Hi Dylan - Can you send your trac-all.log file? (When the baselist is included in the dmrirc, otherwise you're just running the cross-sectional tractography.)
Thanks, a.y
On Mon, 8 Apr 2013, Dylan Nielson wrote:
I'm running CentOS 6.4. I don't know if it matters, but I tried running the command from both bash and tcsh and they both give an error. Also, I did the bedpost outside of freesurfer and then copied the outputs from that into the freesurfer directories where they're supposed to go. The dcmric file will run if I take out the baselist portion. Any ideas you have would be great.
Thanks,
Dylan
On Mon, Apr 8, 2013 at 8:04 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Dylan - First of all kudos for being a brave early adopter :) The only thing wrong with the dmrirc that I see is that there can be only one bvecfile and bvalfile, not one per time point (it's assumed that you used the same protocol for all time points). That said, I don't think that's what's causing the error. What operating system and version are you running this on? a.y On Sat, 6 Apr 2013, Dylan Nielson wrote: I am trying to run Tracula on a single subject with two time points. I get the following Error below. I suspect it is because I am not setting my dmrirc file up correctly, but I cannot figure out what the error is. I've copied my dmrirc file below as well. Thanks, Dylan Command: trac-all -prep -nocorr -nointra -c dmrirc.long.RP0603 Error: trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ; dmrirc.long setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer set dtroot = ~/fmri/RP0629_3T/freesurfer set subjlist = ( tp1002.long.002 \ tp2002.long.002 ) set baselist = ( 002 002 ) set dcmroot = ~/fmri/RP0629_3T/freesurfer/ set dcmlist = ( tp1002.long.002/dmri/dwi.nii.gz \ tp2002.long.002/dmri/dwi.nii.gz ) set bvecfile = ( tp1002.long.002/dmri/bvec \ tp2002.long.002/dmri/bvec ) set bvalfile = ( tp1002.long.002/dmri/bval \ tp2002.long.002/dmri/bval ) set dob0 = 0 set doeddy = 0 set thrbet = 0.5 set doregflt = 0 set doregbbr = 1 set doregmni = 0 set doregcvs = 1 set cvstemp = cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects set usemaskanat = 1 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS \ lh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5) set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt set nstick = 2 set nburnin = 200 set nsample = 7500 set nkeep = 5 set reinit = 0The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.