External Email - Use Caution Yes, my original config file works with 7.2
� I really appreciate your help. � Thanks. � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 9:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � I don't know; Anastasia is the author. She's busy today and tomorrow, I was just trying to push it forward. Does it work with the given config file in 7.2? On 7/25/2022 5:46 PM, kingwai....@gmail.com <mailto:kingwai....@gmail.com> wrote: � � � � � � � �External Email - Use Caution � � � � � � � � I added it to the config file, then it complains interreg: Undefined variable. � When I added interreg = 5, then it complains subj: Undefined variable. � Should I continue fixing it until no more Undefined variable? � From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:42 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � I think the wiki is wrong. Try setting it to 3 in the config On 7/25/2022 5:30 PM, kingwai....@gmail.com <mailto:kingwai....@gmail.com> wrote: � � � � � � � �External Email - Use Caution � � � � � � � � Hi Douglas, � According to TRACULA tutorial <https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1zSA_b4ezKCEwgchIiEjJkTpIEBtecsFaamd9vKJ9u9cVmSkAQgnUAuAvI4uXSMMmrEh26h_MAYnwauVVNGcw_oVyzeG7nY4f4TYvyUJszcbvL5b-cNT2d4mQCl-LlqWW-RDYZFsXRUkKcKMPqtGKZp3Dqr-WlgKEC85pfBEmYQv0KLDuoSU6SnwmafZ-Og9_oDVRrW47SZYBDmLTpOZ9f5US6U7H7cfq5fcq90pyh6d6f9Afsp7QX1KObzxlMYnaAXoq4fcvax2sgQF3nWNcyL1jU3-TmppzASKqM6L-nhXvFTBDq2BGxf1pLOVNxwG2l2s-Nv6Maq6oR8gHg8tDCw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula � A very simple configuration file, where only the absolutely necessary inputs are specified, intrareg is not there. and it works on v7.2.0. w/o it explicitly specified. � From the same site above, Step 12: Specify the intra-subject registration method “The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a mutual information cost), and 3 (bbregister, which uses a boundary-based cost). The default is option 3 (bbregister).” � If I don’t specify it in the config file, it should automatically use the default setting which is intrareg = 3. � I will add it to the config file and try again. � Thanks, � King-Wai � � � � � From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:02 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � are you sure the config file is right? it should be defining the intrareg variable On 7/25/2022 2:11 PM, kingwai....@gmail.com <mailto:kingwai....@gmail.com> wrote: � � � � � � � �External Email - Use Caution � � � � � � � � Hi Douglas, � Thank you for looking into this. It gives the following error. � trac-preproc.sh -c config.file intrareg: Undefined variable. � Thanks, � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 1:55 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)? On 7/22/2022 8:36 AM, kingwai....@gmail.com <mailto:kingwai....@gmail.com> wrote: � � � � � � � �External Email - Use Caution � � � � � � � � Hi Anastasia, � Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz �from segmentThalamicNuclei.sh which doesn’t exist. Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � trac-all finished w/o problem. � trac-all -version trac-all 7.3.0 � I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file. Or it is looking for v12 for a reason? � Is my fix correct? � Thanks, � King-Wai https://secure-web.cisco.com/1AQOqrVn211CtYM48OjffKrqb_crYJt6lw0JJYnqHW3zvTL13nvECnbFiTu9iDrU6EFFZHsQDOypgR2qtXkx0u1lUCSu_fTzllVij8gGPVuMeyXIPA8bqg9dFXGq-tLMtX3rsyMzjU2fYHgwAaM0XtPYJCjopSjXdiTBZfczPDiDp534ViQ8JKkRg5WlpzQB8f0jZZZlULvBWERgMdpvUlXc5YK7UW6nM9a-dbvrB9tH5Xm6U51aldQTxeX9H5eV4B4rbc6a3Vj8PqUz-lN9i0M4CwEojVlij11s_8-VxY0P5_yRpS4M6ztQTMMz0oj_R9c0sGbN1FhFkRo8fiwcddA/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.
