Hi Maya, the problem is that the wm.dat file, by default, only has one column (just the mean of the WM). It is possible to have the top N principle components in the wm.dat file, but this needs to be set up when you configure the WM fcseed (it does not really help much). The same goes for VCSF. Try just using 1 (ie, -nuisreg wm.dat 1). doug
Maya Rosen wrote: > Hi all, > > We've been trying to use FsFast for functional connectivity analysis > using the left hippocampus as the seed (isolated from aseg). We used > the following command to make the analysis: > > mkanalysis-sess -fwhm 0 -fsd bold -mcextreg -polyfit 2 -TR 2.6 > -analysis lhippo_fcfsfast-analysis -nuisreg wm.dat 3 -nuisreg vcsf.dat > 3 -nuisreg global.waveform.dat 1 -taskreg l_hippo.dat 1 -notask -native > > Note that we specified -notask. This ran fine. > > We then tried to run selxavg3-sess using this command: > > selxavg3-sess -s . -a lhippo_fcfsfast-analysis/ -no-preproc -no-con-ok > > and get this error: > > ERROR: not enough columns > /r2/users/fspace2/RestData/091208RU_MR/bold/020/wm.dat > > ans = > > 116 1 > > This file has one column. And I assume that it is looking for multiple > columns with which to do contrasts. However, this is resting-state > data so there are no contrasts. Looking deeper into the selxavg3-sess > code it seems that the -no-con-ok flag sets RequireContrast to 0. > However, this does not get transferred to fast_selxavg3.m. DoContrasts > = 1 in fast_selxavg.m. I think this is the problem. Any help would be > greatly appreciated!!! > > Maya > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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 . 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.
