seed masks will have different voxels numbers?
Thanks again,
Sarina
On Tue, Jul 12, 2011 at 6:44 PM, Matt Glasser <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hmm, I think I would have say the opposite (also, posts from years ago must be interpreted in the context of the capabilities of the software that existed at that time). Because the brain is not made of spherical areas, I suggest you take your thresholded t-stat map and intersect it with a 1-voxel thick layer representing the white matter surface and just use those voxels present in both. Maybe one day we will all do our task fMRI analyses on the surface and be able to track from task activations that represent proper areal extents.
Peace,
Matt.
________________________________
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of Sarina Iwabuchi
Sent: Monday, July 11, 2011 10:16 PM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: [FSL] functional ROIs for probtrackx
Hi there,
I'm not sure that there is a straight answer for this but any help/suggestions would be greatly appreciated!
I've run an fMRI task that shows bilateral activation. I've used the peaks as centrepoints for spherical ROIs (in SPM and marsbar) which I have then run tractography on using probtrackx. However, I've come across a few problems. Some of the masks were so cortical that they overlap over the brain edge and most tend to comprise a reasonable amount of gray matter, which I have read in previous posts could actually cause more errors than anything useful. So from what I have read through the forum posts, it would be best to project these cortical ROIs into white matter using Freesurfer (as suggested by Cherif here https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=FSL&P=R101079&1=FSL&9=A&J=on&X=2CF1366F2F0D769872&Y=sarinaiwabuchi%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4) and track from white matter. My question though is whether I should still use:
1. the whole spherical mask as a seed including grey and white (as I am also getting parameter estimates from these masks form the fmri data) or,
2. use only WM voxels within the sphere as the ROI, however this would leave me with different ROI sizes/shapes (i.e. voxels numbers) which perhaps would not be ideal especially if I am comparing pathways, say, between hemispheres for example?
I also remember reading one of Matt Glasser's posts discouraging tracking from/into grey matter and using a WM segmentation mask instead of the nodif_brain_mask during tracking.
Thanks in advance for any help!
Sarina
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