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