Re: [Freesurfer] problems with analysis after using fslmaths

isxavg-fe-sess is an out-dated program that won't give you what you want. If you do the -per-run option, you are sort of on your own in that you'll have to run mri_glmfit, then that the results from that and concatenate across subject. A different question is why do you want to do this? doug O

Re: [Freesurfer] problems with analysis after using fslmaths

You can run selxavg3-sess with -per-run and it will give you a different output for each run. These results can then be combined in a fixed effects analysis using mri_glmfit. doug On 05/09/2012 03:09 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I have done some more debugging of my analysis and

Re: [Freesurfer] problems with analysis after using fslmaths

Hi Doug, I have done some more debugging of my analysis and tried different filters. If I understand slxavg-sess correctly, the runs are concatenated, and the pcc is computed over all runs. Is it possible to run a single subject FFX instead (e.g., by uncommenting lines 205-217, 305-310)? Thanks, Ca

Re: [Freesurfer] problems with analysis after using fslmaths

Hi Doug, I have done some more debugging of my analysis and tried different filters. If I understand slxavg-sess correctly, the runs are concatenated, and the pcc is computed over all runs. Is it possible to run a single subject FFX instead (e.g., by uncommenting lines 205-217, 305-310)? Thanks, Ca

Re: [Freesurfer] problems with analysis after using fslmaths

Hi, is it possible that it is a data format problem? I tried forcing fslmaths to give float output using -odt float. This changed mostly the autocorrelations computed during selxavg, but not the pcc. Caspar 2012/5/7 Caspar M. Schwiedrzik > the cutoff frequencies are 0.0025 Hz and 0.25 Hz. > Cas

Re: [Freesurfer] problems with analysis after using fslmaths

the cutoff frequencies are 0.0025 Hz and 0.25 Hz. Caspar 2012/5/7 Douglas N Greve > The mkanalysis command looks ok. I don't know how to interpret those > numbers for fslmaths. What are the cutoff frequencies? > doug > > > On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote: > >> Hi Doug, >> I u

Re: [Freesurfer] problems with analysis after using fslmaths

The mkanalysis command looks ok. I don't know how to interpret those numbers for fslmaths. What are the cutoff frequencies? doug On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I use the following command for fslmaths > fslmaths fmc.nii -bptf 200 2 fmcfilt.nii > > where 200*(TR+

Re: [Freesurfer] problems with analysis after using fslmaths

Hi Doug, I use the following command for fslmaths fslmaths fmc.nii -bptf 200 2 fmcfilt.nii where 200*(TR+2) is 400s, and 2*(TR=2)=4s. and for mkanalysis-sess -force -fsd bold -funcstem fmcfilt -analysis name -notask -tr 2 -runlistfile name -native -nskip 5 -mask brain -tpef name -taskreg name fo

Re: [Freesurfer] problems with analysis after using fslmaths

What frequencies did you chose for the FSL bandpass filter? What is you mkanalysis-sess command? On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote: > yes > > 2012/5/7 Douglas N Greve > > > Did you regenerate the seeds after filtering? > > > On 05/07/20

Re: [Freesurfer] problems with analysis after using fslmaths

Did you regenerate the seeds after filtering? On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote: > I have tried analyses with only one seed time course (either 1 voxel, > mean of a sphere of 1 voxel radius, or mean of a functionally defined > roi), as well as several seeds within the same desi

Re: [Freesurfer] problems with analysis after using fslmaths

Is this doing all of those seeds simultaneously or one seed at a time? On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote: > Hi, > I am trying to use fslmaths to filter my data before I plug it into a > resting state analysis. However, once I obtain a pcc map, all > correlation coefficients are

[Freesurfer] problems with analysis after using fslmaths

Hi, I am trying to use fslmaths to filter my data before I plug it into a resting state analysis. However, once I obtain a pcc map, all correlation coefficients are <0.1, even the autocorrelation with the seed voxel. The data look fine when I open them in Matlab using MRIread; the correlations betw