External Email - Use Caution Hi Chiara -
Please ignore the previous email. I set my doB0 = 0, but it gives me this error message: copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_4 ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction Where does one get details of the phase encoding direction? Thanks, Alan On Tue, Jul 18, 2023 at 1:24 PM Maffei, Chiara,PHD <cmaf...@mgh.harvard.edu> wrote: > 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://secure-web.cisco.com/1qtDPkVR503XpTKb0eRbENyT6pCNxZxQEcVnEsTT-MQBb8Jh_6vGfdxTPjXp75GqA3QqXrH8-lFfZupEgBY4659iHs4y4CdgLxW7VJJxO5uZmkUmrXDsH5gh-tuZDdoSeKMNQnixvnzXIsIRbjchh2Er7JMUXnE69SzL6UpXSHtrXZU5jbHoBp_Op2vjYWNVA5iaOfWwPnZh_e1WwzzD60RpsG1shWeO88183W-Kct5_n1npK5Hk5_q0FK3yJ1LGXPcW18QFPBRfxw8lUbvWJfz8j8yQt1GzkYLBpV2ulDBoWo3nByvBAFDNlFlVw1JMPw6xnM1Hye_n7ORTXaPne4A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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://secure-web.cisco.com/1FRoViSNbY5JlGIDZlb1RcMEgaaFu4H8Nnv4Sz06kn0RiOLyZNL7m4g-jFCIiy8ae08WqVQakgUTgJzFhSxOmtggzEponbx9ESQKgNme2S6XqJ9CLjDGNkdtx7YzM8t5heZLFBPjqpnGbTFPYKOo-Sa3EWbRp5OlLyHTxQmw7vCnk4il1OthbR0vDVO9jiAQBjUrkV6LkRkMNDWXBxAyJbaxiJF_FbJ-wWmGv21BzkSR3FtXcifkEhiu6Rc8RAHKKVL8ua1GQq-hZc3DqjPz3tXyHo3w64Yuzv4Xv-MgHFQ_gQYzZMUjYBSpBXdjzQXhgRZJU8yFwjQuVpuNAsX2KrQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1FRoViSNbY5JlGIDZlb1RcMEgaaFu4H8Nnv4Sz06kn0RiOLyZNL7m4g-jFCIiy8ae08WqVQakgUTgJzFhSxOmtggzEponbx9ESQKgNme2S6XqJ9CLjDGNkdtx7YzM8t5heZLFBPjqpnGbTFPYKOo-Sa3EWbRp5OlLyHTxQmw7vCnk4il1OthbR0vDVO9jiAQBjUrkV6LkRkMNDWXBxAyJbaxiJF_FbJ-wWmGv21BzkSR3FtXcifkEhiu6Rc8RAHKKVL8ua1GQq-hZc3DqjPz3tXyHo3w64Yuzv4Xv-MgHFQ_gQYzZMUjYBSpBXdjzQXhgRZJU8yFwjQuVpuNAsX2KrQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > > -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*
dmrirc-109123_7T_4
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