You don't need all that stuff. You should remove everything below the bvalfile line and use the default parameters. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkene...@gmail.com> Sent: Friday, August 5, 2022 2:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula Config file.
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<mailto: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<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alan Francis <alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>> Sent: Thursday, August 4, 2022 12:23 PM To: Freesurfer <freesurfer@nmr.mgh.harvard.edu<mailto: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. 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Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
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