Not sure what is going wrong with the 1st cmd, but the 2nd has a double dash just before Sess49 (--s) that is causing the problem
doug On 03/31/2015 07:55 AM, std...@virgilio.it wrote: > Hi list, > > I'm performing the FS-FAST analysis. > > Some months ago, I have already preformed this analysis on some > subjects without problem. > > Now, I have added some subjects. When I rerun the analysis i have > these error: > > for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh > -contrast L_Thalamus -o my-group_thal_LH > > ERROR: finding sessions > > Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15 > /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48 > /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49 > /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50 > > [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano% > > > and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s > Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s > Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s > Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s > Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s > Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh > -contrast L_Thalamus -o my-group_THAL_LEFT > > ERROR: Flag —s unrecognized. > > > FUNCTIONAL_DATA directory contains: > > > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201 > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess45/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess46/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess47/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/sessidlist > > for each subject, i.e. within > Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01: > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/002/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/003/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/fc.lthalseed.surf.lh/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/fc.rthalseed.surf.rh/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/masks/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/template.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/template.nii.gz > > i.e. within Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/001: > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/f.nii.gz > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.mat.aff12.1D > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.mcdat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.nii.gz > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.nii.gz.mclog > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.sm5.fsaverage.lh.nii.gz > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.sm5.fsaverage.rh.nii.gz > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.sm5.mni305.2mm.nii.gz > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/global.meanval.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/global.waveform.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/init.register.dof6.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/L_Thalamus.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/L_Thalamus.dat.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/masks/ > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/mcdat2extreg.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/mcprextreg > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/R_Thalamus.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/R_Thalamus.dat.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/register.dof6.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/register.dof6.dat.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/register.dof6.dat.mincost > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/register.dof6.dat.param > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/register.dof6.dat.sum > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/template.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/template.nii.gz > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/vcsf.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/vcsf.dat.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/vcsf.dat.pca-stats.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/wm.dat > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/wm.dat.log > file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/wm.dat.pca-stats.dat > > Is possible that some folders are lacking? > > Kind regards and thanks, > > > Stefano > > > _______________________________________________ > 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: 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 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.
