External Email - Use Caution Dear FreeSurfer TRACULA team
I have processed subjects using TRACULA on FS6.0 and 7.2. With both pipelines all the steps are completed without errors but for most subjects when I checked the pathstats.overall.txt file volume of the tract is almost equal to the length average. (unlike the example in Freesufer Wiki) I have attached pathstats for two people with (ID30720) and without (ID 30018) that problem (also attached one of my configuration files). Does this mean the tracts are not fully constructed? I was referring tracula freesurfer page and the following paper https://secure-web.cisco.com/1dIfxly6kRVrrbDgNkmQxrmTgb-DRd5cF1t7FkABP7tQosKUizgyMUWBx6hITrcmfSzRIl4pxl9LDRAwHZ5Ow0-ADMs_HaG-rwy14B2Y03rCPJQund4JmkSYDTsm4ozwRaMczRnzDMvr0D0ahgbfOV8MtCX-wSOmu2zF09pEO996UcVTtDOg4ReK_YFL_cskM_vn9DBaz1AjEOhiDcr-LV_3eojajF2sdNWTIr1Ny7s1ifLYosseu0eVTui7pr0dNO2-tj57d6jBRF_Y_pZrqlW-q4m7LMLMmKTvGTwnvwTy6evufcONsn1rARKuneDYwLE8dY6DF4CrOmwNpjD4Fxg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0165027021000340 I have done re-initializing of the tracts too without any luck of improving Even in freeview the tracts for 30720 looks like thin lines. I have been having this problem for a while and any suggestion to correct it will be much appreciated! Regrards Shanika
# Title Pathway Statistics # # generating_program /public/apps/freesurfer/7.2.0//bin/dmri_pathstats # cvs_version 7.2.0 # cmdline /public/apps/freesurfer/7.2.0//bin/dmri_pathstats --intrc /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/lh.ilf_avg16_syn_bbr --dtbase /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/dtifit --path lh.ilf --subj 30018 --invox path.ref.txt --out /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/lh.ilf_avg16_syn_bbr/pathstats.overall.txt --outvox /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/lh.ilf_avg16_syn_bbr/pathstats.byvoxel.txt # sysname Linux # hostname cpu-731.cluster.local # machine x86_64 # user sjayakody # anatomy_type pathway # # subjectname 30018 # pathwayname lh.ilf # Count 1500 Volume 1877 Len_Min 62 Len_Max 104 Len_Avg 80.7613 Len_Center 89 AD_Avg 0.000585198 AD_Avg_Weight 0.000572661 AD_Avg_Center 0.000399619 RD_Avg 0.000249489 RD_Avg_Weight 0.00024237 RD_Avg_Center 0.000166555 MD_Avg 0.000361392 MD_Avg_Weight 0.000352467 MD_Avg_Center 0.000244243 FA_Avg 0.599611 FA_Avg_Weight 0.601226 FA_Avg_Center 0.618726
# Title Pathway Statistics # # generating_program /public/apps/freesurfer/7.2.0//bin/dmri_pathstats # cvs_version 7.2.0 # cmdline /public/apps/freesurfer/7.2.0//bin/dmri_pathstats --intrc /gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dpath/lh.ilf_avg16_syn_bbr --dtbase /gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dmri/dtifit --path lh.ilf --subj 30720 --invox path.ref.txt --out /gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dpath/lh.ilf_avg16_syn_bbr/pathstats.overall.txt --outvox /gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dpath/lh.ilf_avg16_syn_bbr/pathstats.byvoxel.txt # sysname Linux # hostname cpu-782.cluster.local # machine x86_64 # user sjayakody # anatomy_type pathway # # subjectname 30720 # pathwayname lh.ilf # Count 1500 Volume 58 Len_Min 58 Len_Max 58 Len_Avg 58 Len_Center 89 AD_Avg 0.000937952 AD_Avg_Weight 0.000937952 AD_Avg_Center 0.000931482 RD_Avg 0.000740375 RD_Avg_Weight 0.000740375 RD_Avg_Center 0.000719722 MD_Avg 0.000806234 MD_Avg_Weight 0.000806234 MD_Avg_Center 0.000790309 FA_Avg 0.16653 FA_Avg_Weight 0.16653 FA_Avg_Center 0.183197
setenv SUBJECTS_DIR /gs/gsfs0/users/helena_blumen_lab/TRACULA/ set dtroot = /gs/gsfs0/users/helena_blumen_lab/TRACULA/ set subjlist = 30018 set runlist = 1 set dcmroot = /gs/gsfs0/users/helena_blumen_lab/TRACULA/ set dcmlist = 30018/30018_WIP_110_DTI66d_2mm_SF3_SENSE_20190520152420_1201.nii set bvecfile = 30018/bvecs.txt set bvalfile = 30018/bvals.txt set dob0 = 0 set doeddy = 0 set intrareg = 3 set intradof = 9 set intrarot = 90 set interreg = 5 set intertrg = /public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz set segname = aparc+aseg set usethalnuc = 0 set usemaskanat = 1 set thrbet = 0.3 set trainfile = /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt set nstick = 2 set nburnin = 200 set nsample = 7500 set nkeep = 5 set reinit = 0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
