Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

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OHBM Brainhack registration is open!
by Remi Gau 22 May '20

22 May '20

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circular/cyclic color map for polar data in freeview
by Devavrat Vartak PhD 22 May '20

22 May '20

External Email - Use Caution Hello freesurfer community, I am trying to setup a retinotopy pipeline. I have analysed pRF data generating polar angle and eccentricity maps which I project onto an inflated surface / flattened surface in freeview. Is there a way to display a circular/cyclic colour map (for the polar angle data) in the overlay screen?, the existing 'colour wheel' option seems to be linear? Thank you! Best, DV

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Re: [Freesurfer] Infant Freesurfer: infant_recon_all error
by fsbuild 21 May '20

21 May '20

External Email - Use Caution Hello Fleur, You should be able to do, $ file `which infant_recon_all` .... and the output should tell you if it it is a csh script, a Bourne shell script, a binary, etc. Unless you explicitly made csh or bash your default shell, then at the dollar sign prompt the default shell in Ubuntu is "dash" and not bash or Bourne shell.   If the file command reports it's a Bourne shell then it might be a bash script.  Or a bash script with a hash bang line of /bin/sh will run using dash shell on Ubuntu and can exit with that error on bash syntax/grammar.  You can eliminate that possibility by first running bash, and then the script, $ bash $ infant_recon_all --s SUBJ --age AGE (with I presume arguments substituted for SUBJ and AGE) - R. Fleur Warton May 20, 2020 at 04:05         External Email - Use Caution        Hi, I recently installed the Infant FreeSurfer package. When I try to run infant_recon_all (specific command: infant_recon_all --s SUBJ --age AGE)  I get the error  if: Expression Syntax I tried switching shells from bash to tcsh but got the same error. The FreeSurfer version is freesurfer-infant-20200205My platform is Ubuntu 18.04 Any suggestions how to fix this? Kind regards, Fleur   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Open Postdoctoral Scholar Position
by Neva M Corrigan 21 May '20

21 May '20

External Email - Use Caution Open Postdoctoral Scholar Position The University of Washington Institute for Learning & Brain Sciences (I-LABS; http://ilabs.washington.edu/) located in Seattle, WA is seeking a Postdoctoral Scholar to conduct analyses of human MRI brain imaging data. I-LABS is an interdisciplinary research unit dedicated to discovering the fundamental principles of human learning, with a special emphasis on early learning and brain development. The Postdoctoral Scholar will contribute to a team responsible for creating breakthrough findings in infant, child and adolescent brain development. Applicants should have a Ph.D. in Psychology, Linguistics, Cognitive Science, Biomedical Engineering, Neuroscience, or relate field. Extensive prior experience in analysis of MRI data in a scientific setting is essential. Programming and scripting skills are required, with Matlab or Python as well as Unix scripting experience at a minimum. Familiarity with common MRI image processing software packages (such as FSL, SPM, ANTS, FreeSurfer, or AFNI) is a must. Previous experience in working with pediatric MRI data is highly desired. Full position details and application submission are available at: https://apply.interfolio.com/75530. Review of applications will begin May 1st, 2020; applications will be accepted until the position is filled.

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mris_register intermediate results display
by Chris Adamson 21 May '20

21 May '20

External Email - Use Caution Freesurfer devs, Apologies if this has already been asked. I'm looking for a way that I can look at the progress of mris_register to investigate the accuracy of registration. Given that the registration is done on the 2D parameterisations of the curvature maps, how can I take a spherical surface and write out a tif file with the curvature maps of the surface that I'm registering and the target surface. I presume I need to use mrisp_write but it is unclear how I choose the curvature map to write in the image. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 21 May '20

21 May '20

External Email - Use Caution I apologize for resending all of this info, but my email is acting up and every time I try to respond to the other email, my Outlook freezes. Here is info from our thread. I modified it to include the analysis in which I found significant clusters (i.e., looking at thickness with only age and sex as covariates and not ICV): After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age and sex (this is a three group design). The X matrix was 240x12 (see attached file) * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3 * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3 * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3 * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3 * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3 * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3 Your code: There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[1 2 3]*beta([1 2 3]) When running your code, below are the errors I got in Matlab. Do you know how I can fix the code? >> X = load('Xg.dat'); >> y = load('perm.th30.abs.y.ocn.dat'); >> y = load('perm.th30.abs.y.ocn.dat'); >> beta = inv(X'*X)*X'*y; >> yhat = X(:,[1 2 3]*beta([1 2 3]) yhat = X(:,[1 2 3]*beta([1 2 3]) ↑ Error: Invalid expression. When calling a function or indexing a variable, use parentheses. Otherwise, check for mismatched delimiters. Did you mean: >> yhat = X(:,[1 2 3]*beta([1 2 3])) Error using * Incorrect dimensions for matrix multiplication. Check that the number of columns in the first matrix matches the number of rows in the second matrix. To perform elementwise multiplication, use '.*'. >> yhat = X(:,[1 2 3].*beta([1 2 3])) Index in position 2 is invalid. Array indices must be positive integers or logical values. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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question on partial volume correction
by Barletta, Valeria 21 May '20

21 May '20

Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface? Thanks a lot, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

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TRACULA Segmentation Fault
by Batra, Vinita R. 21 May '20

21 May '20

External Email - Use Caution Hello FS Team and Anastasia, I am processing a subject in TRACULA and came across the error Segmentation fault for the rh.cst tract. A screenshot of the overlay of aparc+aseg and T1 revealed the registration is off. I have also tried running the other tracts independent of rh.cst to see if that works but could not resolve the issue. Please advise as to how to best resolve this. I have pasted the output from trac-all -path below. /Applications/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri May 15 13:39:58 CDT 2020 rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cst_AS_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cst_AS_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.ilf_AS_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.ilf_AS_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.unc_AS_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.unc_AS_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/fmajor_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/fminor_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.atr_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.atr_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.ccg_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.ccg_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cab_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cab_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.slfp_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.slfp_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.slft_PP_avg33_mni_bbr rm -rf /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.slft_PP_avg33_mni_bbr /Applications/freesurfer/bin/dmri_paths --outdir /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cst_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cst_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.ilf_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.ilf_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.unc_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.unc_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/fmajor_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/fminor_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.atr_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.atr_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.ccg_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.ccg_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cab_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cab_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.slfp_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.slfp_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.slft_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.slft_PP_avg33_mni_bbr --dwi /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/dwi.nii.gz --grad /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/bvecs --bval /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/bvals --mask /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/xfms/diff2mni.bbr.mat --init /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt 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/Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt sysname Darwin hostname Suns-iMac-Pro.local machine x86_64 user sunlab Output directory: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cst_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cst_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.ilf_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.ilf_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.unc_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.unc_AS_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/fmajor_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/fminor_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.atr_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.atr_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.ccg_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.ccg_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cab_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cab_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.slfp_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.slfp_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.slft_PP_avg33_mni_bbr /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.slft_PP_avg33_mni_bbr DWIs: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/dwi.nii.gz Gradients: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/bvecs B-values: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/bvals Mask: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/aparc+aseg_mask.bbr.nii.gz BEDPOST directory: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri.bedpostX Max number of tracts per voxel: 2 Tract volume fraction threshold: 0.05 Initial control point file: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt End ROI 1: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz End ROI 2: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz Neighbor aseg prior: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all Neighbor aseg label ID list: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all Neighbor aseg prior set: 14 Local aseg prior: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all Local aseg label ID list: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all Local aseg prior set: 15 Segmentation map: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/aparc+aseg.nii.gz DWI-to-atlas affine registration: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/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: /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Loading DWIs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/dwi.nii.gz Loading mask from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri.bedpostX Loading b-values from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/bvals Loading gradients from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/bvecs INFO: Found 1 baseline images (b = 0) out of a total of 33 frames INFO: Found 210632 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading affine registration from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dmri/xfms/diff2mni.bbr.mat Loading segmentation map from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/aparc+aseg.nii.gz Creating output directory /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cst_AS_avg33_mni_bbr Loading end ROI from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading end ROI from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz Loading control points from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_1_0_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_0_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_0_1_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_-1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_0_-1_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_0_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_0_0_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_0_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_0_0_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_1_1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_1_-1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_-1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_1_1_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_1_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_1_-1_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_-1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_0_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_0_0_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_1_0_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_-1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_-1_0_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_0_1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_0_1_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_0_-1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_0_-1_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_0_0_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_0_0_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_0_0_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_0_0_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_1_1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_-1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_-1_1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_1_-1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_-1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_-1_-1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_1_1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_-1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_-1_1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_1_-1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all_-1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all_-1_-1_-1.txt Loading initial proposal SD's from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt Processing pathway 1 of 18... Initializing MCMC INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 1 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 4 INFO: Attempting to perturb control points INFO: Path from initial control points is not entirely in white matter INFO: in segment 4 INFO: Attempting to perturb control points INFO: Reverting to original control points Running MCMC burn-in jumps Running MCMC main jumps Writing output files to /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/lh.cst_AS_avg33_mni_bbr Done in 33.457 sec. Creating output directory /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dpath/rh.cst_AS_avg33_mni_bbr Loading end ROI from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading end ROI from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz Loading control points from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt WARN: Initial start point 74 68 12 is not in start ROI WARN: Replacing with closest point in start ROI (74 68 11) Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_1_0_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_0_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_0_1_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_-1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_0_-1_0.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_0_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_0_0_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_0_0_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_0_0_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_1_1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_1_-1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_-1_1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_1_1_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_1_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_1_-1_-1.txt Loading nearest neighbor prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all_-1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all_-1_-1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_0_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_0_0_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_1_0_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_-1_0_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_-1_0_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_0_1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_0_1_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_0_-1_0.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_0_-1_0.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_0_0_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_0_0_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_0_0_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_0_0_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_1_1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_-1_1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_-1_1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_1_-1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_-1_-1_1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_-1_-1_1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_1_1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_-1_1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_-1_1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_1_-1_-1.txt Loading local prior from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all_-1_-1_-1.txt with label IDs from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all_-1_-1_-1.txt Loading initial proposal SD's from /Users/sunlab/Documents/FreeSurferDirs/subjects_109/109_KW_PD803_M/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt Processing pathway 2 of 18... Initializing MCMC Darwin Suns-iMac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Oct 10 23:06:14 PDT 2018; root:xnu-4570.71.13~1/RELEASE_X86_64 x86_64 trac-paths exited with ERRORS at Fri May 15 13:40:53 CDT 2020 Thank you so much, Vinita

1 0

Rescale question in PETsurfer
by Vicky Shi 21 May '20

21 May '20

External Email - Use Caution Dear Freesurfer experts, I am using gtm.stats.dat file generated by command mri_gtmpvc. I want it scaled by the mean intensity of whole brain. Is there an easy way to achieve this? Thank you in advance for your help. Best regards, Vicky

2 3

Using PD Scans for Inhomogeneity Correction
by Tali Weiss 21 May '20

21 May '20

External Email - Use Caution Dear all, 1. BV have a tool: https://www.brainvoyager.com/bv/doc/UsersGuide/HighResDataAnalysis/UsingPDS… Is freesurfer have something similar for MPRAGE (i use recon-all) 2.Is PD is suitable also to correct MP2RAGE on 7T? My resolution 1mm, I use recon-all.v6.hires (freesurfer/6.0.0-patch/hcp/) Still, the segmentation in the inferior temporal and frontal pole are very bad... Is it make sense to use PD in MP2RAGE sequence? Tali

2 1

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Freesurfer May 2020