I've found that when using the Bash shell, putting multiple subjects in the config file doesn't work. Maybe that's the issue here? Although, I simply never bothered to look into it any more.
Chris
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of David Soto [d.soto@imperial.ac.uk] Sent: Friday, August 02, 2013 5:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all inquiry
Hi,
I have successfully run recon-all in my dataset and now am attempting to use trac-all on my diffusion data obtained on a Siemens scanner.
Diffusion dicoms were transformed to .nii using MRIConverter and then to .mnc using
nii2mnc output.nii output_t.mnc.
I am trying to run trac-all on a single subject and for this I have created the configuration file attached (tracula02ST)
As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui and within each subject the T1 serving as input for recon-all are in mri/orig
while the diffusion images are in a folder call diffdata (named output_t.mnc) which also contains the bvecs and bvals files, which were transposed and organised according to the tutorial (named as bvecs_t.txt and bvals_t.txt)
When I run: trac-all -c tracula02ST.txt
I get: ERROR: no analysis step (-{prep,bedp,path}) has been selected
THEN I run: trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so and then gives the long output text below with an error message.
Segmentation fault (core dumped) foreach: No match.
The trac-all.log is attached also.
Could you please help?
Cheers
David
-- http://www1.imperial.ac.uk/medicine/people/d.soto/
wmen-dsoto3:~/Documents/fmri/rsdtianawmgui> trac-all -prep -bedp -path -c tracula02ST.txt INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui Actual FREESURFER_HOME /usr/local/freesurfer trac-paths -c /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/dmrirc.local -log /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.log -cmd /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Aug 2 09:44:20 BST 2013 /usr/local/freesurfer/bin/dmri_paths --outdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cst_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cst_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ilf_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ilf_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.unc_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.unc_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fmajor_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fminor_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.atr_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.atr_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ccg_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ccg_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cab_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cab_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slfp_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slfp_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slft_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slft_PP_avg33_mni_bbr --dwi /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz --grad /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs --bval /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals --mask /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz --bpdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz 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/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids --seg /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 Segmentation fault (core dumped) foreach: No match. wmen-dsoto3:~/Documents/fmri/rsdtianawmgui>