Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Download freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
by ye tian 14 Aug '13

14 Aug '13

Dear Freesurfers, Has anyone recently downloaded freesurfer for Mac OS X 10.6? I tried downloading on two computers, and they gave errors of "no mountable file systems" and "not recognized" respectively. If someone has happened to download the same version, would you please let me know whether your download has worked? Thank you very much! Sincerely, Ye

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Re: [Freesurfer] trac-all download
by Anastasia Yendiki 14 Aug '13

14 Aug '13

If you already have the 5.1 version and have used it on some subjects, you can of course use the same version on the other subjects. But if you're going to download something new, that should be the 5.3 version, not an intermediate update to 5.1. It's highly recommended to use the 5.3 version of tracula b/c there are several improvements to it. On Wed, 14 Aug 2013, ana ;osp wrote: > thanksbut i'have all the data processed with 5.1 and i still have a few subjects to process so i didn't want to > download the 5.3 and mix versions... is there anyway to have it without download the 5.3? > thanks > > > > On Wed, Aug 14, 2013 at 11:11 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Ana - If you notice the release notes, this was relevant to an old version of tracula. You should now > be using the latest version of tracula that's included in freesurfer 5.3, in which case you don't need any > extra downloads. > > a.y > > On Wed, 14 Aug 2013, ana ;osp wrote: > > hi'm trying to download the trac-all file from the site in the tracula release notes, it is the > download from > 2012/1/09 recommended for all, but hen i click it open a page and gives me an errorshould i do something > different > than just click? > thanks > > > > > > 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. > > > >

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Re: [Freesurfer] Path analysis
by Anastasia Yendiki 14 Aug '13

14 Aug '13

This has to do with this error, which happened at an earlier step, during preprocessing (which is why checking all of the trac-all.log is important): /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train: Command not found. You mentioned this problem last week, and there's an email from you on August 6th stating that the problem was fixed. How was the problem fixed? On Wed, 14 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Attached please find the trac-all log. > > thanks, > > Alan > > > On Wed, Aug 14, 2013 at 1:51 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Alan - As I asked before, please attach the entire file scripts/trac-all.log. Add it to your messaage as a > file attachment, don't paste any of it in the message. Is this clear? > > a.y > > > On Wed, 14 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > One of my brains had a problem when doing trac-all -path analysis. Please see below the complete > pathway. Thanks so > much for your help. > > Alan > > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -path > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-104 > INFO: SUBJECTS_DIR is > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons > INFO: Diffusion root is > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ > Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 > trac-paths -c > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/dmrirc.local > -log > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/trac-all.log > -cmd > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/trac-all.cmd > #------------------------------------- > /usr/local/freesurfer/stable5_3_0//bin/trac-paths > #------------------------------------- > #@# Path reconstruction Wed Aug 14 13:36:21 EDT 2013 > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni > _bb > r > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mn > i_b > br > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mn > i_b > br > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mn > i_b > br > rm-rf/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mn > i_b > br > /usr/local/freesurfer/stable5_3_0//bin/dmri_paths--outdir/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg3 > 3_mni_bb > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_ > b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni > _b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni > _b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni > _b > br --dwi > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz > --grad /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs > --bval > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals--mask/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg > _mask. > bbr.nii.gz --bpdir > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX > --ntr 2 --fmin > 0.05--roi1/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS_a > vg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cst_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.unc_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.unc_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ilf_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ilf_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fmajor_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fminor_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.atr_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.atr_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ccg_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ccg_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.cab_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cab_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.slfp_PP_avg33_ > mni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slfp_PP_avg33_ > mni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/lh.slft_PP_avg33_ > mni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slft_PP_avg33_ > mni_bbr_end1_dil.nii.gz--roi2/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS_a > vg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cst_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.unc_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.unc_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ilf_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ilf_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fmajor_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fminor_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.atr_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.atr_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ccg_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ccg_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.cab_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cab_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.slfp_PP_avg33_ > mni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slfp_PP_avg33_ > mni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/lh.slft_PP_avg33_ > mni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slft_PP_avg33_ > mni_bbr_end2_dil.nii.gz --reg > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/diff2mni.bbr.mat > --init/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cst_AS_ > avg33_ > mni_bbr_cpts_6.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.cst_AS_avg33_ > mni_bbr_cpts_6.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.unc_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.unc_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.ilf_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.ilf_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/fmajor_PP_avg33_ > mni_bbr_cpts_7.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/fminor_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.atr_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.atr_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.ccg_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.ccg_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.cab_PP_avg33_ > mni_bbr_cpts_4.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.cab_PP_avg33_ > mni_bbr_cpts_4.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.slfp_PP_avg33 > _mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/di > ff/rh.slfp_PP_avg33 > _mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/di > ff/lh.slft_PP_avg33 > _mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/di > ff/rh.slft_PP_avg33 > _mni_bbr_cpts_5.txt--nprior/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS > _avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.cst_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cst_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.cst_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.unc_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.unc_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.unc_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.unc_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ilf_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.ilf_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ilf_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.ilf_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fmajor_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/fmajor_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fminor_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/fminor_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.atr_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.atr_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.atr_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.atr_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ccg_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.ccg_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ccg_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.ccg_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.cab_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.cab_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cab_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.cab_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.slfp_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/lh.slfp_PP_avg33_ > mni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slfp_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/rh.slfp_PP_avg33_ > mni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/lh.slft_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/lh.slft_PP_avg33_ > mni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slft_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/rh.slft_PP_avg33_ > mni_bbr_fsnnids_all--lprior/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS > _avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.cst_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.cst_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cst_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.unc_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.unc_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.unc_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.unc_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.ilf_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ilf_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.ilf_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ilf_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/f > major_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fmajor_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/f > minor_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fminor_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.atr_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.atr_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.atr_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.atr_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.ccg_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ccg_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.ccg_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ccg_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.cab_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.cab_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.cab_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cab_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.slfp_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/lh.slfp_PP_avg33_ > mni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/ > rh.slfp_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slfp_PP_avg33_ > mni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/ > lh.slft_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/lh.slft_PP_avg33_ > mni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/ > rh.slft_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slft_PP_avg33_ > mni_bbr_fsids_all--seg/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/aparc+aseg.n > ii.gz > --nb 200 --ns 7500 --nu 0 --nk 5--sdp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cst_AS_a > vg33_ > mni_bbr_cpts_6_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.cst_AS_avg33_ > mni_bbr_cpts_6_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.unc_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.unc_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.ilf_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.ilf_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/fmajor_PP_avg33_ > mni_bbr_cpts_7_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/fminor_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.atr_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.atr_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.ccg_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.ccg_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.cab_PP_avg33_ > mni_bbr_cpts_4_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.cab_PP_avg33_ > mni_bbr_cpts_4_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.slfp_PP_avg33 > _mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/diff/rh.slfp_PP_avg33 > _mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/diff/lh.slft_PP_avg33 > _mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/diff/rh.slft_PP_avg33 > _mni_bbr_cpts_5_std.txt > > > cwd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons > cmdline /usr/local/freesurfer/stable5_3_0//bin/dmri_paths--outdir/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg3 > 3_mni_bb > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_ > b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni > _b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni > _b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni > _b > br --dwi > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz > --grad /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs > --bval > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals--mask/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg > _mask. > bbr.nii.gz --bpdir > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX > --ntr 2 --fmin > 0.05--roi1/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS_a > vg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cst_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.unc_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.unc_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ilf_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ilf_AS_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fmajor_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fminor_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.atr_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.atr_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ccg_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ccg_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.cab_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cab_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.slfp_PP_avg33_ > mni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slfp_PP_avg33_ > mni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/lh.slft_PP_avg33_ > mni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slft_PP_avg33_ > mni_bbr_end1_dil.nii.gz--roi2/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS_a > vg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cst_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.unc_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.unc_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ilf_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ilf_AS_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fmajor_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/fminor_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.atr_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.atr_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.ccg_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.ccg_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.cab_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/rh.cab_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /mni/lh.slfp_PP_avg33_ > mni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slfp_PP_avg33_ > mni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/lh.slft_PP_avg33_ > mni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/mni/rh.slft_PP_avg33_ > mni_bbr_end2_dil.nii.gz --reg > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/diff2mni.bbr.mat > --init/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cst_AS_ > avg33_ > mni_bbr_cpts_6.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.cst_AS_avg33_ > mni_bbr_cpts_6.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.unc_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.unc_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.ilf_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.ilf_AS_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/fmajor_PP_avg33_ > mni_bbr_cpts_7.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/fminor_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.atr_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.atr_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.ccg_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.ccg_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.cab_PP_avg33_ > mni_bbr_cpts_4.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/rh.cab_PP_avg33_ > mni_bbr_cpts_4.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/dif > f/lh.slfp_PP_avg33 > _mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/di > ff/rh.slfp_PP_avg33 > _mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/di > ff/lh.slft_PP_avg33 > _mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/di > ff/rh.slft_PP_avg33 > _mni_bbr_cpts_5.txt--nprior/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS > _avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.cst_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cst_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.cst_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.unc_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.unc_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.unc_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.unc_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ilf_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.ilf_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ilf_AS_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.ilf_AS_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fmajor_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/fmajor_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fminor_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/fminor_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.atr_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.atr_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.atr_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.atr_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ccg_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.ccg_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ccg_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.ccg_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.cab_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/lh.cab_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cab_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/m > ni/rh.cab_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.slfp_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/lh.slfp_PP_avg33_ > mni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slfp_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/rh.slfp_PP_avg33_ > mni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/lh.slft_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/lh.slft_PP_avg33_ > mni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slft_PP_avg33_ > mni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/ > mni/rh.slft_PP_avg33_ > mni_bbr_fsnnids_all--lprior/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS > _avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.cst_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.cst_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cst_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.unc_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.unc_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.unc_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.unc_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.ilf_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ilf_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.ilf_AS_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ilf_AS_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/f > major_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fmajor_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/f > minor_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /fminor_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.atr_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.atr_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.atr_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.atr_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.ccg_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.ccg_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.ccg_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.ccg_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.cab_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /lh.cab_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/r > h.cab_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni > /rh.cab_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/l > h.slfp_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/lh.slfp_PP_avg33_ > mni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/ > rh.slfp_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slfp_PP_avg33_ > mni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/ > lh.slft_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/lh.slft_PP_avg33_ > mni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/ > rh.slft_PP_avg33_ > mni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mn > i/rh.slft_PP_avg33_ > mni_bbr_fsids_all--seg/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/aparc+aseg.n > ii.gz > --nb 200 --ns 7500 --nu 0 --nk 5--sdp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cst_AS_a > vg33_ > mni_bbr_cpts_6_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.cst_AS_avg33_ > mni_bbr_cpts_6_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.unc_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.unc_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.ilf_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.ilf_AS_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/fmajor_PP_avg33_ > mni_bbr_cpts_7_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/fminor_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.atr_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.atr_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.ccg_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.ccg_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.cab_PP_avg33_ > mni_bbr_cpts_4_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/rh.cab_PP_avg33_ > mni_bbr_cpts_4_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel > /diff/lh.slfp_PP_avg33 > _mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/diff/rh.slfp_PP_avg33 > _mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/diff/lh.slft_PP_avg33 > _mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabe > l/diff/rh.slft_PP_avg33 > _mni_bbr_cpts_5_std.txt > sysname Linux > hostname cerebro > machine x86_64 > user alanf > Outputdirectory:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_av > g33_mni_bb > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_b > b > r/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_ > b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni > _b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni > _b > br/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni > _b > br > DWIs: > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz > Gradients: > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs > B-values: > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals > Mask:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_ > mask. > bbr.nii.gz > BEDPOST directory: > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX > Max number of tracts per voxel: 2 > Tract volume fraction threshold: 0.05 > Initial control pointfile:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cst_AS_av > g33_m > ni_bbr_cpts_6.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > rh.cst_AS_avg33_m > ni_bbr_cpts_6.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > lh.unc_AS_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > rh.unc_AS_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > lh.ilf_AS_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > rh.ilf_AS_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > fmajor_PP_avg33_m > ni_bbr_cpts_7.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > fminor_PP_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > lh.atr_PP_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > rh.atr_PP_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > lh.ccg_PP_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > rh.ccg_PP_avg33_m > ni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > lh.cab_PP_avg33_m > ni_bbr_cpts_4.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > rh.cab_PP_avg33_m > ni_bbr_cpts_4.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/ > lh.slfp_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff > /rh.slfp_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff > /lh.slft_PP_avg33_ > mni_bbr_cpts_5.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff > /rh.slft_PP_avg33_ > mni_bbr_cpts_5.txt > End ROI1:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_ > mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.cst_AS_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.unc_AS_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.unc_AS_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.ilf_AS_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.ilf_AS_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/fmajor_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/fminor_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.atr_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.atr_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.ccg_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.ccg_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.cab_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.cab_PP_avg33_mn > i_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.slfp_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > mni/rh.slfp_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > mni/lh.slft_PP_avg33_m > ni_bbr_end1_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > mni/rh.slft_PP_avg33_m > ni_bbr_end1_dil.nii.gz > End ROI2:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_ > mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.cst_AS_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.unc_AS_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.unc_AS_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.ilf_AS_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.ilf_AS_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/fmajor_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/fminor_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.atr_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.atr_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.ccg_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.ccg_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.cab_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/rh.cab_PP_avg33_mn > i_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/m > ni/lh.slfp_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > mni/rh.slfp_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > mni/lh.slft_PP_avg33_m > ni_bbr_end2_dil.nii.gz/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > mni/rh.slft_PP_avg33_m > ni_bbr_end2_dil.nii.gz > Neighbor asegprior:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_av > g33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /rh.cst_AS_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /lh.unc_AS_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /rh.unc_AS_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /lh.ilf_AS_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /rh.ilf_AS_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /fmajor_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /fminor_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /lh.atr_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /rh.atr_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /lh.ccg_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /rh.ccg_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /lh.cab_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /rh.cab_PP_avg33_mn > i_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni > /lh.slfp_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mn > i/rh.slfp_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mn > i/lh.slft_PP_avg33_m > ni_bbr_fsnnprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mn > i/rh.slft_PP_avg33_m > ni_bbr_fsnnprior_all > Neighbor aseg label IDlist:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg > 33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.cst_AS_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.unc_AS_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.unc_AS_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.ilf_AS_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.ilf_AS_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/f > major_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/f > minor_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.atr_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.atr_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.ccg_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.ccg_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.cab_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.cab_PP_avg33_mn > i_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.slfp_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/ > rh.slfp_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/ > lh.slft_PP_avg33_m > ni_bbr_fsnnids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/ > rh.slft_PP_avg33_m > ni_bbr_fsnnids_all > Neighbor aseg prior set: 14 > Local asegprior:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_av > g33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.cst_AS_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.unc_AS_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.unc_AS_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.ilf_AS_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.ilf_AS_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/f > major_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/f > minor_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.atr_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.atr_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.ccg_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.ccg_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.cab_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/r > h.cab_PP_avg33_mn > i_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/l > h.slfp_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/ > rh.slfp_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/ > lh.slft_PP_avg33_m > ni_bbr_fsprior_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/ > rh.slft_PP_avg33_m > ni_bbr_fsprior_all > Local aseg label IDlist:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg > 33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh. > cst_AS_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh. > unc_AS_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh. > unc_AS_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh. > ilf_AS_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh. > ilf_AS_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fma > jor_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmi > nor_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh. > atr_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh. > atr_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh. > ccg_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh. > ccg_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh. > cab_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh. > cab_PP_avg33_mn > i_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh. > slfp_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh > .slfp_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh > .slft_PP_avg33_m > ni_bbr_fsids_all/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh > .slft_PP_avg33_m > ni_bbr_fsids_all > Local aseg prior set: 15 > Segmentation map: > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/aparc+aseg.nii.gz > DWI-to-atlas affine registration: > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dmri/xfms/diff2mni.bbr.mat > Number of burn-in samples: 200 > Number of post-burn-in samples: 7500 > Keep every: 5-th sample > Update proposal every: 0-th sample > Initial proposal SDfile:/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cst_AS_av > g33_m > ni_bbr_cpts_6_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/rh.cst_AS_avg33_m > ni_bbr_cpts_6_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/lh.unc_AS_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/rh.unc_AS_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/lh.ilf_AS_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/rh.ilf_AS_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/fmajor_PP_avg33_m > ni_bbr_cpts_7_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/fminor_PP_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/lh.atr_PP_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/rh.atr_PP_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/lh.ccg_PP_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/rh.ccg_PP_avg33_m > ni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/lh.cab_PP_avg33_m > ni_bbr_cpts_4_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/rh.cab_PP_avg33_m > ni_bbr_cpts_4_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/d > iff/lh.slfp_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > diff/rh.slfp_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > diff/lh.slft_PP_avg33_ > mni_bbr_cpts_5_std.txt/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/ > diff/rh.slft_PP_avg33_ > mni_bbr_cpts_5_std.txt > Loading DWIs from > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz > Loading maskfrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_m > ask. > bbr.nii.gz > Loading BEDPOST parameter samples from > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX > Loading b-values from > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals > Loading gradients from > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs > INFO: Found 10 baseline images (b = 0) out of a total of 70 frames > INFO: Found 182362 voxels in brain mask > INFO: Resolution of DWI space relative to base space is (1, 1, 1) > Loading atlas reference volumefrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg3 > 3_mn > i_bbr_end1_dil.nii.gz > niiRead(): error openingfile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg3 > 3_mn > i_bbr_end1_dil.nii.gz > ERROR: Could notread/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg3 > 3_mn > i_bbr_end1_dil.nii.gz > Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > trac-paths exited with ERRORS at Wed Aug 14 13:37:20 EDT 2013 > > > > > > 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. > > > >

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TCL script not exiting
by Greg Book 14 Aug '13

14 Aug '13

I have a bash script which calls a .tcl script through which I'm running tksurfer. It works, except the script is no longer exiting when it reaches the end. Instead, it displays the tksurfer window and stays open. After I click the menu option to Quit, the script continues. Below is the script open_window set lablpth "$env(SUBJECTS_DIR)/$env(SUBJECT_NAME)/label" set outpth "$env(SUBJECTS_DIR)/$env(SUBJECT_NAME)/shots" labl_import_annotation "$lablpth/$hemi.$env(PARC).annot" redraw UpdateAndRedraw puts "Taking Snapshots..." if {![file exists "$outpth/$env(SUBJECT_NAME)_${hemi}_$env(SURF)_$env(PARC)_lat.tif"]} { make_lateral_view redraw set tiff "$outpth/$env(SUBJECT_NAME)_${hemi}_$env(SURF)_$env(PARC)_lat.tif" save_tiff $tiff } if {![file exists "$outpth/$env(SUBJECT_NAME)_${hemi}_$env(SURF)_$env(PARC)_med.tif"]} { make_lateral_view rotate_brain_y 180 redraw set tiff "$outpth/$env(SUBJECT_NAME)_${hemi}_$env(SURF)_$env(PARC)_med.tif" save_tiff $tiff } exit(0)

2 3

Re: [Freesurfer] Tracula failed
by Anastasia Yendiki 14 Aug '13

14 Aug '13

Why do you want to use a '$'? On Wed, 14 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Yes the path that you pointed out is the one I presently use. Is there no way to use the '$' as a substitute? > > thanks, > > Alan > > > On Wed, Aug 14, 2013 at 1:46 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Alan - Where is the location that has plenty of space? You should set your SUBJECTS_DIR to that location, > e.g., > > setenv SUBJECTS_DIR /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons > > > On Wed, 14 Aug 2013, Alan Francis wrote: > > Hi Anastasia/ FreeSurfers > > I did not use the conventional path usr/local/freesurfer. since there is very little disc space in > this location. > Alternately I set the environment at a location where is plenty of disc space and then sourced it. > > For the SUBJECTS_DIR I set the environment without using the dollar sign $. > > The Freesurfer recons and Tracula ran without problem and saved the processed data to this > location. So the > FReeSurfer recons and tracula data are in the same location. > > Now I am trying to use the dollar sign, so that I can extract the trac data, but I keep getting the > error message. > > csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : > setenv > SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons > > FreeSurfer_Data: Undefined variable. > > > thanks, > > Alan > > > On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Where did you get this command line? You should set the SUBJECTS_DIR to the location on disk where > your > freesurfer recons are. > > > On Wed, 14 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > I fixed that problem - thank you. However, I have another question. i am trying extract trac data > but when I set > environment, I get an error message: > > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv > SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons > > FreeSurfer_Data: Undefined variable. > > How do I solve this? > > Thanks again, > > Alan > > > > On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Alan - I'm not sure where the output from the one subject ends the the other starts. For > future > reference, it's best to attach the entire trac-all.log files instead of copying and pasting > parts of them > into your message. > > I see two error messages here: > 1. "ERROR: must specify as many DWI dicoms as subjects" > This is as it says. Check your configuration file and see if the numbers of entries in > subjlist and > dcmlist are the same. > > 2. "ERROR: reading > > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz" > I'm guessing the problem is in the b-value table. How many entries are there that correspond > to low-b > images? > > a.y > > On Tue, 13 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > Thanks to your advice most of the data have been processed using Tracula. Two brains gave me > error > messages that are > as follows: > > > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all > -prep > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 > ERROR: must specify as many DWI dicoms as subjects > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all > -prep > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 > INFO: SUBJECTS_DIR is > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons > INFO: Diffusion root is > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ > Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 > trac-preproc -c > > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local > -log > > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log > -cmd > > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd > #------------------------------------- > /usr/local/freesurfer/stable5_3_0//bin/trac-preproc > #------------------------------------- > #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 > mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 > > > 90224_14110 > 2DIFFUSIONHighRess016a001.nii > > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz > mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 > > > 90224_14110 > 2DIFFUSIONHighRess016a001.nii > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > readingfrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 > > 90224_1 > 4110 > 2DIFFUSIONHighRess016a001.nii... > TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.997762, -0.0667414, -0.00403802) > j_ras = (-0.0662713, 0.979101, 0.192276) > k_ras = (0.00887916, -0.192114, 0.981333) > writing to > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz... > cp > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs > cp > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals > flip4fsl > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz > INFO: input image orientation is LAS > INFO: input image determinant is -6.8719 > fslswapdim > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz > x y z > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz > fslorient -forceradiological > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz > INFO: found > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals, > converting to FSL format > INFO: found > > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs, > converting to FSL format > mv-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.b > > ve > cs > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs > mv-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.b > > va > ls > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvals > eddy_correct > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz 0 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0000 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0001 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0002 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0003 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0004 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0005 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0006 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0007 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0008 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0009 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0010 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0011 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0012 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0013 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0014 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0015 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0016 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0017 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0018 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0019 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0020 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0021 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0022 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0023 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0024 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0025 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0026 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0027 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0028 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0029 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0030 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0031 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0032 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0033 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0034 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0035 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0036 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0037 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0038 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0039 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0040 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0041 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0042 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0043 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0044 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0045 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0046 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0047 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0048 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0049 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0050 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0051 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0052 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0053 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0054 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0055 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0056 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0057 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0058 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0059 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0060 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0061 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0062 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0063 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0064 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0065 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0066 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0067 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0068 > processing > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0069 > mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot > xfmrot > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.ecclog > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs > ln -sf > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/data.nii.gz > awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) > mri_concat --i > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz > --mean --o > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/lowb.nii.gz > niiRead(): error opening file > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz > ninputs = 1 > Checking inputs > ERROR: reading > /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz > Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > trac-preproc exited with ERRORS at Mon Aug 12 17:30:05 EDT 2013 > > As always - thanks for your help, > > best, > > Alan > > Martinos Center. > > > > > > 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. > > > > > > > >

1 0

Path analysis
by Alan Francis 14 Aug '13

14 Aug '13

Hi Anastasia: One of my brains had a problem when doing trac-all -path analysis. Please see below the complete pathway. Thanks so much for your help. Alan csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -path -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-104 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-paths -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable5_3_0//bin/trac-paths #------------------------------------- #@# Path reconstruction Wed Aug 14 13:36:21 EDT 2013 rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni_bbr rm -rf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni_bbr /usr/local/freesurfer/stable5_3_0//bin/dmri_paths --outdir /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni_bbr --dwi /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz --grad /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs --bval /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals --mask /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt cwd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons cmdline /usr/local/freesurfer/stable5_3_0//bin/dmri_paths --outdir /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs --bval /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals --mask /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/diff2mni.bbr.mat --init /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt 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/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt sysname Linux hostname cerebro machine x86_64 user alanf Output directory: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cst_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.unc_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.unc_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ilf_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ilf_AS_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fmajor_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/fminor_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.atr_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.atr_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.ccg_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.ccg_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.cab_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.cab_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slfp_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slfp_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/lh.slft_PP_avg33_mni_bbr /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dpath/rh.slft_PP_avg33_mni_bbr DWIs: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz Gradients: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs B-values: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals Mask: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_mask.bbr.nii.gz BEDPOST directory: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX Max number of tracts per voxel: 2 Tract volume fraction threshold: 0.05 Initial control point file: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt End ROI 1: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz End ROI 2: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz Neighbor aseg prior: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all Neighbor aseg label ID list: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all Neighbor aseg prior set: 14 Local aseg prior: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all Local aseg label ID list: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all Local aseg prior set: 15 Segmentation map: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/aparc+aseg.nii.gz DWI-to-atlas affine registration: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dmri/xfms/diff2mni.bbr.mat Number of burn-in samples: 200 Number of post-burn-in samples: 7500 Keep every: 5-th sample Update proposal every: 0-th sample Initial proposal SD file: /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Loading DWIs from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/dwi.nii.gz Loading mask from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri.bedpostX Loading b-values from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvals Loading gradients from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/bvecs INFO: Found 10 baseline images (b = 0) out of a total of 70 frames INFO: Found 182362 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/BW_104/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Wed Aug 14 13:37:20 EDT 2013

2 1

Tracula failed
by Alan Francis 14 Aug '13

14 Aug '13

Hi Anastasia: Thanks to your advice most of the data have been processed using Tracula. Two brains gave me error messages that are as follows: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124 ERROR: must specify as many DWI dicoms as subjects csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118 INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable5_3_0//bin/trac-preproc #------------------------------------- #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_141102DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_141102DIFFUSIONHighRess016a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_141102DIFFUSIONHighRess016a001.nii... TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997762, -0.0667414, -0.00403802) j_ras = (-0.0662713, 0.979101, 0.192276) k_ras = (0.00887916, -0.192114, 0.981333) writing to /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals flip4fsl /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -6.8719 fslswapdim /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz x y z /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvals eddy_correct /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz 0 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0000 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0001 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0002 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0003 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0004 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0005 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0006 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0007 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0008 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0009 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0010 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0011 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0012 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0013 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0014 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0015 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0016 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0017 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0018 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0019 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0020 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0021 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0022 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0023 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0024 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0025 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0026 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0027 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0028 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0029 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0030 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0031 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0032 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0033 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0034 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0035 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0036 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0037 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0038 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0039 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0040 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0041 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0042 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0043 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0044 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0045 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0046 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0047 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0048 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0049 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0050 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0051 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0052 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0053 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0054 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0055 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0056 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0057 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0058 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0059 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0060 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0061 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0062 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0063 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0064 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0065 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0066 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0067 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0068 processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0069 mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot xfmrot /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.ecclog /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs ln -sf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/data.nii.gz awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz --mean --o /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/lowb.nii.gz niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Aug 12 17:30:05 EDT 2013 As always - thanks for your help, best, Alan Martinos Center.

2 5

Expert opts
by Victor Kovac 14 Aug '13

14 Aug '13

Dear Freesurfer experts, I am needing to manually re-set T1.mgz intensity ranges in recon-all, because, currently, only voxels under 80 are getting segmented as gray matter, which is generally outside of the brain. Additionally, all voxels with an intensity of 80 or more are segmented as wm. I have attached an image of what this looks like. I looked through this page ( http://ftp.nmr.mgh.harvard.edu/fswiki/recon-all#Arguments) but did not recognize a command that corresponds to what I need. Could any of you tell me how to use expert options to set intensity ranges for wm or gm? I need to re-set both, I think. Thank you so much! Victor

1 0

Fornix labelled as corpus callosum in patient with periventricular leukomalacia
by Corinna Bauer 14 Aug '13

14 Aug '13

Hello all, I am examining diffusion tracking in the corpus callosum of individuals with periventricular leukomalacia (PVL). The corpus callosum is particularly small and the anterior and mid-anterior labels are being applied to the fornix (see attached Fornix_labelled_as_CC.png). The midposterior and posterior look ok, while the central is very small, maybe one voxel in size. The wm segmentation, seen with ?l.white, also shows segmentation defaults with the anterior corpus callosum (see attached images). I tried to correct this using control points, which you can see did not fix the segmentation. Any suggestions? Corinna

2 1

MCSRCH ERROR
by Eli Fredman 14 Aug '13

14 Aug '13

I ran 10 cases through freesurfer5.3 last night and found that they all exited with the same error. This is the input that I used: recon-all -i /projects/schiz/NFL/case01409/strct/align-space/01409-t1w-realign-masked.nii.gz -autorecon1 -noskullstrip -subjid 01409 && cp subjects/01409/mri/T1.mgz subjects/01409/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01409 && recon-all -autorecon3 -subjid 01409 I've attached the recon-all.log file which shows the following error: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 (as a side note, the reason I don't simply run recon-all -all is because this doesn't seem to acknowledge the -noskullstrip tag). Thanks for the help! -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150

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