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
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 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/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_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>
hi - I note though I changed the shell to tcsh before running the code and performed all the relevant setenv Also a single subject but not multiple subjs, is being entered cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ On 02/08/13 10:19, Watson, Christopher wrote:
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 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_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>
Hi David - You need to run each of the steps (-prep, -bedp, -path) separately. You can't run them all at the same time. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
Hope this helps, a.y
On Fri, 2 Aug 2013, David Soto wrote:
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
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
David Soto -
Watson, Christopher