One more question, actually; if my seed were in structural space, and the output file was thus in structural space, how would I convert the output file into standard space?

Thanks,

Crystal

On Mon, Jun 25, 2012 at 4:23 PM, Crystal Zhou <[log in to unmask]> wrote:
Thanks!

Crystal


On Mon, Jun 25, 2012 at 4:18 PM, Matt Glasser <[log in to unmask]> wrote:

The output should already be in standard space then.


Peace,

 

Matt.

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Crystal Zhou
Sent: Monday, June 25, 2012 5:03 PM
To: [log in to unmask]
Subject: Re: [FSL] Averaging tracks across participants

 

I provided Probtracks with a transformation matrix (standard2diff.mat - this came from the Registration step). There is only one output file - fdt_paths.nii.gz. I was under the impression that this file is in diffusion space. Is automatically changed standard space? If not, is there a way to convert it to standard space?

 

I have included the probtrackx.log and the fdt.log below if they're of any help.

 

Thanks!

 

Crystal

 

probtrackx.log

 

/usr/local/fsl/bin/probtrackx --mode=seedmask -x /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/AXIAL_T1_MPRAGE_Series_3/P1_L_insula.nii -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --xfm=/Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/xfms/standard2diff.mat --forcedir --opd -s /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/merged -m /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/nodif_brain_mask --dir=/Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/L_insula 

 

fdt.log

 

set tool probtrackx

set probtrack(usereference_yn) 1

set probtrack(xfm) /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/xfms/standard2diff.mat

set probtrack(bedpost_dir) /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX

set probtrack(xfm) /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/xfms/standard2diff.mat

set probtrack(mode) seedmask

set probtrack(exclude_yn) 0

set probtrack(usereference_yn) 1

set probtrack(verbose_yn) 0

set probtrack(loopcheck_yn) 1

set probtrack(modeuler_yn) 0

set probtrack(curvature) 0.2

set probtrack(nsteps) 2000

set probtrack(steplength) 0.5

set probtrack(nparticles) 5000

set probtrack(reference) /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/AXIAL_T1_MPRAGE_Series_3/P1_L_insula.nii

set probtrack(output) /Users/jclab/Desktop/Crystal_2012/Summer_2012/Data/Chinese/P1_Chinese/DTI_Series_CorrectedDICOMImport/DTI.bedpostX/L_insula

 

On Mon, Jun 25, 2012 at 10:32 AM, Matt Glasser <[log in to unmask]> wrote:

That isn’t the right procedure for what you want, it is for something else I think.  You should provide probtrackx a transformation matrix or warpfield from standard space to diffusion space for each subject.  This will cause it to output the results from your standard space seed in standard space as well.  You could then just average the tracking results with fslmaths, or do something more complicated (like divide by the waytotal, threshold at some level, and binarize on each subject before averaging).  

 

Peace,


Matt.

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Crystal Zhou
Sent: Monday, June 25, 2012 11:05 AM
To: [log in to unmask]
Subject: [FSL] Averaging tracks across participants

 

Hello there,

 

I was wondering if anyone had any ideas about how to average ProbtrackX results across participants? Basically, what I'm interested in is if there's a way to average the tracks found using one seed in MNI space for all participants. I found this thread below, but it seems to stop at one participant, and (barring a general idea) I'm also not entirely sure what all the steps does and what it is each step is producing.

 

Any help would be greatly appreciated!

 

Crystal

 

On 10/19/09 2:49 PM, "Matt Glasser" <[log in to unmask]" target="_blank">[log in to unmask]> wrote:
This thread is getting difficult to follow without all of the previous messages below.  Here is the procedure you should be using:
 
Create Transforms:
 
Create affine transform between FA and Template FA using FLIRT (lets call this diff2standard.mat), also output the linearly transformed FA map in the template space (lets call this data_FA2standard_affine.nii.gz)
Create nonlinear transform between data_FA2standard_affine.nii.gz and the template FA (lets call this diff2standardwarp.nii.gz)
 
Invert Transforms:
Use convert_xfm -omat standard2diff.mat -inverse diff2standard.mat
Use invwarp -w diff2standardwarp.nii.gz -o standard2diffwarp.nii.gz -r <native diffusion space file, e.g. nodif_brain_mask>
 
Move ROIs from Standard Space to Structural Space:
applywarp -i <ROI in standard space> -r <native diffusion space file, e.g. data_FA> -o <ROI in native space> -w standard2diffwarp.nii.gz --postmat=standard2diff.mat --interp=nn
 
To test, you can do the following test to verify that you did everything correctly:
applywarp -i <data_FA in diffusion space> -r <template FA> -o <data_FA in standard space> --premat=diff2standard.mat -w diff2standardwarp.nii.gz --interp=trilinear
applywarp -i < data_FA in standard space > -r <native diffusion space file, e.g. data_FA> -o <data_FA in diffusion space 2> -w standard2diffwarp.nii.gz --postmat=standard2diff.mat --interp=trilinear
 
The output image <data_FA in diffusion space 2> should line up exactly with the original image <data_FA in diffusion space> as you will have transformed the FA into standard space and then back again into diffusion space.  Note that I use trilinear interpolation instead of nearest neighbour because the FA is an image with continuous values.
 
Peace,
 
Matt.