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Re: [Freesurfer] Xhemi stat questions
by Gabriel Gonzalez Escamilla 27 Mar '13

27 Mar '13

2 1

Fwd: Cortical thickness in average space
by Rafa X 27 Mar '13

27 Mar '13

Thanks Bruce for your answer, as you asked I'm forwarding this question to the list in case any other can answer this. We already have the surface generated by mri_preproc, now we are trying to read it using the matlab function read_mgh. It returns a 4-D matrix, how can we interpret this data to get the cortical thickness values at each vertex of every subject? Rafa & Gabi 2013/3/26 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Rafa and Gabi > > yes, that's pretty much what the -qcache flag does in recon-all. Or you can > use mri_surf2surf to do it. > > cheers > Bruce > > On Tue, 26 Mar 2013, Rafa X wrote: > >> Hi Freesurfers, >> We would need to obtain the cortical thickness of each subject in the >> space of the average subject (built from our subject population), Does >> it exists? >> If so, Can I use the label files produced by mri_surfcluster to >> directly extract the mean cortical thickness of each ROI in each >> subject? We want to avoid to trasform each cluster to every subject. >> >> Thank you all in advance, >> Rafa & Gabi. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >

2 1

question regarding creating Brodmann area
by Ji Won Bang 27 Mar '13

27 Mar '13

Dear. freesurfer users. I'm trying to make a label for Brodmann area 44. According to the freesurfer manual, I've run, recon-all -s subjid -ba-labels However, it says Flag -ba-labels unrecognized. I'm using freesurfer version 4.5.0. By default, recon-all is supposed to create Brodmann areas under label directory. However, inside the lable directory, I see only aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label Please leave me any comment!! I appreciate it a lot! Best regards, Ji Won Bang

2 1

memory allocation errors on Snow Leopard running dmri_train
by Ping-Hong Yeh 27 Mar '13

27 Mar '13

Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc sysname Darwin hostname twbrkmp2s-Mac-Pro-5.local machine x86_64 user twbrkmp2 Output directory: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni Output directory in test subject's space: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff Output base: lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt Training subject directory list: /private/tmp/subj33.NCNC2348.61836.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz Affine registration from atlas to base for output subject: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat Number of control points for initial spline: 10 Exclude previously chosen center streamlines: 0 Use truncated streamlines: 1 Loading brain mask of output subject from /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz Loading affine registration from /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat Loading streamline start ROI from /apps/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk INFO: Rejected 587 streamlines for straying off mask INFO: Rejected 77 streamlines for reversing direction INFO: Rejected 36 streamlines as length outliers INFO: Have 7732 total streamlines (min/mean/max length: 59/99/129) Loading segmentation from /apps/freesurfer/trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc005/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc005/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc006/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc006/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc007/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc007/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc008/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc008/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc009/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc009/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc010/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc011/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc011/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc012/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc012/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc013/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc013/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc014/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc014/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc015/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc015/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc016/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc016/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc017/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc017/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc018/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc018/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc019/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc019/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc020/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc020/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc021/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc021/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc022/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc022/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc023/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc023/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc024/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc024/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc025/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc025/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc026/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc026/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc027/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc027/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc028/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc028/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(63678) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 138th slice Cannot allocate memory Darwin twbrkmp2s-Mac-Pro-5.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Mar 26 14:40:16 EDT 2013 Any suggestions? Thanks. ping

2 4

Problems with recon-all--won't generate wm or surf files
by Hayley Dorfman 27 Mar '13

27 Mar '13

Hello, I've been having problems with recon-all for only 1 of my 50 subjects. Recon-all is failing somehow before white matter or surf files are generated. The T1 and nu.mgz files look fine. Below are the files that my subject is missing in the 'mri' subdirectory (they are also missing the entire surfs directory): filled.mgz lh.ribbon.mgz rh.ribbon.mgz ribbon.mgz wm.asegedit.mgz wm.mgz wmparc.mgz Below is the last few lines of output from my recon-all log file: "#@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.6 +- 4.9 [80.0 --> 125.0] GM (72.0) : 69.4 +- 10.8 [30.0 --> 96.0] setting bottom of white matter range to 80.2 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5962 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3294 filled 117 bright non-wm voxels segmented. 4879 diagonally connected voxels added... white matter segmentation took 3.4 minutes writing output to wm.seg.mgz... changing input type from 3 to UCHAR mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR reading wm segmentation from wm.seg.mgz... Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013 For more details, see the log file /ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting make: *** [/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz] Error 1" Any ideas as to what might be failing? Thanks for your help! Hayley

2 1

CT as covariate
by Rafa X 27 Mar '13

27 Mar '13

Dear Freesurfers I will introduce the mean cortial thickness as covariate into my statistical model, but I'm wonderind which way will be the best. To get the cortical thickness in individual space, or in AVG space? Thank you all in advanced, Rafa.

2 1

June course on structural and functional connectivity at the Martinos Center
by Anastasia Yendiki 27 Mar '13

27 Mar '13

Dear Freesurfistas - This new course, offered at the Martinos Center right before the OHBM meeting, may be of interest to some of you. There are some open spots left. For info on how to register and a tentative schedule, see the web page at the end of the announcement. a.y --- STRUCTURAL AND FUNCTIONAL BRAIN CONNECTIVITY AS REVEALED BY MRI Dates: June 3-7, 2013 Themes: Resting State Functional Connectivity and DTI/DSI/Tractography Location: Martinos Center for Biomedical Imaging of the Massachusetts General Hospital; Boston/Charlestown Massachusetts Program Director: Robert L. Savoy In December 2012 the Martinos Center for Biomedical Imaging introduced a new, 5-day program on functional and structural connectivity using MRI. The next edition of this program will be held June 3-7 (two weeks prior to the Organization for Human Brain Mapping annual meeting). There is likely to be an additional program in 2013, to be held near the end of October or early November, 2013. Issues associated with connectivity in the human brain are of increasing importance, as reflected in the large number of abstracts, research articles, and even entire journals devoted to this area, as well as the increased emphasis on lesions within the white matter as being a source of many neuro-psychiatric disorders. MRI has proven to be a valuable tool for examining connectivity both in terms of the coordinated activities of neural networks (using BOLD-based fMRI data collected during rest and during tasks) and also in terms of the structural anatomy of white matter pathways of the brain (using Diffusion Tensor Imaging (DTI), Diffusion Spectrum Imaging (DSI), and tractography programs to analyze and visualize the resulting data). Participants will learn about the technical challenges in acquisition, data processing and visualization of brain networks via the data from fMRI during the so-called resting state, but also available during experimenter-initiated cognitive tasks. Participants will also receive a firm grounding in the power and limitations associated with using diffusion-sensitive MRI to detect and organize the anatomical structure of white matter tracts in the living human brain. The primary goal of this program is to give researchers and clinicians a good start for their investigations using these tools. In that sense, it serves a purpose analogous to that of the Functional MRI Visiting Fellowship Program (fMRIVFP) also offered at the Martinos Center, except that the domain will be structural and functional connectivity of myelinated fiber tracts within the living human brain. The active component of the program will be the use of software tools to promote quality assurance in the data, detect outliers and other problematic attributes of the data, optimize data acquisition, and flexibly visualize the data in the service of asking and answering specific questions. Participants will be expected (though not required) to bring a suitable laptop computer for engaging in the hands-on exercises of the program. There will also be a section on the Connectome MRI Machine that uses exceptionally strong gradients to enhance data acquisition of strutural and functional images. The core faculty is drawn from the staff of the Athinoula A. Martinos Center (of the Massachusetts General Hospital and Massachusetts Institute of Technology) and affiliated faculty from Harvard University, McLean Hospital and other local institutions. Guest lecturers (at the Dec, 2012 program) included faculty from the Child Mind Institute of New York, NIH, Stanford University, The Donders Institute, the University of Cambridge and others. For questions, e-mail: fmrivfp(a)nmr.mgh.harvard.edu For more information and registration, see: http://martinos.org/ConnectivityCourse

1 0

Incomplete and poorly formed tracts
by Susan Kuo 27 Mar '13

27 Mar '13

Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH

2 10

Question regarding the subject directory
by Lukas.Scheef＠ukb.uni-bonn.de 27 Mar '13

27 Mar '13

Hi folks! I would like to use a different subject dirctory (setenv SUBJECTS_DIR <full path to subject dir>). Does freesurfer still finds the folders which are located in the default subjects directory of the FS installation? Or are they simply not needed for the recon-all process ? I refer to cvs_avg35 etc. not to the test data sets. Please excuse if this question is stupid ... but considering the processsing time ... Many thanks in advance, Luke

2 1

getting started with ROI & labels
by Fred Lado 27 Mar '13

27 Mar '13

Dear Freesurfers, I'm interested in using FS identified labels, such as Brodman areas in the anatomical volume, to measure a feature, say mean intensity in V1, in a second volume registered to the first. I'm new to the use of labels, so some advice on where to start would be appreciated. Thanks, Fred Lado, MD PhD Director, Neurology Service - Moses & North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: flado(a)montefiore.org Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately.

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