Hi using Philips scanner (interleaved)Therefore, I'm running preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -sliceorder odd However, as you can see below stc has been not produced.
file:///Applications/freesurfer/subjects/Sess101/rest/001/f.niifile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.mat.aff12.1Dfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.mcdatfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.nii.gz.mclogfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.nii.gz.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.fsaverage.lh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.fsaverage.rh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.mni305.1mm.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.fsaverage.lh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.fsaverage.rh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.mni305.2mm.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/global.meanval.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/global.waveform.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/init.register.dof6.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Amygdala.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Amygdala.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_orbitofrontal.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_orbitofrontal.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Thalamus.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Thalamus.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/masks/file:///Applications/freesurfer/subjects/Sess101/rest/001/mcdat2extreg.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/mcprextregfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Amygdala.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Amygdala.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_orbitofrontal.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_orbitofrontal.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Thalamus.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Thalamus.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.mincostfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.paramfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.sumfile:///Applications/freesurfer/subjects/Sess101/rest/001/template.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/template.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat.pca-stats.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/wm.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/wm.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/wm.dat.pca-stats.dat Thanks, Stefano what slice order was the data created with? Find out and then use that slice order in the commandOn 8/26/15 4:14 AM, [email protected] wrote: Hi list,I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run. I have acquired data using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder siemens"?The command line: preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -sliceorder siemensproduces the files reported below. fmcstc files are lacking. Please, give me an help. Thanks, Stefano file:///Applications/freesurfer/subjects/Sess201/rest/001/f.nii file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.mat.aff12.1D file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.mcdat file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.nii.gz.mclog file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.nii.gz.log file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.sm5.fsaverage.lh.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.sm5.fsaverage.rh.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.sm5.mni305.1mm.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.sm5.fsaverage.lh.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.sm5.fsaverage.rh.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.sm5.mni305.1mm.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/global.meanval.dat file:///Applications/freesurfer/subjects/Sess201/rest/001/global.waveform.dat file:///Applications/freesurfer/subjects/Sess201/rest/001/init.register.dof6.dat file:///Applications/freesurfer/subjects/Sess201/rest/001/masks/ file:///Applications/freesurfer/subjects/Sess201/rest/001/mcdat2extreg.log file:///Applications/freesurfer/subjects/Sess201/rest/001/mcprextreg file:///Applications/freesurfer/subjects/Sess201/rest/001/register.dof6.dat file:///Applications/freesurfer/subjects/Sess201/rest/001/register.dof6.dat.log file:///Applications/freesurfer/subjects/Sess201/rest/001/register.dof6.dat.mincost file:///Applications/freesurfer/subjects/Sess201/rest/001/register.dof6.dat.param file:///Applications/freesurfer/subjects/Sess201/rest/001/register.dof6.dat.sum file:///Applications/freesurfer/subjects/Sess201/rest/001/template.log file:///Applications/freesurfer/subjects/Sess201/rest/001/template.nii.gz file:///Applications/freesurfer/subjects/Sess201/rest/001/tmp.mc-afni2.6432/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] 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. 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