Hi Stefano, Just use the cp command to move your recon-all directories to the Diff01 directory and source it from there.
HTH, Shantanu On Tue, February 5, 2013 3:38 pm, 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 . 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 . 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 . 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 -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
