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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.**** >> >> **** >> >> ** ** >> > >