External Email - Use Caution Good thing it's not the software :) Also makes it easier for me to fix. In my script there was one tiny mistake - the anatomical image for one subject was repeated each time instead of using the files for different subjects. I ran recon-all 100+ times on the same subject!! Checking the registration was definitely worthwhile. Thanks again for the help, it made me look at the problem in a different.
On Fri, Jan 25, 2019 at 6:34 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes, that file is the only thing linking the functional to the anatomical. > It's too bad you messed up the files, but I'm relieved it was not my > software:). > > On 1/25/19 5:09 AM, Keri Woods wrote: > > External Email - Use Caution > Hi Douglas > > Thanks very much for getting back to me. I created new separate > directories and re-processed one of the problem subjects individually, and > the registration worked well. So the problem is that the anatomical and > functional images come from different subjects. But I've checked and the > subjectname files are correct. That's the only thing linking the anatomical > and functional images? Thanks very much, you've helped me a lot. Now I just > have to go and see where I mixed up the files! > > Thanks again, > Keri > > On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> 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 > > > _______________________________________________ > 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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