Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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 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/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

QDEC error Two Groups three covariates
by Mikael Novén 21 May '20

21 May '20

External Email - Use Caution Dear FreeSurfer Developers, I’m attempting to run a cortical thickness correlation analysis regressing out the effect of brain size, age and gender. However, when attempting to run this analysis in qdec (or trying to use mri_glmfit separately) I get the following error: "MatrixMultiplyD(): m2 is null break matrix.c:415 No such file or directory” Full output from the mri_glmfit call is last in this mail. The first lines of my fsgd files look like this: "GroupDescriptorFile 1 Title RTfMRI Class M Class F Variables RT eICV Age Input 101 M 36.767 1046505.93 25 Input 102 F -58.589 955597.34 30 Input 103 M 68.883 1107660.32 22” My contrast matrix looks like this: "+0.00000 +0.00000 +1.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000” Any help is much appreciated. Kind regards, Mikael mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex --glmdir fMRIRT_revision_test2 gdfRead(): reading fMRIRT_age_gender_eICV.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 RT 82.6508 76.4669 1 eICV 980394 122148 2 Age 24.5294 3.23797 Class Means of each Continuous Variable 1 M 97.4687 1037828.2188 25.0000 2 F 74.5684 949066.0966 24.2727 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex --glmdir fMRIRT_revision_test2 sysname Darwin hostname LUMAC1089 machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh logyflag 0 usedti 0 FSGD fMRIRT_age_gender_eICV.fsgd labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir fMRIRT_revision_test2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory fMRIRT_revision_test2 Loading y from /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to fMRIRT_revision_test2/Xg.dat Computing normalized matrix Normalized matrix condition is 3815.6 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149078 voxels in mask Saving mask to fMRIRT_revision_test2/mask.mgh Reshaping mriglm->mask... search space = 74130.630564 DOF = 9 Starting fit and test Fit completed in 0.0511667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361 Writing results RT_covNI_cp maxvox sig=-4.61019 F=62.3686 at index 156731 0 0 seed=1590285961 MatrixMultiplyD(): m2 is null break matrix.c:415 No such file or directory

2 1

Recon-all error in CA Normalize (FreeSurfer V 7.1)
by Schranzer René 21 May '20

21 May '20

External Email - Use Caution Dear Freesurfer experts, I'm trying to recon-all (-hires) for a new subject (mp2rage image) using the FreeSurfer Version 7.1. However, the recon-all exited with errors at the "mri_ca_normalize". I also processed the same subject from different timepoints and they finished without errors. The error log is as following: #@# CA Normalize Sat May 16 12:43:31 CEST 2020 /data/disk_1/IP/MS/freesurfer/MS_MRS_03_TP1_MP2RAGE/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (74, 87, 47) --> (250, 243, 247) finding center of left hemi white matter using (133, 139, 147) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (111,120,122) --> (154, 158,171) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 4.3 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246437 sample points... INFO: compute sample coordinates transform 0.82947 -0.03916 0.01418 -3.56121; 0.02560 0.95026 0.20358 -65.47982; -0.02149 -0.16312 0.83311 18.21485; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (162, 90, 50) --> (242, 211, 245) double free or corruption (out) Command terminated by signal 6 @#@FSTIME 2020:05:16:12:43:32 mri_ca_normalize N 8 e 52.08 S 0.30 U 41.78 P 80% M 793644 F 0 R 213860 W 0 c 1239 w 3 I 0 O 0 L 10.49 12.64 12.79 @#@FSLOADPOST 2020:05:16:12:44:24 mri_ca_normalize N 8 10.29 12.25 12.65 Linux twodogs 4.15.0-88-generic #88-Ubuntu SMP Tue Feb 11 20:11:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MS_MRS_03_TP1_MP2RAGE exited with ERRORS at Sat May 16 12:44:24 CEST 2020 I am thankful for any help. Best, René

2 1

-T2pial after white matter edits
by Octavian Lie 21 May '20

21 May '20

External Email - Use Caution Dear All, I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits, when running recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz it throws an error ~ 'flag volT2.mgz not recognized'. When reruning recon-all as above, do we need to include the T2pial flag to make use of the t2 pial information? If not, is the previous T2pial output used to regenerate the pia? Thank you, OL

2 3

Problem with single subject retinotopy visualization using tksurfer-sess
by Kasia Siuda-Krzywicka 21 May '20

21 May '20

External Email - Use Caution Dear FreeSurfer community, I am running a retinotopy analysis using FSFAST and I encountered a problem with data visualisation. To perform my analysis I followed the official guidelines found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and the following tutorial: https://kylemathewson.com/retinotopy-in-freesurfercnl-protocol/#FUNC The pipeline worked and I didn't get any error messages. I now want to visualise my single subject data to make sure that everything worked fine. As suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I run a command: tksurfer-sess -s 2016_09_23_NBI_AMJU -hemi lh -analysis retino.self.lh Unfortunately, it doesn't work and returns the following error message: /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' I attached in this mail a print screen with the logs of the operation. I believe that the program is supposed to create a file: retino.self.lh/tksconcat.nii but I don't find it in my analysis folder. Could anyone help me resolve this issue? Thank you! Kasia [image: image.png]

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