Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Re: [Freesurfer] Tracula Cluster Question
by Anastasia Yendiki 28 Mar '13

28 Mar '13

Hi Sal, 1. I have no experience with the sun grid engine, perhaps someone else on the list can help with that. 2. The -bedp step needs the outputs from the -corr and -masks steps. The -path step needs the outputs from the -bedp step. The output files from each part are listed here: http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles 3. Checking the aparc+aseg should be enough for tracula purposes as well, since that's the freesurfer output that tracula uses. Keep in mind that DWI resolution is usually lower than T1 resolution, so tiny changes in the aparc+aseg might not affect tracula at all. 4. Yes, I do recommend using bbregister. It's not surprising that it would give better results since it uses the additional information of the surfaces. If I remember correctly, Doug didn't manage to replicate your bbregister error, right? I'd check if you get the same error with the 5.1 version of bbregister. Hope this helps, a.y On Wed, 27 Mar 2013, Salil Soman wrote: > Hi, > I have been able to implement FS 5.2 on our Sun Grid Engine Cluster using the CentOS 6 > distribution. After modifying the fsl_sub_mgh file to work with out cluster queue > names and to modify the email notifications, I am able to run the entire processing > pipeline using FLT. (Everytime I try bbr I get errors. I had email doug about this but > have not heard any response). > > I am submitting the jobs to the cluster as follows > > recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm -openmp 50 > -hippo-subfields -all > trac-all -prep -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -bedp -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -path -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > > There are a few issues I am trying to sort out: > > 1) how should one conifigure the openmp flag for the Sun Grid Engine? the flag I used > did not change processing time, and each subject is still taking ~24 hrs? > > 2) once the script starts bedpost, bedpost has controller code which paralelizes all > of the slices (which has been great going from 12 hrs of processing to 1.5 hrs). > However, my original script goes on to execute trace-all -path ... before bepost is > done, generating errors. I have gotten around this by running the trace-all -path > command again after bedpost sends me an email confirming completion. Is there a way to > more cleanly do this (some kind of hold command I can do based on output from > bedpost)? > > 3) In your experience, how important is quality control of freesurfer on tracula > results? We have come to the compromise for freesurfer output to manually check the > segmentation of aparc+aseg.mgz using free view, only correcting and rerunning steps of > freesurfer when there are specific structures we want the volumes of (eg hippocampus). > > 4) have you found a significant benefit of bbr over flt? If so, any suggestions on > things I may need to check to get bbr to work (given flt works)? > > Best wishes, > > Sal > > > > > >

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trac-all -path error
by Nawaf Yassi 28 Mar '13

28 Mar '13

Dear mailing list I am encountering an error at the trac-all path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error ³Segmentation fault² (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help? I am using freesurfer 5.2 and FSL 5.0.2.1 (linux) Regards Nawaf ATTACHED: ERROR MESSAGE + config file below ========================================================= [nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject Too many )'s. INFO: SUBJECTS_DIR is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer INFO: Diffusion root is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.2 trac-paths -c /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/dmrirc.local -log /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/trac-all.log -cmd /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer5.2/bin/trac-paths #------------------------------------- #@# Path reconstruction Thu Mar 28 10:01:34 EST 2013 rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.cst_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.cst_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.ilf_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.ilf_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.unc_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.unc_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/fmajor_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/fminor_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.atr_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.atr_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.ccg_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.ccg_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.cab_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.cab_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.slfp_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.slfp_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.slft_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.slft_PP_avg33_mni_bbr /usr/local/freesurfer5.2/bin/dmri_paths --outdir /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.cst_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.cst_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.ilf_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.ilf_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.unc_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.unc_AS_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/fmajor_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/fminor_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.atr_PP_avg33_mni_bbr /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.atr_PP_avg33_mni_bbr 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/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dmri/bvecs --bval /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dmri/bvals --mask /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lowb_brain_mask.nii.gz --bpdir /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz 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/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Segmentation fault (core dumped) foreach: No match. ============================================================================ ========================================================= [nyassi@bee1 scripts]$ cat dmrirc_single_subject # # dmrirc.example # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2013/02/16 22:49:06 $ # $Revision: 1.3.2.4 $ # # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" # # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer(a)nmr.mgh.harvard.edu # # # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # # Subject IDs # set subjlist = (C01) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile, bvalfile, and nb0 must be specified (see below) # set dcmroot = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/DICOMS/raw_dti/HURLE_LISA set dcmlist = (IM-0001-0001.dcm) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # # set bvecfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvecs.txt # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # # set bvalfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvals.txt # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 0 # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 5000 # # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # # set reinit = 0

2 1

error during trac-all -prep
by Jon Wieser 28 Mar '13

28 Mar '13

i ran trac-all -prep -c dmrirc_single_subject and got the error : fslmaths /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask.nii.gz -mul /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/notventricles.nii.gz /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask-vent.nii.gz Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort I have attached the trac-all .log and trac-all.error files I don't know how to fix this error Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

2 2

Problem with tracula: incomplete or lacking tracts
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

Hi Analstasia, as you suggest, adjusting brain mask the tracts are better. Now I'd like to perform trac-all with new version by using a new configuration file. I do not understand what I should do for: 1- set b0mlist2- set b0plist Thanks. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 25-mar-2013 20.22 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: Problem with tracula: incomplete or lacking tracts Yes, it's a warning, not an error. On Mon, 25 Mar 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia,now I have correct the nodif mask and run again trac-all. > > Is normal "WARN: Could not find satisfactory control point fit - try 83Finding center streamline" during > -prior? > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 25-mar-2013 18.02 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts > > > I also remember that your brain masks had some big chunks of brain > missing. Was whatever caused that fixed as well? > > On Mon, 25 Mar 2013, stdp82(a)virgilio.it wrote: > > > Yes, I fix them. I'm attacking the maps after the last trac-all. > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 25-mar-2013 17.26 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: Problem with tracula: incomplete or lacking tracts > > > > > > Hi Stefano - As I recall, we established that your bvecs were wrong. Did > > you fix them? > > > > a.y > > > > On Mon, 25 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > Hi Anastasia, > > > > > > I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends > from > > > an error in my configuration file? > > > > > > I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > Thank you Anastasia. > > > > I'm checking bvecs/bvals. I obtain it by DTI table creator > > > > (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) > > > > > > > > bvecs/bvals should be done. > > > > > > > > Gradients can be the unique responsable? > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 22-mar-2013 17.07 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > Your gradient table is wrong. See where I've marked the corpus callosum in > > > > your screenshot. The eigenvectors are not pointing along the corpus > > > > callosum, but perpendicular to it. So they're off by 90 degrees, which > > > > means the same is true about the vectors in your gradient table. > > > > > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Hi Anastasia - I attacked the screenshots. > > > > > Thanks, > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 22-mar-2013 1.39 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > > > > Hi Stefano - There's nothing in these screenshots that tells you that the > > > > > eigenvectors are correct. These are vectors, so the way to check them is > > > > > to display them as lines. You display dtifit_V1 as lines, overlaid on > > > > > dtifit_FA. Then you see if the lines point in the right direction. > > > > > > > > > > a.y > > > > > > > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > Here they are attacked. > > > > > > Thanks, > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > Data: 21-mar-2013 21.50 > > > > > > A: <stdp82(a)virgilio.it> > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > > > > > lacking tracts > > > > > > > > > > > > > > > > > > Can you send a screenshot that shows dtifit_V1 and dtifit_FA? > > > > > > > > > > > > On Thu, 21 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > I have checked the gradient directions. How can I resolve the brain mask > > > > > > > problem. > > > > > > > Can I send you my files of this subject? > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > Data: 20-mar-2013 22.46 > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > > > > > lacking > > > > > > > tracts > > > > > > > > > > > > > > > > > > > > > There are chunks of the brain missing from the brain mask. This may cause > > > > > > > some tracts to be incomplete or missing. > > > > > > > > > > > > > > But you should still check that the gradient directions are correct, so > > > > > > > you know if you have multiple problems or just one. The FA map can't tell > > > > > > > you if the gradient table was correct, you have to check the eigenvectors > > > > > > > in dtifit_V1 for that. > > > > > > > > > > > > > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > File attacked > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > Da: stdp82(a)virgilio.it > > > > > > > > Data: 20-mar-2013 22.34 > > > > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking > > > > > > > tracts > > > > > > > > > > > > > > > > Thank you Anastasia. I'm checking gradient table but I would like > > > > > > > underline that I'm noting some holes in > > > > > > > > dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative > > > > > > > images). > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > > Data: 20-mar-2013 16.40 > > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > > > > > > > > > > > > > Hi Stefano - Have you checked that your gradient table is correct by > > > > > > > > looking at the output of the tensor fit? > > > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > > > Hi list and Anastasia, > > > > > > > > > if you remember the last week I had same problems with tracula output: > > > > > > > the final tract are lacking or > > > > > > > > > incomplete for same subjects. Some of these are less wrong (only > > > > > > forceps > > > > > > > major), other have more evident > > > > > > > > > error (you can see this in picture that I have attacked). > > > > > > > > > > > > > > > > > > To resolve this issue I have: > > > > > > > > > > > > > > > > > > 1-checked the correct overlap of dwi and dwi_mask > > > > > > > > > 2-rerun data with new version 5.2 > > > > > > > > > 3-rerun new registration using bbregister (fsl/spm option): for > > > > > > example, > > > > > > > in the subject of the picture > > > > > > > > > attacked, the .mincost file now contains as first value 0.87 (previous > > > > > > > it was 1.1) > > > > > > > > > > > > > > > > > > Please, give me an advise > > > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > > Da: stdp82(a)virgilio.it > > > > > > > > > Data: 12-mar-2013 17.47 > > > > > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > > Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > I got it from mri directory but I'm understanding that this directory > > > > > > > isn't ok.I'm attacking the image > > > > > > > > > from dlabel/diff/aparc+aseg.bbr.nii > > > > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > > > Data: 12-mar-2013 17.19 > > > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > > Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > > > > > > > > > > Can you please answer my question? I can't really tell if the issue is > > > > > > > due > > > > > > > > > poor dwi-aseg overlap unless you tell me where you got that aseg > > > > > > volume > > > > > > > > > from. > > > > > > > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > > > > > Thank you Anastasia. What do you think about the issue in the file > > > > > > > attacked > > > > > > > > > > (I'm noting that same subjects are lacking of same > > > > > > > > > > tracts or same tracts are incomplete) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > > > > Data: 12-mar-2013 17.02 > > > > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > > > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's > > > > > > > in > > > > > > > > > > the dlabel/diff/ directory has been mapped to the same space as the > > > > > > > DWI, > > > > > > > > > > so those are the volumes that can be compared directly to > > > > > > dwi.nii.gz. > > > > > > > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > Hi list, > > > > > > > > > > > > > > > > > > > > > > I have two questions, please. > > > > > > > > > > > > > > > > > > > > > > I'm using version 5.1 to complete my analysis. > > > > > > > > > > > > > > > > > > > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of > > > > > > the > > > > > > > same > > > > > > > > > > > subject (figure 1 and 3). You can note the dwi do not overlap to > > > > > > the > > > > > > > aseg. > > > > > > > > > > > How can I resolve this issue? > > > > > > > > > > > > > > > > > > > > > > 2-After TRACULA analysis, I'm noting that same subjects are > > > > > > lacking > > > > > > > of > > > > > > > > > > same > > > > > > > > > > > tracts or same tracts are incomplete (figure 3). > > > > > > > > > > > > > > > > > > > > > > Could it depends from the issue in question 1? I'm thinking to > > > > > > rerun > > > > > > > all > > > > > > > > > > > using version 5.2 but before starting new analyses, I'd like to > > > > > > ask > > > > > > > you > > > > > > > > > > > which is the possible error. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > > > > whom > > > > > > > it is > > > > > > > > > > addressed. If you believe this e-mail was sent to you in error and > > > > > > the > > > > > > > > > > e-mail > > > > > > > > > > contains patient information, please contact the Partners Compliance > > > > > > > > > > HelpLine at > > > > > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > > > > you > > > > > > > in > > > > > > > > > > error > > > > > > > > > > but does not contain patient information, please contact the sender > > > > > > > and > > > > > > > > > > properly > > > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > > > Freesurfer mailing list > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > > > > > > > it is > > > > > > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > > > > e-mail > > > > > > > > > contains patient information, please contact the Partners Compliance > > > > > > > HelpLine at > > > > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you > > > > > > > in error > > > > > > > > > but does not contain patient information, please contact the sender > > > > > > and > > > > > > > properly > > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > > Freesurfer mailing list > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > > > > > > it > > > > > > > is > > > > > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > > > > e-mail > > > > > > > > contains patient information, please contact the Partners Compliance > > > > > > > HelpLine at > > > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you > > > > > > in > > > > > > > error > > > > > > > > but does not contain patient information, please contact the sender and > > > > > > > properly > > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > > > > > > is > > > > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > > > > e-mail > > > > > > > contains patient information, please contact the Partners Compliance > > > > > > > HelpLine at > > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > > > > > > error > > > > > > > but does not contain patient information, please contact the sender and > > > > > > > properly > > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it is > > > > > addressed. If you believe this e-mail was sent to you in error and the e-mail > > > > > contains patient information, please contact the Partners Compliance HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you in error > > > > > but does not contain patient information, please contact the sender and properly > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it is > > > > addressed. If you believe this e-mail was sent to you in error and the e-mail > > > > contains patient information, please contact the Partners Compliance HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was sent to you in error > > > > but does not contain patient information, please contact the sender and properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the person to whom it is > > > addressed. If you believe this e-mail was sent to you in error and the e-mail > > > contains patient information, please contact the Partners Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to you in error > > > but does not contain patient information, please contact the sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Incorporating (high resolution) T2- and FLAIR volumes
by Lukas.Scheef＠ukb.uni-bonn.de 28 Mar '13

28 Mar '13

Hi FreeSurfer experts! We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions: 1) How do I incorporate T2/Flair volumes into the recon all processing stream? a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ? b) What is expected to get the better results regarding the pial surface: FLAIR or T2? (both are at 1x1x1mm) 2) Is there any module in FS to detect white matter lesions? 3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do I have to switch to Caret? Many thanks in advance for your help and advice! Best wishes, Luke

3 3

Bug in DOSS implementation in QDEC
by Douglas N Greve 28 Mar '13

28 Mar '13

Dear FreeSurferers, it has just come to my attention that there may be a bug in the way that QDEC computes contrasts for DOSS. If you are using QDEC in this way, please hold off until I track down the problem. Also, please let me know if you are using it in this way. thanks and sorry for the inconvenience doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 2

Recon-all errors (reposting)
by Marcos Martins da Silva 28 Mar '13

28 Mar '13

Hi, freesurferers I am trying to execute the post installation tests as recommended at Freesurfer Wiki. Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over Fedora 18 using VirtualBox 4.2.8. Freesurfer version is 5.2. Tkmedit, Tksurfer, qdec and freeview all work great. However, recon-all tests return errors. Thank you for your attention. _______________________________________ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! _______________________________________ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log _______________________________________ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

1 0

Re: [Freesurfer] Underestimated Pial surface - after deleting problematic voxels
by Bruce Fischl 28 Mar '13

28 Mar '13

well, something is really wrong. Did you happen to change the voxel type of brain.finalsurfs.mgz? Can you run mri_info on it and send us the results? If not, then upload the tarred and gzipped subject dir and I'll take a look. I don't think it will be hard to fix On Thu, 28 Mar 2013, preciado(a)nmr.mgh.harvard.edu wrote: > A) Log attached. > B) That was my next step but I wanted to check first to see if there was > something obvious I was missing. > > I actually ran "recon-all -autorecon-pial -subjid subject_name" twice. I > thought the first time, that it was the result of some process failing/not > completing along the way without entirely crashing freesurfer. I ran it > again in the hopes that it was some crazy fluke but the result is exactly > the same. > > -Ronny > >> eek, that's pretty bad. No idea why that would happen. Can you send us >> the recon-all.log? If you rerun with the original brain.finalsurfs.mgz >> does it restore good surfaces? >> On Thu, 28 Mar 2013, >> preciado(a)nmr.mgh.harvard.edu wrote: >> >>> Hello Freesurfers, >>> >>> I ran recon-all on a subject's structural data like so: >>> recon-all -autorecon-all -subjid subect_name >>> >>> The resulting pial surface looked pretty good except that there were a >>> few >>> voxels of dura and cerebellum that were included in the pial surface. >>> not >>> a big deal. I deleted some voxels of dura from brainmask.mgz and deleted >>> voxels of from the cerebellum by creating and saving a copy of >>> brain.finalsurfs.mgz. >>> /subject_name/mri/ >>> cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz >>> >>> >>> Then I ran recon all to regenerate the pial surface: >>> recon-all -autorecon-pial -subjid subject_name >>> >>> >>> The results from the pial surface redrawing are now totally wrong and >>> completely underestimated. The weird thing is that it looked perfectly >>> fine before and removing some problematic voxels caused this result. >>> >>> Any insights as to how/why this occurred and how to fix it? Images of >>> the >>> AFTER picture attached. >>> >>> Thanks! >>> -Ronny >> >> >> >

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Underestimated Pial surface - after deleting problematic voxels
by preciado＠nmr.mgh.harvard.edu 28 Mar '13

28 Mar '13

Hello Freesurfers, I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result. Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached. Thanks! -Ronny

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qdec covariates
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

Hi list,I'm performing qdec. This my file.dat1 diagnosis discrete 2 1 Pathology 2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203Number of subjects: 31Number of factors: 4 (1 discrete, 3 continuous)Number of classes: 2Number of regressors: 8NPStest is scored from 0 to 8 and for controls it is all 0.Previously I have performed qdec without problem but I'm noting that when I use covariates that contains all 0 in a group, qdec give me an error. What's happen?Thanks, Stefano

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