External Email - Use Caution Hi Alan,
It looks like you have specified the ncpts variable but not the pathlist. If you do not specify pathlist, TRACULA will include all 42 tracts by default, so your pathlist and ncpts variables will have different lengths. If you want to focus your analysis on a subset of tracts, specify those using pathlist (e.g., set pathlist = (rh.uf lh.uf)). If not, do not specify ncpts either (comment out or remove line 59 from your config file) and TRACULA will reconstruct all 42 tracts. I also noticed you specified dob0 = 2 but did not set pedir. If you want to use topup to correct for b0 inhomogeneity distortions you need to provide the PE direction of your volumes. Best, Chiara > On Jul 18, 2023, at 1:01 PM, Alan Francis <alandarkene...@gmail.com> wrote: > > External Email - Use Caution > > > Hi King-Wai: > > I have been running Tracula on 7T images and it keeps giving me an error. The > error is as follows: > > copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2 > Unmatched '"'. > > I have attached my config file. Can you please let me know what I am doing > wrong? > > Thanks, > > Alan > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > Alan N. Francis PhD > Assistant Professor of Neuroscience > Institute of Neuroscience > University of Texas, School of Medicine > Rio Grande Valley > Texas. > > > <dmrirc-109123_7T_2>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1h22qW5Sk61PyGDT0hI--uUXJRRi9PeS5yoZ8404dlD1_0z1vAdJHl1DSpAqKmEr1hMw7AHcy6yirr0NYNit9csau7I6MRWk77WhWAAhQTuLcyo2n86A2QHHKc-53-D_zI7-rM2_ZWYUkzRli4sN32dybyt33eKgN2UpIvFcpfCX-dtKnx6TO5KCZ1rvxgIFHpm0XTqdjKoiHX1VMJRH0SQcD8n8BQi7PewsKGWAsYE-IPebIoEzDOOhAnxToInngV3WHF6lj1NheRbrqV_Ui1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
