External Email - Use Caution
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
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >
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