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Hi - you will already have the source code, which ever distribution you took. look in fsl/stable-src/avwutils I suggest that a good program to edit would be avwstats - add a new option to output a text line for every non-zero voxel. If you have any queries on editing avwstats and recompiling, it might be best to email me directly rather than bother the list with the details. Good luck! On Mon, 10 Feb 2003, Wei Qiu wrote: > Thanks Steve. I think avwroi just gives the single voxel image. This is > the too slow to run. I would like to try the second way by writtng some > c/c++ code. In the avwutils, there are lots commond there. Could you > please tell me which one is the best one to modify and how can I get the > source code? Also what's mean "add in that functionlity"? I am looking > forward to hearing from you. wei > > > On Mon, 10 Feb 2003, Stephen Smith wrote: > > > Hi - there's currently not a program to do this directly. You could quite > > easily script this (eg in tcl) to call, inside a loop, avwroi to give a > > single-voxel image and then extract the values using avwstats. this would > > be very slow to run, but would at least be easy! A better thing would be > > to just edit one of the avwutils C/C++ programs and add in that > > functionality. > > > > Thanks, Steve. > > > > > > > > On Sun, 9 Feb 2003, Wei Qiu wrote: > > > > > Hi, > > > > > > In my cluster_mask_zstat1.hdr file in the .feat directory, I have two > > > clusters: cluster 1 and cluster 2. Using the following command, I > > > generate a mask for cluster 2: > > > > > > avwmaths cluster_mask_zstat1.hdr -mult -1 -thr -2 -mult -1 -thr 2 > > > mask_cluster2 > > > > > > Appy this mask to thresh_zstat1.hdr: > > > > > > avwmaths thresh_zstat1 -mas mask_cluster2 cluster2output.hdr > > > > > > Then convert the cluster2output.hdr to a text file: > > > > > > avw2ascii cluster2putput.hdr cluster2output.txt > > > > > > I found the text file (cluster2output.txt) contails Z values for all > > > voxels in cluster 2, setting Z values to 0 for other voxels. My quesion > > > is: How can I get the coordinates (x, y, and z values for each voxel) of > > > all voxels in cluster 2? And the same thing for cluster 1? > > > > > > Any suggestion for this purpose (finding coordinates (x, y, z) of all > > > voxels in a specific cluster) is greatly appreciated. > > > > > > Thanks, > > > > > > Wei > > > > > > > Stephen M. Smith MA DPhil CEng MIEE > > Associate Director, FMRIB and Analysis Research Coordinator > > > > Oxford University Centre for Functional MRI of the Brain > > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > > +44 (0) 1865 222726 (fax 222717) > > > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > Stephen M. Smith MA DPhil CEng MIEE Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve