25 Jan
2019
25 Jan
'19
11:50 a.m.
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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