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Hi Steve, Thanks for looking into this. I started over from scratch, just to make sure I didn't do something wrong. And, of course, after posting a problem, I discover it was user error... I don't know where I messed it up, but I'm getting the expected values now. Here's what I'm doing and the results I'm getting, if interested: I'm trying to count the number of voxels above a given threshold. I'm using a t map from an individual analysis in spm, thresholding it to only leave t values above 2.6259 (p=.01, df=100, uncorrected) and masking it to look at things only within a given roi (that's already been converted to a binary mask). So, to do this, at the terminal I type: avwmaths_16SI <spmT map>.hdr -thr 2.6259 -mul <roi mask> <output>. If I check the header info with avwhd, I get: bash-2.05b$ avwhd masked_t.nii.gz filename masked_t.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 79 dim2 95 dim3 69 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 2.0000000000 pixdim2 2.0000000000 pixdim3 2.0000000000 pixdim4 1.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 1.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Unknown qform_code 0 qto_xyz:1 2.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 2.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 2.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -2.000000 0.000000 0.000000 78.000000 sto_xyz:2 0.000000 2.000000 0.000000 -112.000000 sto_xyz:3 0.000000 0.000000 2.000000 -50.000000 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip FSL3.2beta aux_file The output from avwstats++ is: bash-2.05b$ avwstats++ masked_t.nii.gz -v -V -r -R -m -M 517845 4142760.000000 440 3520.000000 765 1276 0 1530 0.760305 894.818182 Thanks for your help and sorry about wasting your time... Pat On 5/19/07, Steve Smith <[log in to unmask]> wrote: > Hi - sounds odd - can you send the output from: > > avwhd <input> > avwstats++ <input> -v -V -r -R -m -M > > Cheers. > > > On 18 May 2007, at 21:36, Pat Vee wrote: > > > Hi Steve, > > > > Thanks for the quick reply. One follow up question though... For > > avwstats, I'm still confused b/c my voxels are 2x2x2mm (confirmed > > by avwhd). Therefore, if I multiply that by the number of voxels, > > I shouldn't get a decimal. And, the number ( e.g., 13560.75) is > > much larger than my number of voxels (826) times the volume > > (8mm^3). Am I doing something wrong? > > > > Thanks, > > Pat > > > > On 5/18/07, Steve Smith <[log in to unmask]> wrote:Hi, > > > > On 18 May 2007, at 02:23, Pat Vee wrote: > > > > > Hi all, > > > > > > I'm trying to use avwstats to count the number of voxels and find > > > the mean > > > within a masked image. What I've done is created a binary mask, > > then > > > multiplied that by an image to only leave values in the non-masked > > > regions. > > > > > > So, to count voxels I'm typing: > > > avwstats <input> -V > > > It outputs 2 values; I understand that the 1st value is the number > > > of voxels > > > that are non-zero. I've been getting whole numbers for this on the > > > order of > > > hundreds (e.g., 826), which is what I expect. However, I don't > > > understand > > > what the 2nd value is. I've been getting numbers on the order of > > > thousands, > > > with decimals for this (e.g., 13560.75). Can someone explain what > > > this > > > number is? > > > > If you just type "avwstats" you get the usage; > > the second number is the volume, i.e. the first number X voxel volume. > > > > > To find the mean, I'm typing: > > > avwstats <input> -M > > > It outputs a value that I believe is the mean for all the non-zero > > > voxels. > > > However, I realized that it's possible that some of the volumes > > > will have > > > zero values within the non-masked regions. So, is there some way > > > to mask > > > regions so that the masked area is converted to NaNs - or some > > > other method > > > that would allow me to include zeros when calculating the mean? > > > > We don't use NaNs, This is easy in avwstats++ with the -k (masking) > > option. > > > > Cheers. > > > > > > ---------------------------------------------------------------------- > > -- > > --- > > 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 > ------------------------------------------------------------------------ > --- >