Hi Danny,
Please find attached the registration log files (OK and strange), and the difference between them. I checked through the difference file, but am not sure which is the cause.
Best regards,
Jun
2016/02/16 20:13$B!"(BJun Miyata <[log in to unmask]> $B$N%a!<%k!'(B
> Hi Danny,
>
> Sorry for confusing description. This subject was included in both trial. The previously attached results are of this single subject with the same parameters. I'm now away from lab so I will send you the registration log tomorrow.
> Thank you very very much,
>
> Jun
>
>
>> Hi Jun
>> You said earlier that parameters were the same except for number of subjects - are the two results of different subjects then?
>>
>> Nonetheless, could you show the reg log files so that I can see what was run.
>>
>> Thanks
>>
>> Danny Kim
>> ________________________________________
>> From: FSL - FMRIB's Software Library [
>> [log in to unmask]] On Behalf Of Jun Miyata [[log in to unmask]
>> ]
>> Sent: Monday, February 15, 2016 7:38 PM
>> To:
>> [log in to unmask]
>>
>> Subject: Re: [FSL] highres2standard registration works strangely
>>
>> Dear Danny,
>>
>> Thank you very much for your interest. I attached the enlarged versions. In the Overlay_color file, the skewed result (gray scale) is displayed on normal result (red-yellow). These are results of the same subject, with the same melodic parameters.
>> The FSL version is 5.0.5, melodic 3.1.4 on OSX 10.9.5. I confirmed the same issue occurs on FSL 5.0.9 on OSX 10.10.
>> Best regards,
>>
>> Jun
>>
>>
>> Hard to tell from small snapshots.. do you have a better resolution snaps?
>>
>> Danny Kim
>> On 2016-02-15, at 5:03 PM, Jun Miyata wrote:
>>
>> Dear FSL experts,
>>
>> I attached the PNG files. The highres2standard_OK and highres2standard_strange files show differences in frontal and parietal convexities, though they may be a bit difficult to distinguish. The overlay file shows strange result (gray scale) overlaid on normal result (red). This would be easier to see the difference.
>> Best regards,
>>
>> Jun
>>
>> 2016/02/15 13:52$B!"(BJun Miyata <[log in to unmask]> $B$N%a!<%k!'(B
>>
>> Dear FSL experts,
>>
>> I have run Melodic group ICA for the same rsfMRI data twice, but I had different results for highres2standard registration. For the 1st trial it worked well, but for the 2nd the final highres2standard.nii.gz was skewed like diamond shape.
>> I performed ICA from Melodic GUI. The parameters were the same except for the number of subjects. I confirmed that highres2standard_linear.nii.gz, highres2standard.mat, and standard2highres.mat files are identical between two trials, whereas highres2standard_warp.nii.gz and highres2standard.nii.gz are different. Thus I think the problem is in nonlinear registration.
>> I appreciate if anyone could explain the reason. I would like to attach the files but it exceed the maximum size.
>>
>> Thanks in advance,
>>
>> Jun
8c8
< Started at 2016年 1月15日 金曜日 15時54分45秒 JST<p>
---
> Started at 2016年 2月12日 金曜日 18時01分56秒 JST<p>
11c11
< /bin/cp /tmp/feat_gH8K3t.fsf design.fsf
---
> /bin/cp /tmp/feat_FXop3f.fsf design.fsf
15c15
< /usr/local/fsl5.0.5/fsl/bin/mainfeatreg -F 6.00 -d /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica -l /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/logs/feat5_reg -R /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/report_unwarp.html -r /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/report_reg.html -i /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/example_func.nii.gz -n 10 -h /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/MPRAGE/FEP1005_struct_brain -w BBR -x 90 -s /usr/local/fsl5.0.5/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 -a /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap/FEP1005_fieldmap_rads -b /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap_mag/FEP1005_fieldmap_mag_brain -e 30 -f 10 -g 0.3018 -p y -w BBR
---
> /usr/local/fsl5.0.5/fsl/bin/mainfeatreg -F 6.00 -d /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica -l /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/logs/feat5_reg -R /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/report_unwarp.html -r /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/report_reg.html -i /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/example_func.nii.gz -n 10 -h /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/MPRAGE_VBM8_brain/FEP1005_struct_brain -w BBR -x 90 -s /usr/local/fsl5.0.5/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 -a /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap/FEP1005_fieldmap_rads -b /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap_mag/FEP1005_fieldmap_mag_brain -e 30 -f 10 -g 0.3018 -p y -w BBR
17,21c17,21
< Option -d ( output directory ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica"
< Option -l ( logfile )input with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/logs/feat5_reg"
< Option -R ( html unwarping report ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/report_unwarp.html"
< Option -r ( html registration report ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/report_reg.html"
< Option -i ( main input ) input with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/example_func.nii.gz"
---
> Option -d ( output directory ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica"
> Option -l ( logfile )input with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/logs/feat5_reg"
> Option -R ( html unwarping report ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/report_unwarp.html"
> Option -r ( html registration report ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/report_reg.html"
> Option -i ( main input ) input with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/example_func.nii.gz"
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< Option -h ( high-res structural image ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/MPRAGE/FEP1005_struct_brain"
---
> Option -h ( high-res structural image ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/MPRAGE_VBM8_brain/FEP1005_struct_brain"
29,30c29,30
< Option -a ( fieldmap image ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap/FEP1005_fieldmap_rads"
< Option -b ( field ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap_mag/FEP1005_fieldmap_mag_brain"
---
> Option -a ( fieldmap image ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap/FEP1005_fieldmap_rads"
> Option -b ( field ) selected with argument "/Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap_mag/FEP1005_fieldmap_mag_brain"
38c38
< /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D prefiltered_func_data -odt float
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D prefiltered_func_data -odt float
489c489
< 0.000000 1485.488647
---
> 0.000000 1485.962646
491c491
< /usr/local/fsl5.0.5/fsl/bin/fslmaths prefiltered_func_data_bet -thr 148.5488647 -Tmin -bin mask -odt char
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths prefiltered_func_data_bet -thr 148.5962646 -Tmin -bin mask -odt char
494c494
< 1168.454834
---
> 1169.240601
502c502
< /usr/local/fsl5.0.5/fsl/bin/susan prefiltered_func_data_thresh 876.3411255 2.12314225053 3 1 1 mean_func 876.3411255 prefiltered_func_data_smooth
---
> /usr/local/fsl5.0.5/fsl/bin/susan prefiltered_func_data_thresh 876.93045075 2.12314225053 3 1 1 mean_func 876.93045075 prefiltered_func_data_smooth
506c506
< /usr/local/fsl5.0.5/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 8.55831112082 prefiltered_func_data_intnorm
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 8.55255966261 prefiltered_func_data_intnorm
517c517
< /bin/mkdir -p /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/4D/FEP1005_4D_groupICA.ica/reg
---
> /bin/mkdir -p /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/test9_auto_2/4D/FEP1005_4D_groupICA.ica/reg
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< /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap/FEP1005_fieldmap_rads FM_UD_fmap
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap/FEP1005_fieldmap_rads FM_UD_fmap
526c526
< /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap_mag/FEP1005_fieldmap_mag_brain FM_UD_fmap_mag_brain
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap_mag/FEP1005_fieldmap_mag_brain FM_UD_fmap_mag_brain
529c529
< /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/fieldmap_mag/FEP1005_fieldmap_mag FM_UD_fmap_mag
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/fieldmap_mag/FEP1005_fieldmap_mag FM_UD_fmap_mag
626c626
< /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/MPRAGE/FEP1005_struct_brain highres
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/MPRAGE_VBM8_brain/FEP1005_struct_brain highres
629c629
< /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_matched_FEP24_HC54/MPRAGE/FEP1005_struct highres_head
---
> /usr/local/fsl5.0.5/fsl/bin/fslmaths /Volumes/MacintoshHD4/dual_reg/JHU_FEP/FEP_3T_dual_reg/age_gender_FEP38_HC68/MPRAGE_VBM8_brain/FEP1005_struct_brain highres_head
643c643
< Running FAST segmentation FLIRT pre-alignment Registering fieldmap to structural Running BBR with fieldmap 0.443029 0.999787 0.006807 0.019500 0.000000 -0.006989 0.999933 0.009255 0.000000 -0.019436 -0.009390 0.999767 0.000000 2.599002 0.971926 2.075908 1.000000 Making warp fields and applying registration to EPI series
---
> Running FAST segmentation FLIRT pre-alignment Registering fieldmap to structural Running BBR with fieldmap 0.444300 0.999788 0.006001 0.019687 0.000000 -0.006168 0.999946 0.008420 0.000000 -0.019635 -0.008540 0.999771 0.000000 2.521120 0.894109 2.175205 1.000000 Making warp fields and applying registration to EPI series
658c658
< -20.209295 29.070723 -2.816948 12.768369
---
> -18.513517 24.757313 -3.931181 17.075397
666c666
< /usr/local/fsl5.0.5/fsl/bin/overlay 1 0 EF_UD_fmap_mag_brain -a FM_UD_fmap2epi_shift 0.0001 12.768369 grot 0.0001 2.81695 EF_UD_shift+mag
---
> /usr/local/fsl5.0.5/fsl/bin/overlay 1 0 EF_UD_fmap_mag_brain -a FM_UD_fmap2epi_shift 0.0001 17.075397 grot 0.0001 3.93118 EF_UD_shift+mag
743c743
< Warning, Jacobian not within prescribed range. Prescription is 0.01 -- 100 and obtained range is 0.00753912 -- 2.78686
---
>
|