Can you tar up the anatomical and functional analyses and send them to me through our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/ when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu On 1/23/19 5:57 AM, Keri Woods wrote: > > External Email - Use Caution > > I meant some are nearly perfect. > > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.wo...@gmail.com > <mailto:keri.wo...@gmail.com>> wrote: > > Hi Douglas > > Thanks for the response. > > No, some of the registrations are fine. Some are close, but not > perfect, while others are very bad. > > I've checked the subjectname file for some subjects with poor > registration (eg 20_101), and they are correct. > > Thanks, > Keri > > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > Are you saying that all of them have bad registrations? Some > of them > (eg, 20_1, 20_10) look like they should be good. Others (eg, > 20_101) > look like they could be bad. For the bad ones, are you totally > sure that > the subjetname file has the correct name of the subject? > > On 1/21/19 3:19 AM, Keri Woods wrote: > > > > 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 <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu > <mailto: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 list > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
