 |
 |
Hi Mark, I think it may be because the voxels I'm using are all near the frontal poles. It seems to work fine with the other flirt option by transforming to subject space earlier so I'll just do it that way instead. thanks for all your help! Mengfei On Mon, Aug 10, 2009 at 10:01 PM, Mark Jenkinson <[log in to unmask]>wrote: > Hi, > > I'm surprised that a coordinate within the brain will be transformed > outside > the FOV. Have you checked coordinates that are not near the edge of the > brain? > > Your flirt call is fine if you want to do that instead. > > All the best, > Mark > > > > On 10 Aug 2009, at 20:27, Mengfei Huang wrote: > > Hi Mark, >> >> I just tried that and ended up with coordinates that fell off of my >> highres brain (y coordinate). Is this a reasonable problem to encounter due >> to inaccuracies in the transformation matrix, or would this indicate that >> something has gone wrong? >> >> If it's the former, I'll go back and just transform the original mask into >> subject space first before picking the peak voxel. i believe that would be: >> flirt -in [mask in standard space] -ref reg/standard -applyxfm -init >> standard2highres.mat -out [mask in subject space] correct? >> >> thanks! >> Mengfei >> >> On Mon, Aug 10, 2009 at 7:41 PM, Mark Jenkinson <[log in to unmask]> >> wrote: >> Hi, >> >> That's not quite right. >> The syntax is: >> std2imgcoord -img reg/highres -std reg/standard -xfm >> reg/highres2standard.mat -vox coordfile >> where coordfile contains your input coordinates (in standard space) as >> text. >> The output goes to the screen. >> To capture it in a file just end the line with: > outputfile.txt >> as the ">" operator in Unix directs the output (of any command) into the >> following file. >> >> You are right that you give it the highres2standard.mat transformation, >> which it internally >> inverts, to convert coordinates from standard to highres space. >> >> All the best, >> Mark >> >> >> >> On 10 Aug 2009, at 19:34, Mengfei Huang wrote: >> >> Hi Mark, >> >> so just to double check the syntax would be: >> >> std2imgcoord -img <text file containing voxel coordinates> -std >> reg/standard -xfm <subject's hires2standard.mat> <output coordinate file in >> subject space> -vox (to output coordinates in voxels) >> >> Is this correct? So even though you're using the hires2standard matrix, it >> converts from standard to hires? >> >> Thank you! >> Mengfei >> >> On Mon, Aug 10, 2009 at 6:08 PM, Mark Jenkinson <[log in to unmask]> >> wrote: >> Hi, >> >> Just use the tool std2imgcoord. >> >> All the best, >> Mark >> >> >> >> On 10 Aug 2009, at 18:04, Mengfei H wrote: >> >> Dear FSL, >> >> Is it possible to use FLIRT to transform voxel coordinates (x,y,z) from >> standard >> space back into subject space? If so, what would be appropriate syntax? >> >> I've seen it done for nii.gz images but not specific coordinates >> >> Many thanks! >> Mengfei >> >> >> >> >> -- >> Mengfei Huang >> Fulbright Scholar (UK) 2008-2009 >> MSc Neuroscience >> Oxford University >> BS Biological Sciences >> Stanford University >> >> >> >> >> -- >> Mengfei Huang >> Fulbright Scholar (UK) 2008-2009 >> MSc Neuroscience >> Oxford University >> BS Biological Sciences >> Stanford University >> >> -- Mengfei Huang Fulbright Scholar (UK) 2008-2009 MSc Neuroscience Oxford University BS Biological Sciences Stanford University