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Thank you! Crystal On Mon, Jun 25, 2012 at 4:25 PM, Matt Glasser <[log in to unmask]> wrote: > ** ** ** > > You would use applywarp or flirt to transform the data according to the > structural to standard transformation matrix. > > **** > > Peace,**** > > > Matt.**** > > ** ** > ------------------------------ > > *From:* **FSL - FMRIB's Software Library** [mailto:[log in to unmask]] *On > Behalf Of *Crystal Zhou > *Sent:* Monday, June 25, 2012 5:25 PM > > *To:* [log in to unmask] > *Subject:* Re: [FSL] Averaging tracks across participants > **** > > ** ** > > 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]<https:[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.**** > > **** > > **** > > ** ** > > ** ** >