thanks Anastasia, I have some problems however- could you help please?
as said, I am not using the DICOMS, my diffusion data has been converted to nii and then to mnc my config file mostly accepts the defaults, and is simple as follows. There is a folder 'diffree' which contains the dmri config file, the becs and bvals and the mnc difffusion file $$$$$$$$ setenv SUBJECTS_DIR /home/dsoto/Documents/fmri/rsdtianawmgui set dtroot = /home/dsoto/Documents/fmri/rsdtianawmgui set subjlist = (02ST) set runlist = (1) set dcmroot = /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree set dcmlist = (diffdata.mnc) set bvecfile = /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/bvecs_t set bvalfile = /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/bvals_t set mnitemp = /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain $$$$$$$$
When i run trac-all -c tracula02ST.txt -prep I get some errors such as
1. fslmaths /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -Tmean /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz Cannot open volume /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb for reading! bet /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain.nii.gz -m -f 0.3
Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid
mv -f /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_mask.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff mv: cannot stat `/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_mask.nii.gz': No such file or directory
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_anat.flt.nii.gz -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.flt.mat -cost mutualinfo
Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped)
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.flt.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.flt.mat Could not open matrix file /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.flt.mat Cannot read input-matrix convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.flt.mat -concat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.flt.mat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2anat.mat Could not open matrix file /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.flt.mat Cannot read concat-matrix convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anatorig.flt.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.flt.mat Could not open matrix file /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.flt.mat Cannot read input-matrix
Intriguinly, the script completes with the message
trac-preproc finished without error at Tue Aug 6 03:02:08 BST 2013
HOWEVER, when I attempt the next step trac-all -c tracula02ST.txt -bedp it aborts saying "/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/nodif_brain_mask not found"
I am running FSL 5.0.4 under Ubuntu 12.04
cheers ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: 02 August 2013 19:15 To: Soto, David Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all inquiry
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
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