Hi Jun
In one of your trial, FEP1005_struct_brain is being used as highres_head by FNIRT (the one called from VBM8 folder).
Non-skull stripped brain must be used as highres_head and I have a feeling that in that folder it's missing (thus FSL will make do with the skull stripped brain).
Try with the skull-intact brain provided in the VBM8 folder, named following the required convention (i.e. FEP1005_struct) and should work.
Danny Kin
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Jun Miyata [[log in to unmask]]
Sent: Tuesday, February 16, 2016 11:24 PM
To: [log in to unmask]
Subject: Re: [FSL] highres2standard registration works strangely
Hi Danny,
I found that the 743 rd line is different between two trials, where the "OK" version reports warning message regarding FNIRT in line 742. That means, FNIRT command seems to output two different results for the same inputs and parameters. I confirmed that FLIRT for highres to standard output the same results for both trials.
Best ragards,
Jun
2016/02/17 13:34$B!"(BJun Miyata <[log in to unmask]> $B$N%a!<%k!'(B
> 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
> <difference.txt><report_log_OK.html><report_log_strange.html>
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