External Email - Use Caution Hi King-Wai -
First of all, thank you so much for taking the time to investigate my RC file. I made the changes that you suggested, but the error keeps coming up. I have attached the file. Thanks again, Alan On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu <kingwai....@gmail.com> wrote: > External Email - Use Caution > > Hi Alan, > > They still don't match. > See attached excel file. > > Best, > > King-Wai > > On Fri, Aug 5, 2022 at 2:35 PM Alan Francis <alandarkene...@gmail.com> > wrote: > >> External Email - Use Caution >> >> Hello King-Wai - >> >> I made the change to the ncpts. But still an error message persists. >> >> ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm >> cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af >> <http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af> >> rh.af >> <http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af> >> lh.ar >> <http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar> >> rh.ar >> <http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar> >> lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc >> lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 >> rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID >> list >> ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 >> 0 0 10 49 0 0 0 0 0 0 0 0) do not match >> >> >> >> I have attached the RC file. Could you please shed some light on this? >> >> Thank you >> >> Alan >> >> On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu <kingwai....@gmail.com> >> wrote: >> >>> External Email - Use Caution >>> >>> Hi Alan, >>> >>> Your pathlist and "Number of path control points"(ncpts) don't match. >>> You have more than 3 paths in the pathlist and only 3 numbers in ncpts. >>> >>> Best, >>> >>> King-Wai >>> >>> >>> >>> >>> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis <alandarkene...@gmail.com> >>> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Good morning Anastasia - >>>> >>>> I made the changes you suggested and removed "extraneous" commands. But >>>> the error message still persists. Could you please shed some light on this? >>>> Attached - latest RC file. >>>> >>>> The error message is : unmatched ' " ' >>>> >>>> Thank you >>>> >>>> Alan >>>> >>>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < >>>> ayend...@mgh.harvard.edu> wrote: >>>> >>>>> Hi Alan - dcmroot is the root directory under which the dicom files >>>>> are saved. It's actually optional. In your case, either of the following >>>>> will have the same, correct effect: >>>>> >>>>> set dcmroot = /home/afrancis/Imaging >>>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz) >>>>> >>>>> OR >>>>> >>>>> set dcmlist = >>>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz) >>>>> >>>>> In addition, there are *a lot *of things that you left in there from >>>>> the example RC file. You should delete them entirely, unless you >>>>> specifically want to set one of those things to something other than the >>>>> default. These are examples that may not give you the default behavior. >>>>> Also the field mapping files - delete those lines because you're just >>>>> using >>>>> the example names and they're not going to work. You want your RC file to >>>>> have the minimum necessary for your analysis. >>>>> >>>>> Best, >>>>> Anastasia. >>>>> >>>>> >>>>> ------------------------------ >>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < >>>>> alandarkene...@gmail.com> >>>>> *Sent:* Thursday, August 4, 2022 12:23 PM >>>>> *To:* Freesurfer <freesurfer@nmr.mgh.harvard.edu> >>>>> *Subject:* [Freesurfer] Tracula Config file. >>>>> >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi Anastasia - >>>>> >>>>> Hope you are well. I am running tracula on FS 7.2. I created the RC >>>>> file based on your recommendations. However it is giving me an error >>>>> message when I run it. The error is : Unmatched ' " " >>>>> >>>>> I have attached the RC file. Could you please see where I have made an >>>>> error. >>>>> >>>>> Thanks so much, >>>>> >>>>> Best regards, >>>>> >>>>> Alan >>>>> >>>>> -- >>>>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* >>>>> >>>>> >>>>> >>>>> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of >>>>> Neuroscience* >>>>> *University of Texas, School of Medicine* >>>>> >>>>> *Rio Grande Valley * >>>>> >>>>> *Texas. * >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> *MailScanner has detected a possible fraud attempt from >>>>> "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> <https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/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 *MailScanner has detected a possible >>>>> fraud attempt from "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >>>>> <https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >>>>> <*MailScanner has detected a possible fraud attempt from >>>>> "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >>>>> <https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/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.* >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> <https://secure-web.cisco.com/147r4yKWXDa0ksyQ_uy68dtWkcYD3-JmqjORDjb8wn1yq_rsrwgA_BsryMv4A4tG4MDuknwm94cEnJDZbHhKopKetiFD1jOAz8LydOql5U6nIxNQOmhIOpsL546Pz2jHWWcBaCjM9zwxc1v7wLO1YnJ0jwqPjYSuLPLnmU7ik9jKak1dH9olnDiywVCLo2Ki1ikF7Otbd1osYYzRZkuguuxYM8Vjt12MrHYJd34xLd4ZX2a8D7xCcJyH85YOqRe3Mh9k13cvwOa6elIfClYhwJmEeWNZXi2YLSgZHtIrSwwf8lIrX5PE_5CaDIZmPGIwm/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 *MailScanner has detected a possible >>>> fraud attempt from "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >>>> <https://secure-web.cisco.com/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl86MlMfZaWHXtWQ_xvoSoFe19ETRJ0qeFiEx1Mb5d5yKdu6DBbnmZEJcOC5lR-T_11kBRKJX49sFd8PZcKE0FpVoqGN0-yej4ZPiOXCrL76SHzSJJeeIRhWzLGRkxsDbZIAzxCt4NMorpwX2wHW4YsfzLBVVJeBWw_9eyvedZ4NyJutBZuE8aV595Kp2f8I1v_dv3nbu4juE2mdORcvSqy3unc9oTm0a0dhj85ojssfTY7c2-tEPDUYpltXeCOuJ1WkNMDJCEj9YbkeW7V3/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >>>> <*MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >>>> <https://secure-web.cisco.com/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl86MlMfZaWHXtWQ_xvoSoFe19ETRJ0qeFiEx1Mb5d5yKdu6DBbnmZEJcOC5lR-T_11kBRKJX49sFd8PZcKE0FpVoqGN0-yej4ZPiOXCrL76SHzSJJeeIRhWzLGRkxsDbZIAzxCt4NMorpwX2wHW4YsfzLBVVJeBWw_9eyvedZ4NyJutBZuE8aV595Kp2f8I1v_dv3nbu4juE2mdORcvSqy3unc9oTm0a0dhj85ojssfTY7c2-tEPDUYpltXeCOuJ1WkNMDJCEj9YbkeW7V3/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> >>>> . >>>> >>> >>> >>> -- >>> King-Wai Chu, Ph.D. >>> Program Analyst >>> Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) >>> James J. Peters Dept. of Veterans Administration Medical Center (OOMH) >>> 130 W. Kingsbridge Road >>> Bronx, NY 10468 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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. 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Francis PhDAssistant Professor of NeuroscienceInstitute of >> Neuroscience* >> *University of Texas, School of Medicine* >> >> *Rio Grande Valley* >> >> *Texas.* >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/11covYpNG9XogCXNSKkEfQ4sHz7Fzi5j-cYHWmfjoP40VT5S7NUoT7l4Qdc8w5CTdzoEvMGvbWkDJ6h7mTQJg4G4N8Koof6j4ciGfKQ_nkIWuwR1Ek57grNVG-LUEs_K1lVwgxARX5mIjEFhtOc44RfAbPO3lLndNslRdbL6XRDQiwEJSGpsQiceShK8Rmrpm7uqur23comFXbKSMEbuF4UNzihLs2gYSLDZ370VEvkbq1kjGMYn1clW8NuUPzZFRmFM7V3aq_eI9hyvp01p-ekTSBi0u9mLsI2KLrg3uqiyB4tsC9KS-fPZS0ApHWg57F1al6lVcPI3-YsYVwoc2GQ/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. 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Peters Dept. of Veterans Administration Medical Center (OOMH) > 130 W. Kingsbridge Road > Bronx, NY 10468 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/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/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/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.*
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here setenv SUBJECTS_DIR /home/afrancis/Imaging # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/afrancis/Imaging/109123 # Subject IDs # set subjlist = (109123) # Default: Run analysis on all subjects # set runlist = (1) set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz) set bvecfile = /home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP.bvec set bvalfile = /home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP.bval # Perform correction for B0 inhomogeneity distortions? set dob0 = 2 # Perform correction for eddy-current distortions? # 0: No correction # 1: Perform registration-based correction with eddy_correct # 2: Perform model-based correction with eddy (default) set doeddy = 2 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # Degrees of freedom for intra-subject registration # Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine) # Default: 6 for infants, 9 otherwise # set intradof = 6 # Maximum rotation angle (degrees) for intra-subject registration # Default: 3 for infants, 90 otherwise set intrarot = 90 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) set usemaskanat = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 set thrbet = 0.5 set pathlist = ( ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af rh.af lh.ar rh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths set ncpts = ( 5 5 5 5 5 5 4 4 4 4 5 6 6 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 ) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/hcp/trainlist.txt set trainfile = $FREESURFER_HOME/trctrain/hcp/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0
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