Ok, so I will use my own recon-alled data to follow the tutorial and at the same time to wait for the new version of FreeSurfer
Thanks
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Envoyé : dimanche 18 décembre 2016 14:51 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors
Hi Hao - That is strange, thank you for bringing this to our attention. The recons should be there. We're in the process of rerunning everything with version 6.0 in preparation for the release, so all this data will be updated. Thank you for your patience!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hao wen [hao.freesurfer@hotmail.com] Sent: Sunday, December 18, 2016 4:32 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA trac-all preprocessing errors
Hello, Thanks for your reply, that was what I thought, But I just download the tutorial data, and followed your tutorial from this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
FsTutorial/Tracula - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula surfer.nmr.mgh.harvard.edu Back to list of all tutorials | Back to course page | Next. TRACULA tutorial. This tutorial will take you through the steps necessary to run TRACULA (TRActs ...
So I think in the folder tutorial_data/diffusion_recons/elmo.2005/mri, it is empty, do you think before TRACULA, we have to run recon-all for these tutorial subjects??? i thought they are already recon-alled....I defined the SUBJECT_DIR as
export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons
Besides, thanks for the second point:)
Hope to hear from you soon,
Thanks in advance
Hao
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Envoyé : samedi 17 décembre 2016 17:26 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors
Hi Hao - It looks like it didn't find the freesurfer recons of the subjects' structural data. They should be under whatever you have defined as SUBJECTS_DIR.
On a separate note, it looks like you're using an old version of TRACULA. There is an update that you can download from the TRACULA wiki page, or you can wait for freesurfer 6.0, which will hopefully be out in a few days and will include this update. https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Best,
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hao wen [hao.freesurfer@hotmail.com] Sent: Saturday, December 17, 2016 11:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA trac-all preprocessing errors
Hello, Freesurfer experts:
I am new to Tracula, and I followed your tutorial with your tutorial data, and for the preprocessing pipeline, I got some errors when doing the tensor fitting, here is the command:
trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
and I looked over the trac-all.log and found that the problem is from the command dmri_train, here is the errro log information:
'
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.25745.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.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.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc ERROR: fio_pushd: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
cwd /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial cmdline /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.25745.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.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.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc sysname Linux hostname DELLEED1 machine x86_64 user wen Output directory: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni Output directory in test subject's space: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.elmo.2005.25745.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.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: [1] 1065 segmentation fault (core dumped) --outdir --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr '
and in the output structure /dlabel, I dont have the mni sub-folder, so I guess I have some problems when doning the tensor fitting.
And I know in this process, we will need the aparc+aseg.mgz, but the in the tutorial data diffusion_recons , for the subject of elmo.2005, I dont find aparc+aseg.mgz in mri folder, and I just found aparc+aseg2diff.mgz image in Diff001, instead, you use this volume???
I am stuck at this step, any advice will be appreciated:)
Thank in advance
Hao
Good day