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
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < DGREVE@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 CautionHi
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 listFreesurfer@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
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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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> 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
External Email - Use Caution
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. < DGREVE@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 CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 myproblem.
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>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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External Email - Use Caution
I meant some are nearly perfect.
On Wed, Jan 23, 2019 at 11:49 AM Keri Woods keri.woods@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. < DGREVE@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 CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 myproblem.
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>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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
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 greve@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.woods@gmail.com mailto:keri.woods@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. <DGREVE@mgh.harvard.edu <mailto:DGREVE@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. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@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
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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. < DGREVE@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 greve@nmr.mgh.harvard.edu
On 1/23/19 5:57 AM, Keri Woods wrote:
External Email - Use CautionI meant some are nearly perfect.
On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.com mailto:keri.woods@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. <DGREVE@mgh.harvard.edu <mailto:DGREVE@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. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > What version of FS are you using? version 6 initializeswith
> mri_coreg (the FS equivalent of spm_coreg). On whole-brain data, > I've found this to be very robust. Is your datawhole-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
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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. <DGREVE@mgh.harvard.edumailto:DGREVE@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 greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
On 1/23/19 5:57 AM, Keri Woods wrote:
External Email - Use CautionI meant some are nearly perfect.
On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.commailto:keri.woods@gmail.com <mailto:keri.woods@gmail.commailto:keri.woods@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. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@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. > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@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>> <mailto: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>> <mailto: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> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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. < DGREVE@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 CautionHi 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. < DGREVE@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 greve@nmr.mgh.harvard.edu
On 1/23/19 5:57 AM, Keri Woods wrote:
External Email - Use CautionI meant some are nearly perfect.
On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.com mailto:keri.woods@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. <DGREVE@mgh.harvard.edu <mailto:DGREVE@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. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > What version of FS are you using? version 6 initializeswith
> mri_coreg (the FS equivalent of spm_coreg). On whole-brain data, > I've found this to be very robust. Is your datawhole-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
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Keri Woods