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 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, Caspar > > 2012/5/7 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu > <mailto:cschwie...@rockefeller.edu>> > > 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 <cschwie...@rockefeller.edu > <mailto:cschwie...@rockefeller.edu>> > > the cutoff frequencies are 0.0025 Hz and 0.25 Hz. > Caspar > > 2012/5/7 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > 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+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 > > for debugging, I did not include nuisance regressors. > Caspar > > > 2012/5/7 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > > > 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 > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>. edu > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > > > 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 design matrix, with the same problem. > All of these analyses did yield higher > pcc when done > without > filtering. > Caspar > > 2012/5/7 Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>. edu > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>> . edu > > > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>. edu > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>>>> > > > 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 <0.1, even the > autocorrelation > with the > > seed voxel. > > The data look fine when I open them in Matlab using > MRIread; the > > correlations between individual voxel time courses > obtained in > Matlab > > is about 0.6. > > > > My analysis stream is as follows: > > a) I filter the data using "fslmaths input -bptf > highpass > lowpass > > output"; from this I obtain a filtered nii.gz file > > b) I extract a seed timecourse from the filtered > data in Matlab > > c) I run mkanalysis-sess with -notask > > d) I run selxavg3-sess > > e) I overlay the pcc.nii > > > > I have tried this with smoothed and unsmoothed data, > with and > without > > nuisance regressors, with different seeds, with > mri_convert > after step > > a. It is not a problem with the overlay since the > max values > in pcc > > are all <0.1. > > I noticed that there are some differences in the > nifti header > (as read > > with MRIread) before and after filtering, but it > seemed to > me that > > they are gone after I used mri_convert. > > I do find much higher correlations with unfiltered data. > > Any advice what could be going wrong here? I am using > Freesurfer 5.1 > > and FSL 4.1.9 on Linux. > > Thanks, Caspar > > > > > > > > ______________________________ _________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:freesur...@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesur...@nmr.mgh > <mailto:freesur...@nmr.mgh>. harvard.edu > <http://harvard.edu> > <mailto:freesur...@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:freesur...@nmr.mgh <mailto:freesur...@nmr.mgh> > <mailto:freesur...@nmr.mgh <mailto:freesur...@nmr.mgh>>. > harvard.edu <http://harvard.edu> <http://harvard.edu> > > <mailto:freesur...@nmr.mgh > <mailto:freesur...@nmr.mgh>. harvard.edu > <http://harvard.edu> > <mailto:freesur...@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>. edu > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>> . edu > > > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>. edu > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>>> > > Bugs: surfer.nmr.mgh.harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/> > <http://surfer.nmr.mgh. harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/>> fswiki/BugReporting > > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > <http://harvard.edu/fswiki/> BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > <http://harvard.edu/fswiki/> > <http://harvard.edu/fswiki/> BugReporting > > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > <http://harvard.edu/fswiki/> BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > FileDrop: www.nmr.mgh.harvard.edu/ > <http://www.nmr.mgh.harvard.edu/> > <http://www.nmr.mgh.harvard. edu/ > <http://www.nmr.mgh.harvard.edu/>> > facility/filedrop/index.html > > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > ______________________________ > _________________ > > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:freesur...@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesur...@nmr.mgh > <mailto:freesur...@nmr.mgh>. harvard.edu > <http://harvard.edu> > <mailto:freesur...@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:freesur...@nmr.mgh <mailto:freesur...@nmr.mgh> > <mailto:freesur...@nmr.mgh <mailto:freesur...@nmr.mgh>>. > harvard.edu <http://harvard.edu> <http://harvard.edu> > > <mailto:freesur...@nmr.mgh > <mailto:freesur...@nmr.mgh>. harvard.edu > <http://harvard.edu> > <mailto:freesur...@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > The information in this e-mail is > intended only for the > person to > whom it is > addressed. If you believe this e-mail > was sent to you in > error and > the e-mail > contains patient information, please > contact the > Partners > Compliance HelpLine at > http://www.partners.org/ complianceline > <http://www.partners.org/ complianceline > <http://www.partners.org/ complianceline > <http://www.partners.org/complianceline>>> . If the > e-mail was > sent to > you in error > but does not contain patient > information, please > contact the > sender and properly > dispose of the e-mail. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard > <mailto:gr...@nmr.mgh.harvard>. edu > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: surfer.nmr.mgh.harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/> > <http://surfer.nmr.mgh. harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/>> fswiki/BugReporting > > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > <http://harvard.edu/fswiki/> BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > FileDrop: www.nmr.mgh.harvard.edu/ > <http://www.nmr.mgh.harvard.edu/> > <http://www.nmr.mgh.harvard. edu/ > <http://www.nmr.mgh.harvard.edu/>> > facility/filedrop/index.html > > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard. edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/> fswiki/BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: www.nmr.mgh.harvard.edu/ > <http://www.nmr.mgh.harvard.edu/> > facility/filedrop/index.html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/ > facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
