26 Apr
2013
26 Apr
'13
11:53 a.m.
Hi Dylan - Thanks for your patience.
There was a small scripting bug that was causing trac-all in longitudinal mode not to process the command line properly on some systems. Can you please copy the two modified scripts I'm attaching to your $FREESURFER_HOME/bin, overwriting the existing versions?
Please let me know if that fixes the error, and if so I'll post them to the wiki as an update for anyone else who wants to run longitudinal.
Thanks, a.y
On Tue, 9 Apr 2013, Dylan Nielson wrote:
This should be what you need, Let me know if I've sent the wrong one.
On Tue, Apr 9, 2013 at 11:30 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
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 = 0 The 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.