Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

aseg.mgz altered after auto-recon2?
by Joshua Lee 28 Mar '13

28 Mar '13

Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge.

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FSFAST and octave error dfor fast_selxavg3.m
by Mario Ortega 28 Mar '13

28 Mar '13

Hi Freesurfer group, Im attempting to use FS-FAST with resting BOLD data, and I have come across the following error. I tried changing files to non .gz extension, and still have this error.. $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ `fast_selxavg3' is a script from the file /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m `fast_ldanaflac' is a function from the file /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m ------------------------- outtop = /media/GOLDIN/FSFAST Extension format = nii.gz error: `MRIread' undefined near line 87 column 7 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/flac_customize.m at line 87, column 5 error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 65, column 7 ------------------------------------------ When I attempt to use fast_selxavg3 standalone in octave, I get this error. octave:1> fast_selxavg3; error: `sess' undefined near line 26 column 19 error: evaluating argument list element number 1 error: evaluating argument list element number 1 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 26, column 8 thanks, Mario Ortega GS4 Washington University in St. Louis, Dept. of Neurology

2 1

mris_thickness & qcache for xhemi surfaces
by Ejoe Yizhou Ma 28 Mar '13

28 Mar '13

Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: "mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h" To keep with this protocol, my questions are 1) how do I use "mris_thickness" properly so that I don't overwrite the files registered to fsaverage_510? 2) in "recon-all -qcache", will it do the trick by substituting "fsaverage_sym" for "fsaverage_510"? Thank you in advance, Cherry

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spmregister error
by Borzello, Mia 28 Mar '13

28 Mar '13

Hi Freesurfers, I'm in the middle of coregistering a CT and MRI, and after running spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig I get the error that orig.mgz is not found in COR or MGZ formats, but I have an orig.mgz file in my folder. Any help on this would be awesome! Thanks, Mia

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R: Re: R: Re: perirhinal analysis
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

What's meaning "subjet 2with"?Can you shown the correct command line, please? The wrong command line is mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface Many thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 28-mar-2013 18.32 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] perirhinal analysis If the source subject is subject_prova then you need to spec that subjet 2with --srcsubject (instead of fsaverage) doug On 03/28/2013 01:11 PM, stdp82(a)virgilio.it wrote: > Yes, it is located in > /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. > > > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 28-mar-2013 17.46 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] perirhinal analysis > > It says "no such file or directory" > does rh.perifhyinal.label exist? > > > On 03/28/2013 11:55 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I'm running perirhinal analysis with this error: > > > > mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label > > --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi > > rh --regmethod surface > > > > srclabel = rh.perirhinal.label > > srcsubject = fsaverage > > trgsubject = Con01 > > trglabel = Con01/label/rh.perirhinal.label > > regmethod = surface > > > > srchemi = rh > > trghemi = rh > > trgsurface = white > > srcsurfreg = sphere.reg > > trgsurfreg = sphere.reg > > usehash = 1 > > Use ProjAbs = 0, 0 > > Use ProjFrac = 0, 0 > > DoPaint 0 > > > > SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova > > FREESURFER_HOME /Applications/freesurfer > > Loading source label. > > No such file or directory > > mri_label2label: could not open label file rh.perirhinal.label > > No such file or directory > > ERROR reading rh.perirhinal.label > > > > My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and > > rh.perirhinal.label exist and it is located > > in /Applications/freesurfer/subjects/subject_prova/Con01/label > > > > > > Thanks, > > > > > > Stefano > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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R: Re: perirhinal analysis
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

Yes, it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 28-mar-2013 17.46 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] perirhinal analysis It says "no such file or directory" does rh.perifhyinal.label exist? On 03/28/2013 11:55 AM, stdp82(a)virgilio.it wrote: > Hi list, > > I'm running perirhinal analysis with this error: > > mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label > --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi > rh --regmethod surface > > srclabel = rh.perirhinal.label > srcsubject = fsaverage > trgsubject = Con01 > trglabel = Con01/label/rh.perirhinal.label > regmethod = surface > > srchemi = rh > trghemi = rh > trgsurface = white > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova > FREESURFER_HOME /Applications/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file rh.perirhinal.label > No such file or directory > ERROR reading rh.perirhinal.label > > My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and > rh.perirhinal.label exist and it is located > in /Applications/freesurfer/subjects/subject_prova/Con01/label > > > Thanks, > > > Stefano > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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

perirhinal analysis
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

Hi list, I'm running perirhinal analysis with this error: mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface srclabel = rh.perirhinal.labelsrcsubject = fsaveragetrgsubject = Con01trglabel = Con01/label/rh.perirhinal.labelregmethod = surface srchemi = rhtrghemi = rhtrgsurface = whitesrcsurfreg = sphere.regtrgsurfreg = sphere.regusehash = 1Use ProjAbs = 0, 0Use ProjFrac = 0, 0DoPaint 0 SUBJECTS_DIR /Applications/freesurfer/subjects/subject_provaFREESURFER_HOME /Applications/freesurferLoading source label.No such file or directorymri_label2label: could not open label file rh.perirhinal.labelNo such file or directoryERROR reading rh.perirhinal.label My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and rh.perirhinal.label exist and it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label Thanks, Stefano

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Different MPRAGE sequences
by _andreia_＠sapo.pt 28 Mar '13

28 Mar '13

Hello list, I have a group of subjects (4 patients and 8 controls) in which one MPRAGE sequence was used and another group of subjects (2 patients and 2 controls) where a diffent MPRAGE was used. Both groups were acquired in the same scanner. For each subject I have two anatomical sequences and I'm working with the average dataset. My question is can I put both groups together for comparision? I've thought about this and I can't really be sure... I was thinking that since for group 2 the number of acquisitions is balanced maybe the overall impact of different sequences won't be significative... Patients and subjects are age-matched in both groups. Please, any advice will be greatly appreciated! Thank you!

2 3

Fwd: Re: memory allocation errors on Snow Leopard running dmri_train (fwd)
by zkaufman＠nmr.mgh.harvard.edu 28 Mar '13

28 Mar '13

Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke -------- Original Message -------- Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT) From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> To: Zeke Kaufman <zkaufman(a)nmr.mgh.harvard.edu> ---------- Forwarded message ---------- Date: Wed, 27 Mar 2013 13:44:56 -0400 From: Ping-Hong Yeh <pinghongyeh(a)gmail.com> To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train Hi Anastasia, See the attached. Thank you. ping On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Ping - Can you send us your entire trac-all.log? There's some info in > there about your system and the freesurfer build you're using that we'll > need to try to replicate the problem. > > Thanks, > > a.y > > On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: > >> Hi Anastasia, >> >> It had the same issue before, but worked fine after installing the >> fixed dmri patch for Snow Leopard. >> >> Thanks. >> ping >> >> On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> Hi Ping - Are you running this on the same system where you were running >>> the >>> 5.1 snow leopard build without a problem? >>> >>> a.y >>> >>> >>> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: >>> >>>> 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 >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >

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Re: [Freesurfer] error during trac-all -prep
by Anastasia Yendiki 28 Mar '13

28 Mar '13

You can open them in a viewer, or just run mri_info on them. On Thu, 28 Mar 2013, Jon Wieser wrote: > How do i check the dimensions of the volumes? > > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, March 28, 2013 10:13:19 AM > Subject: Re: [Freesurfer] error during trac-all -prep > > > Hi Jon - The command that fails is trying to multiply 2 volumes and > complains that they have different sizes. Have you checked if these 2 > volumes exist and what their dimensions are? > > a.y > > On Wed, 27 Mar 2013, Jon Wieser wrote: > >> i ran >> trac-all -prep -c dmrirc_single_subject >> and got the error : >> >> fslmaths /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask.nii.gz -mul /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/notventricles.nii.gz /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask-vent.nii.gz >> Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes >> terminate called after throwing an instance of 'RBD_COMMON::BaseException' >> Abort >> >> >> I have attached the trac-all .log and trac-all.error files >> >> I don't know how to fix this error >> >> >> Thanks >> Jon >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > >

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