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
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