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Hi - this is the same issue - if the values are negative then the "maximum" is not defined, hence the cope4 result. Hence this voxel is negative. We'll fix/clarify this in the next release. Cheers. On 19 Apr 2007, at 17:36, Paymon Hosseini wrote: > Dear all, > changing the threshold value in featquery also does not solve the > problem of incorrectly reported voxels. i was wondering if is there > any way around this? > thank you very much for any help, > paymon > > > Paymon Hosseini wrote: >> Dear Steve , >> >> I am having a similar problem. I am trying to find the % signal >> change of several COPE files for one subject for a single voxel >> using featquery. The featquery report uses the correct voxel for >> some COPE files, and not for others. >> >> here is an example featquery output report: >> 1 stats/cope1 1 0.00 0.30 0.30 0.30 0.30 0.30 30 53 15 -2.45 57.30 >> 20.36 (correct voxel) >> 1 stats/cope2 1 0.00 0.36 0.36 0.36 0.36 0.36 30 53 15 -2.45 57.30 >> 20.36 (correct voxel) >> 1 stats/cope3 1 0.00 0.18 0.18 0.18 0.18 0.18 30 53 15 -2.45 57.30 >> 20.36 (correct voxel) >> 1 stats/cope4 1 -0.00 -0.00 -0.00 -0.00 -0.00 0.00 0 0 0 107.32 >> -107.92 -38.02 (incorrect voxel) >> >> for example in the above, stats/cope1 to stats/cope3 are evaluate >> at the voxel i specified, but stats/cope4 is evaluate at some >> other voxel. >> >> Both the mask and the voxel are in standard space, and there are >> no registration problems. All the cope images have an intensity >> value at voxel i am interested in, when viewed in fslview. You >> said "if there are no voxels above the threshold then the co- >> ordinates reported are meaningless". what threshold are you >> referring to? >> Could you please explain in more detail why one cannot get a % >> signal change (e.g stats/cope4 above), even though the stats/ >> cope4.nii.gz has a valid intensity value at the given voxel of >> interest? >> >> thanks >> paymon hosseini >> >> >> >> >> Steve Smith wrote: >>> Hi - yes, sorry, if there are no voxels above the threshold then >>> the co-ordinates reported are meaningless - we'll get that fixed >>> in the next release. >>> Cheers. >>> >>> >>> On 4 Apr 2007, at 00:24, Sang Lee wrote: >>> >>>> Hi Steve, >>>> >>>> The mask image was set to the standard space reference image >>>> used in the registrations, and the mm coordinates were in the >>>> space of this image. Also, there were no registration failure >>>> nor that the voxel that I specified was outside the field-of- >>>> view-of the datasets. >>>> >>>> Possible that this error is generated when there is no real >>>> activation in the voxel that I soecified? Looking at each >>>> individuals that had these errors, all of them did not have any >>>> activations in the specified voxel. i.e. no activation in the >>>> voxel is generating these errors. If so, for these individuals, >>>> would it be ok to assume that the mean % signal change is zero >>>> (for the % signal change plot)? >>>> >>>> Thank you again for your help. >>>> >>>> From Sang >>>> Sang Lee >>>> Phenotype Genotype Project >>>> Athinoula Martinos Center for >>>> Biomedical Imaging >>>> 149 13th St. Rm. 2302 >>>> Charlestown, MA 02129 >>>> Fax: 617-726-1351 >>>> >>>> >>>> On Apr 1, 2007, at 5:29 AM, Steve Smith wrote: >>>> >>>>> Hi - did you make sure that the mask image was set to the >>>>> standard space reference image used in your registrations, and >>>>> that the mm co-ordinates were in the space of this image? Also, >>>>> is it possible that the registration had failed for the >>>>> problematic FEAT runs, or that the voxel you specified was >>>>> outside the field-of-view of those datasets? >>>>> >>>>> Cheers, Steve. >>>>> >>>>> >>>>> On 31 Mar 2007, at 21:37, Sang Lee wrote: >>>>> >>>>>> Dear FSL user, >>>>>> >>>>>> I am using PE files to calculate the percentage signal change >>>>>> via featquery for a single voxel for >>>>>> each of my subjects (total n = 28). >>>>>> >>>>>> Given that I am using PE file, an anatomical mask, and a mm >>>>>> coordinate for a single voxel, using >>>>>> featquery tool with convert PE/COPE to % signal change option >>>>>> turned on, I should get % signal >>>>>> change for each of my subjects for that single voxel. >>>>>> >>>>>> However, several of the subjects report file comes out with a >>>>>> coordinate that I did not specify. >>>>>> >>>>>> For example, I specified (-16 -4 -16) for my mm coordinates. >>>>>> However, several of my subjects' >>>>>> report file comes out with % signal change values with the >>>>>> following coordinate (90 -126 -72). >>>>>> This happens with one third of my subjects. Is there something >>>>>> that I am doing wrong? How do I >>>>>> deal with those results with the coordinates that I did not >>>>>> specify? >>>>>> >>>>>> I am trying to plot mean % signal change plot for all 28 >>>>>> subjects, but I am not sure what to do with >>>>>> those subejct's mean % signal change that comes out with a >>>>>> coordinate that I did not specify. >>>>>> >>>>>> Any input would be a great help! >>>>>> >>>>>> Thank you in advance. >>>>>> >>>>>> From Sang >>>>> >>>>> >>>>> ------------------------------------------------------------------ >>>>> --------- >>>>> Stephen M. Smith, Professor of Biomedical Engineering >>>>> Associate Director, Oxford University FMRIB Centre >>>>> >>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>>> +44 (0) 1865 222726 (fax 222717) >>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>>>> ------------------------------------------------------------------ >>>>> --------- >>>> >>>> The information transmitted in this electronic communication is >>>> intended only for the person or entity to whom it is addressed >>>> and may contain confidential and/or privileged material. Any >>>> review, retransmission, dissemination or other use of or taking >>>> of any action in reliance upon this information by persons or >>>> entities other than the intended recipient is prohibited. If you >>>> received this information in error, please contact the >>>> Compliance HelpLine at 800-856-1983 and properly dispose of this >>>> information. >>> >>> >>> -------------------------------------------------------------------- >>> ------- >>> Stephen M. Smith, Professor of Biomedical Engineering >>> Associate Director, Oxford University FMRIB Centre >>> >>> FMRIB, JR 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, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---