Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

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!

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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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Re: [Freesurfer] Tracula Cluster Question
by Anastasia Yendiki 28 Mar '13

28 Mar '13

Hi Sal, 1. I have no experience with the sun grid engine, perhaps someone else on the list can help with that. 2. The -bedp step needs the outputs from the -corr and -masks steps. The -path step needs the outputs from the -bedp step. The output files from each part are listed here: http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles 3. Checking the aparc+aseg should be enough for tracula purposes as well, since that's the freesurfer output that tracula uses. Keep in mind that DWI resolution is usually lower than T1 resolution, so tiny changes in the aparc+aseg might not affect tracula at all. 4. Yes, I do recommend using bbregister. It's not surprising that it would give better results since it uses the additional information of the surfaces. If I remember correctly, Doug didn't manage to replicate your bbregister error, right? I'd check if you get the same error with the 5.1 version of bbregister. Hope this helps, a.y On Wed, 27 Mar 2013, Salil Soman wrote: > Hi, > I have been able to implement FS 5.2 on our Sun Grid Engine Cluster using the CentOS 6 > distribution. After modifying the fsl_sub_mgh file to work with out cluster queue > names and to modify the email notifications, I am able to run the entire processing > pipeline using FLT. (Everytime I try bbr I get errors. I had email doug about this but > have not heard any response). > > I am submitting the jobs to the cluster as follows > > recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm -openmp 50 > -hippo-subfields -all > trac-all -prep -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -bedp -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -path -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > > There are a few issues I am trying to sort out: > > 1) how should one conifigure the openmp flag for the Sun Grid Engine? the flag I used > did not change processing time, and each subject is still taking ~24 hrs? > > 2) once the script starts bedpost, bedpost has controller code which paralelizes all > of the slices (which has been great going from 12 hrs of processing to 1.5 hrs). > However, my original script goes on to execute trace-all -path ... before bepost is > done, generating errors. I have gotten around this by running the trace-all -path > command again after bedpost sends me an email confirming completion. Is there a way to > more cleanly do this (some kind of hold command I can do based on output from > bedpost)? > > 3) In your experience, how important is quality control of freesurfer on tracula > results? We have come to the compromise for freesurfer output to manually check the > segmentation of aparc+aseg.mgz using free view, only correcting and rerunning steps of > freesurfer when there are specific structures we want the volumes of (eg hippocampus). > > 4) have you found a significant benefit of bbr over flt? If so, any suggestions on > things I may need to check to get bbr to work (given flt works)? > > Best wishes, > > Sal > > > > > >

1 0

trac-all -path error
by Nawaf Yassi 28 Mar '13

28 Mar '13

Dear mailing list I am encountering an error at the trac-all path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error ³Segmentation fault² (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help? I am using freesurfer 5.2 and FSL 5.0.2.1 (linux) Regards Nawaf ATTACHED: ERROR MESSAGE + config file below ========================================================= [nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject Too many )'s. INFO: SUBJECTS_DIR is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer INFO: Diffusion root is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.2 trac-paths -c /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/dmrirc.local -log /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/trac-all.log -cmd /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer5.2/bin/trac-paths #------------------------------------- #@# Path reconstruction Thu Mar 28 10:01:34 EST 2013 rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.cst_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.cst_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.ilf_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.ilf_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.unc_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.unc_AS_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/fmajor_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/fminor_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.atr_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.atr_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.ccg_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.ccg_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.cab_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.cab_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.slfp_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.slfp_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.slft_PP_avg33_mni_bbr rm -rf /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/rh.slft_PP_avg33_mni_bbr /usr/local/freesurfer5.2/bin/dmri_paths --outdir /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dpath/lh.cst_AS_avg33_mni_bbr 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/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Segmentation fault (core dumped) foreach: No match. ============================================================================ ========================================================= [nyassi@bee1 scripts]$ cat dmrirc_single_subject # # dmrirc.example # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2013/02/16 22:49:06 $ # $Revision: 1.3.2.4 $ # # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" # # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer(a)nmr.mgh.harvard.edu # # # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # # Subject IDs # set subjlist = (C01) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile, bvalfile, and nb0 must be specified (see below) # set dcmroot = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/DICOMS/raw_dti/HURLE_LISA set dcmlist = (IM-0001-0001.dcm) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # # set bvecfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvecs.txt # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # # set bvalfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvals.txt # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 0 # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 5000 # # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # # set reinit = 0

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Freesurfer March 2013