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 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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