External Email - Use Caution Hi Douglas
Thank you for your reply. I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a I am using whole brain data. The functional and structural images were acquired in different sessions on the same day, I don't know if that complicated things? Each subject has 2 runs of the same task. This is what I get after running the command in the format of tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum 20_1 013 0.5155 20_1 014 0.5090 20_10 013 0.5247 20_10 014 0.5229 20_100 038 0.8420 20_100 040 0.8443 20_101 008 0.9052 20_101 010 0.9289 20_102 058 0.6924 20_102 059 0.6902 20_103 045 0.9778 20_103 046 0.9931 20_104 010 0.9324 20_104 012 0.9413 20_105 013 0.8754 20_105 014 0.8937 20_106 047 0.4433 20_106 048 0.4377 20_107 008 0.9178 20_107 010 0.9238 20_11 013 0.7631 20_11 014 0.7615 20_110 048 0.7687 20_110 049 0.7549 20_112 013 0.8821 20_112 014 0.9161 20_113 052 0.7689 20_113 053 0.7757 20_116 046 1.0072 20_116 047 1.0256 20_117 008 0.7742 20_117 010 0.7826 20_119 013 0.7929 20_119 014 0.7854 20_120 048 0.5090 20_120 049 0.4973 20_126 047 0.8285 20_126 048 0.8281 20_128 046 0.9580 20_128 047 0.9314 20_130 047 0.9439 20_130 048 0.9425 20_132 047 0.8550 20_132 048 0.8558 20_134_1 013 0.5716 20_134_1 015 0.5744 20_135 011 0.8357 20_135 012 0.8401 20_136 044 0.9995 20_136 045 0.9604 20_137 047 0.7922 20_137 048 0.7990 20_142 047 0.5282 20_142 048 0.5278 20_144 013 0.8755 20_144 014 0.8838 20_146 047 0.7997 20_146 048 0.7895 20_149 049 0.9251 20_149 050 0.9408 20_151 048 0.5905 20_151 049 0.5519 20_152 048 0.9024 20_152 049 0.9021 20_155 048 0.5285 20_155 049 0.5324 20_156 048 0.8883 20_156 049 0.9267 20_158 048 0.5404 20_158 049 0.5297 20_159 048 0.8021 20_160 013 0.5002 20_160 014 0.4942 20_162 047 0.5401 20_162 048 0.5401 20_164 047 0.8944 20_164 048 0.8940 20_165 047 0.9163 20_165 048 0.9077 20_166 045 0.8787 20_166 046 0.8848 20_167 050 0.8428 20_167 051 0.8442 20_169 049 0.9407 20_169 050 0.9462 20_170 047 0.8921 20_170 048 0.9113 20_171 013 0.9060 20_171 014 0.9060 20_173 048 0.9193 20_173 049 0.9141 20_177 048 0.8695 20_177 049 0.8600 20_178 048 1.0327 20_178 049 0.8979 20_180 045 0.7999 20_180 046 0.8002 20_182 047 0.9135 20_182 048 0.9130 20_184 048 0.9842 20_184 049 0.9960 20_185 046 0.9640 20_185 047 0.9514 20_187 048 0.8134 20_187 049 0.8082 20_189 047 1.0063 20_189 048 0.9701 20_19 013 0.8485 20_19 014 0.8534 20_190 047 0.9279 20_190 048 0.9169 20_191 046 0.9586 20_191 047 0.9751 20_192 049 0.8544 20_193 013 0.9084 20_193 014 0.9110 20_194 047 0.9220 20_194 048 0.9166 20_195 048 0.9552 20_195 049 0.9508 20_196 047 0.9098 20_196 048 0.9011 20_199 048 0.8569 20_199 049 0.8567 20_20 013 0.8750 20_20 014 0.8749 20_201 048 0.8864 20_201 049 1.0040 20_202 048 0.8542 20_202 049 0.8516 20_203 048 1.0267 20_203 049 1.0060 20_204 048 0.8513 20_204 049 0.8588 20_208 014 0.9130 20_208 015 0.9329 20_209 047 1.0020 20_209 048 1.0120 20_21 027 0.9747 20_21 028 1.0081 20_210 048 0.8607 20_210 049 0.8564 20_220 047 0.8888 20_220 048 0.8903 20_222 047 0.9998 20_222 048 0.8597 20_224 013 0.8122 20_224 014 0.8107 20_226 013 0.7855 20_226 014 0.7845 20_227 013 0.9372 20_227 014 0.9818 20_231 047 0.8355 20_231 048 0.8506 20_232 048 0.9730 20_232 049 0.9591 20_234 048 0.9357 20_234 049 0.9429 20_235 048 0.7528 20_235 049 0.7483 20_236 047 0.8997 20_236 048 0.8922 20_239 049 0.8920 20_239 050 0.8817 20_24 013 0.8197 20_24 014 0.8280 20_240 047 0.9109 20_240 048 0.9231 20_243 013 0.8227 20_243 014 0.8333 20_245 045 0.8620 20_245 046 0.8635 20_246 047 0.8236 20_246 048 0.8269 20_248 053 0.6015 20_248 054 0.6091 20_25 013 0.8676 20_25 014 0.8658 20_250 048 0.9124 20_250 050 0.9090 20_251 048 0.9061 20_251 049 0.9078 20_277 008 0.7923 20_277 010 0.7970 20_278 048 0.4834 20_278 049 0.4845 20_279 008 0.4363 20_279 010 0.4370 20_281 013 0.8672 20_281 014 0.8647 20_282 043 0.8884 20_282 044 0.8886 20_284 052 0.9152 20_284 053 0.9118 20_285 047 0.9546 20_285 048 0.9517 20_286 008 0.9607 20_286 010 0.9596 20_287 055 0.8976 20_287 056 0.8756 20_288 047 1.0127 20_288 048 1.0307 20_290 048 1.0089 20_290 049 1.0391 20_293 052 0.7792 20_293 053 0.7772 20_3 017 0.8530 20_3 018 0.8501 20_40 013 0.9392 20_40 014 0.9787 20_41 013 0.9562 20_41 014 0.9547 20_44 013 0.8725 20_44 014 0.8872 20_51 013 0.9420 20_51 014 0.9417 20_55 013 0.9796 20_55 014 0.9837 20_58 013 0.9677 20_58 014 0.9506 20_59 013 0.9180 20_59 014 0.9157 20_69 013 0.9265 20_69 014 0.9283 20_74 014 0.9476 20_74 015 0.9201 20_78 012 0.9822 20_78 013 0.9501 20_81 013 0.8664 20_81 014 0.8693 20_84 013 0.8827 20_84 014 0.9196 20_86 016 0.9138 20_86 017 0.9152 20_88 039 0.9905 20_88 041 1.0168 20_90 049 0.8263 20_90 050 1.0208 20_95 008 0.8892 20_95 010 0.9359 20_96 013 0.9191 20_96 014 0.9326 20_97 008 0.9569 20_97 010 0.9731 20_98 008 0.9317 20_98 012 0.9409 20_PHRU 047 0.7797 20_PHRU 048 0.7894 So the registration is really poor. I've visually checked the registration for many of the subjects, and the functional data isn't left-right reversed, I've also checked some of the subjectname files (which I created by running a script) and they are correct. I'm new to Freesurfer, so maybe I've made a mistake somewhere? I'm been following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial Thanks, Keri On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > What version of FS are you using? version 6 initializes with mri_coreg > (the FS equivalent of spm_coreg). On whole-brain data, I've found this to > be very robust. Is your data whole-brain? > > On 1/18/19 5:10 AM, Keri Woods wrote: > > External Email - Use Caution > Hi > > I have a problem very similar to this one: > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html > > I've tried the suggestions given there, but it didn't fix my problem. > > I'm running the FSFAST preproc-sess stream and the quality of the > registration is very poor for most of the subjects. > > I've tried initializing the registration differently, using bbregister > with --init-fsl, --init-spm and init-header, which didn't improve the > results at all. > > I've also tried register-sess with --init-fsl, --init-spm and init-header, > as well as spmregister-sess and fslregister-sess. > > Is there anything else I could try? > > Using the SPM GUI, the registration was fine, so I thought that > spmregister-sess would have been an improvement, but it wasn't. Is there > anyway I can import the registration obtained using the SPM GUI? > > Thanks for your help. > > Thanks, > Keri > > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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