they are the files named like "fmcpr.odd.nii.gz"
On 09/04/2015 08:17 AM, [email protected] wrote: > 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.nii > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.mat.aff12.1D > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.mcdat > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.nii.gz.mclog > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.nii.gz.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.fsaverage.rh.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.mni305.1mm.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.fsaverage.lh.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.fsaverage.rh.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.mni305.2mm.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/global.meanval.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/global.waveform.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/init.register.dof6.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/L_Amygdala.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/L_Amygdala.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/L_orbitofrontal.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/L_orbitofrontal.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/L_Thalamus.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/L_Thalamus.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/masks/ > file:///Applications/freesurfer/subjects/Sess101/rest/001/mcdat2extreg.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/mcprextreg > file:///Applications/freesurfer/subjects/Sess101/rest/001/R_Amygdala.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/R_Amygdala.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/R_orbitofrontal.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/R_orbitofrontal.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/R_Thalamus.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/R_Thalamus.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.mincost > file:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.param > file:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.sum > file:///Applications/freesurfer/subjects/Sess101/rest/001/template.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/template.nii.gz > file:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat.log > file:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat.pca-stats.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/wm.dat > file:///Applications/freesurfer/subjects/Sess101/rest/001/wm.dat.log > file:///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 command > On 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 siemens > > produces 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. 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. > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
