You could just move the recon-all output directories from the location where they was originally generated into the Diff01 directory. For the purposes of running trac-all this should not make a difference.
On Tue, 5 Feb 2013, std...@virgilio.it wrote:
Because initially I have run recon-all and trac-all in two separate folder.Now I'd like rerun them in a unique folder. I have put MPRAGE and data.nii.gz in Diff01 When I run: recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd $SUBJECTS_DIR/Diff01 -all I have: ERROR: must specify a subject id I do not understand as I should placed the my file in the folder. Stefano ----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 5-feb-2013 21.08 A: <std...@virgilio.it> Cc: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: tracula and recon-all Why do you want to rerun recon-all after trac-all? You just need to run it before trac-all. On Tue, 5 Feb 2013, std...@virgilio.it wrote: > No, I 'm sorry. I try to reformulate my question. > I have a folder called Diff01 in > my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova) > This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt, > bvals.txt and MPRAGE.nii.gz. > > Which is the exact command line (and the exact files name in the folder) > that you advise me for running recon-all and after trac-all? > > > > Stefano > > > > You mean the exact command line to delete a folder? It's rm -rf. > > On Tue, 5 Feb 2013, std...@virgilio.it wrote: > > > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR > > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have > > data.nii.gz bvecs bvals MPRAGE.nii.gz > > > > If I write on terminal > > > > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject > > $SUBJECTS_DIR/Diff01 > > > > with this ERROR: You are trying to re-run an existing subject with > > (possibly) > > new input data (-i). If this is truly new input data, you should delete > > the subject folder and re-run, or specify a different subject name. > > If you are just continuing an analysis of an existing subject, then > > > > How is the exact command line, please? > > > > Thanks, > > > > > > Stefano > > > > omit all -i flags.The subject name needs to be the same for recon-all and > t > > rac-all. There is > > no way for trac-all to guess that hpth_subj01 and Diff01 are the same > > subject. > > > > > Hi Anastasia, > > > my original folder Diff01 in > > > /Applications/freesurfer/subjects/subject_prova/Diff01 now > > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned > > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject > > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c > > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error: > > > /Applications/freesurfer/bin/dmri_train --outdir > > > /Applications/freesurfer/subjects/subject_prova/Diff01/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.Diff01.21529.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 > > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra > > in_mask.flt.nii.gz > > > --fa > > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA. > > flt.nii.gz > > > --ncpts 5 --debugERROR: fio_pushd: > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR: > > > must specify brain mask volume for output subjectDarwin > > > iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > > > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Tue Feb 5 07:54:09 CET 2013 > > > Why? Can it depends from the files in the original folder Diff01? > Please, > > > if yes, may you explain which is the better arrangement of the MPRAGE > and > > > DWI in the folders. > > > Thank you very much, > > > > > > Stefano > > > > > > > > > > > > > > > ----Messaggio originale---- > > > Da: ayend...@nmr.mgh.harvard.edu > > > Data: 4-feb-2013 4.48 > > > A: <std...@virgilio.it> > > > Cc: <freesurfer@nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: tracula bvecs error > > > > > > > > > No, putting your T1 in a folder is not the same as running freesurfer on > > > it. You need to run recon-all on your T1. This is a piece of software > that > > > will segment your T1 (among other things). Tracula will need that > > > segmentation to reconstruct your tracts. > > > > > > On Sun, 3 Feb 2013, std...@virgilio.it wrote: > > > > > >> Hi Anastasia, > > >> I have put T1 in > /Applications/freesurfer/subjects/subject_prova/Diff01/ > > >> together data.nii.gz, bvals and bvecs. > > >> My $SUBJECTS_DIR=$FREESURFER_HOME/subjects/subject_prova > > >> T1 was called as T1_01.nii.gz. > > >> This is well done? > > >> > > >> Thanks, > > >> > > >> Stefano > > >> > > >> ----Messaggio originale---- > > >> Da: ayend...@nmr.mgh.harvard.edu > > >> Data: 3-feb-2013 20.50 > > >> A: <std...@virgilio.it> > > >> Cc: <freesurfer@nmr.mgh.harvard.edu> > > >> Ogg: Re: [Freesurfer] tracula bvecs error > > >> > > >> > > >> Do you have a freesurfer recon of your subject's T1 in the > > >> $SUBJECTS_DIR? > > >> > > >> On Sun, 3 Feb 2013, std...@virgilio.it wrote: > > >> > > >> > I think that I have resolved the bvecs error by using sudo nano > option > > >> but > > >> > now in the next step I visualize this error: > > >> > ERROR: fio_pushd: > > >> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni > > >> > ERROR: must specify brain mask volume for output subject > > >> > > > >> > Thanks, > > >> > > > >> > Stefano > > >> > > > >> > > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@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. > > >> > > >> > > >> > > >> > > >>_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@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 . 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