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_brain_mask.flt.nii.gz --fa /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug
ERROR: fio_pushd: /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
ERROR: must specify brain mask volume for output subject
Darwin 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: ayendiki@nmr.mgh.harvard.edu
Data: 4-feb-2013 4.48
A: <stdp82@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, stdp82@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: ayendiki@nmr.mgh.harvard.edu
> Data: 3-feb-2013 20.50
> A: <stdp82@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, stdp82@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
> >
> >
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