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Admin: Please unsubscribe this email address
by Dalwani, Manish 27 Mar '13

27 Mar '13

Hello Admin, Please unsubscribe this email address. Regards, Manish

2 1

bbregister error with hardi data
by Corinna Bauer 27 Mar '13

27 Mar '13

Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.15356/template.nii... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) keeping frame 0 writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii... Mov determinant is -6.125 /usr/local/freesurfer/subjects/symmetry/lindsay tkregister2_cmdl --mov ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.15356/fslregister/reg0.15393.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/symmetry/lindsay/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.750 0.000 0.000 112.000; 0.000 0.000 2.000 -60.000; 0.000 -1.750 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; Determinant 1 subject = lindsay RegMat --------------------------- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -6.125, ref det = -1 Mon Mar 25 12:22:34 EDT 2013 /usr/local/freesurfer/subjects/symmetry/lindsay flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.15356/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.15356/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.15356/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Mon Mar 25 12:22:34 EDT 2013 /usr/local/freesurfer/subjects/symmetry/lindsay flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.15356/reg.init.dat.fsl.mat -init ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.15356/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.15356/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.15356/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --fslreg ./tmp.bbregister.15356/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.15356/reg.init.dat.fsl.mat cat: ./tmp.bbregister.15356/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Mon Mar 25 12:22:23 EDT 2013 Ended at Mon Mar 25 12:22:34 EDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg ./tmp.bbregister.15356/reg.init.dat --out-reg ./tmp.bbregister.15356/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15356/reg.init.dat mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg ./tmp.bbregister.15356/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.15356/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15356/bbr.pass1.dat Cleaning up Started at Mon Mar 25 12:22:16 EDT 2013 Ended at Mon Mar 25 12:22:34 EDT 2013 BBR-Run-Time-Sec 18 bbregister Done To check results, run: tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf

2 13

view retinotopy results in version 5
by Y.V. Jiang 27 Mar '13

27 Mar '13

Hi, I was able to view retinotopic mapping results using rtview in version 5. However, the display was on the inflated surface. Is there a way to view the results on the flattened occipital map, similar to version 4's surf-sess -flat? Thanks! -Yuhong

2 2

surf2vol
by Daniel Lumsden 27 Mar '13

27 Mar '13

Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template <path to>/orig.mgz --outvol <path to where I want the file>/leftfrontallobe.nii.gz --surfval <path to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan > Date: Mon, 25 Mar 2013 14:59:28 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: doclumsden(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] surf2vol > > Hi Dan > > try using mri_surf2vol instead (it has a much bigger help, thanks to > Doug0 > Bruce > On Mon, 25 Mar 2013, Daniel Lumsden wrote: > > > Dear All > > > > Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical > > parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the > > parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate > > the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm > > struggling to apply the surf2vol command. > > > > From the terminal window I can see that the commands required are: > > > > surf2vol <surf> <refvol> <outvol> <convention> > > > > I presume that <surf> is the .gii file I'm trying to visualise, and <outvol> is to specify the name of the output volume the > > command will generate, but what should I be using as the <refvol>? I would be very grateful for any guidance. Please accept my > > apologies if I've missed a very obvious online explanation for this and thank you in advance. > > > > Dan Lumsden > > Clinical Research Fellow > > > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.

2 5

Re: [Freesurfer] Xhemi stat questions
by Gabriel Gonzalez Escamilla 27 Mar '13

27 Mar '13

2 1

Fwd: Cortical thickness in average space
by Rafa X 27 Mar '13

27 Mar '13

Thanks Bruce for your answer, as you asked I'm forwarding this question to the list in case any other can answer this. We already have the surface generated by mri_preproc, now we are trying to read it using the matlab function read_mgh. It returns a 4-D matrix, how can we interpret this data to get the cortical thickness values at each vertex of every subject? Rafa & Gabi 2013/3/26 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Rafa and Gabi > > yes, that's pretty much what the -qcache flag does in recon-all. Or you can > use mri_surf2surf to do it. > > cheers > Bruce > > On Tue, 26 Mar 2013, Rafa X wrote: > >> Hi Freesurfers, >> We would need to obtain the cortical thickness of each subject in the >> space of the average subject (built from our subject population), Does >> it exists? >> If so, Can I use the label files produced by mri_surfcluster to >> directly extract the mean cortical thickness of each ROI in each >> subject? We want to avoid to trasform each cluster to every subject. >> >> Thank you all in advance, >> Rafa & Gabi. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

2 1

question regarding creating Brodmann area
by Ji Won Bang 27 Mar '13

27 Mar '13

Dear. freesurfer users. I'm trying to make a label for Brodmann area 44. According to the freesurfer manual, I've run, recon-all -s subjid -ba-labels However, it says Flag -ba-labels unrecognized. I'm using freesurfer version 4.5.0. By default, recon-all is supposed to create Brodmann areas under label directory. However, inside the lable directory, I see only aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label Please leave me any comment!! I appreciate it a lot! Best regards, Ji Won Bang

2 1

memory allocation errors on Snow Leopard running dmri_train
by Ping-Hong Yeh 27 Mar '13

27 Mar '13

Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc sysname Darwin hostname twbrkmp2s-Mac-Pro-5.local machine x86_64 user twbrkmp2 Output directory: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni Output directory in test subject's space: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff Output base: lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt Training subject directory list: /private/tmp/subj33.NCNC2348.61836.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz Affine registration from atlas to base for output subject: /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat Number of control points for initial spline: 10 Exclude previously chosen center streamlines: 0 Use truncated streamlines: 1 Loading brain mask of output subject from /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz Loading affine registration from /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat Loading streamline start ROI from /apps/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /apps/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /apps/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /apps/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk INFO: Rejected 587 streamlines for straying off mask INFO: Rejected 77 streamlines for reversing direction INFO: Rejected 36 streamlines as length outliers INFO: Have 7732 total streamlines (min/mean/max length: 59/99/129) Loading segmentation from /apps/freesurfer/trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc005/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc005/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc006/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc006/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc007/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc007/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc008/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc008/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc009/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc009/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc010/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc011/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc011/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc012/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc012/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc013/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc013/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc014/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc014/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc015/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc015/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc016/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc016/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc017/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc017/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc018/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc018/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc019/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc019/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc020/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc020/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc021/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc021/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc022/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc022/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc023/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc023/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc024/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc024/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc025/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc025/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc026/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc026/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc027/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc027/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc028/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc028/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /apps/freesurfer/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /apps/freesurfer/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(63678) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 138th slice Cannot allocate memory Darwin twbrkmp2s-Mac-Pro-5.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Mar 26 14:40:16 EDT 2013 Any suggestions? Thanks. ping

2 4

Problems with recon-all--won't generate wm or surf files
by Hayley Dorfman 27 Mar '13

27 Mar '13

Hello, I've been having problems with recon-all for only 1 of my 50 subjects. Recon-all is failing somehow before white matter or surf files are generated. The T1 and nu.mgz files look fine. Below are the files that my subject is missing in the 'mri' subdirectory (they are also missing the entire surfs directory): filled.mgz lh.ribbon.mgz rh.ribbon.mgz ribbon.mgz wm.asegedit.mgz wm.mgz wmparc.mgz Below is the last few lines of output from my recon-all log file: "#@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.6 +- 4.9 [80.0 --> 125.0] GM (72.0) : 69.4 +- 10.8 [30.0 --> 96.0] setting bottom of white matter range to 80.2 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5962 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3294 filled 117 bright non-wm voxels segmented. 4879 diagonally connected voxels added... white matter segmentation took 3.4 minutes writing output to wm.seg.mgz... changing input type from 3 to UCHAR mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR reading wm segmentation from wm.seg.mgz... Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013 For more details, see the log file /ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting make: *** [/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz] Error 1" Any ideas as to what might be failing? Thanks for your help! Hayley

2 1

CT as covariate
by Rafa X 27 Mar '13

27 Mar '13

Dear Freesurfers I will introduce the mean cortial thickness as covariate into my statistical model, but I'm wonderind which way will be the best. To get the cortical thickness in individual space, or in AVG space? Thank you all in advanced, Rafa.

2 1

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