Dear Jesper,
It looks like in these cases FNIRT has not finished. In the registration
summary html page there are only images for "Registration of example_func to
highres" and no images for
Summary registration, FMRI to standard space
Registration of highres to standard
Registration of example_func to standard
that are also usually included.
I've attached the report_log.html - please let me know if you need other
information.
thanks,
Mara
On Fri, 19 Jun 2009 20:54:30 +0100, Jesper Andersson <[log in to unmask]>
wrote:
>Dear Mara,
>
>> Thanks for the information about using FNIRT in feat. It works fine
>> for most
>> runs but a few generate this error in the report_log:
>>
>> /usr/share/fsl/bin/fnirt --in=highres_head --aff=highres2standard.mat
>> --cout=highres2standard_warp --iout=highres2standard
>> --jout=highres2standard_jac --config=T1_2_MNI152_2mm --
>> ref=standard_head
>> --refmask=standard_mask --warpres=10,10,10
>> SpMat::SolveForx: Warning requested tolerence not obtained.
>> Requested tolerance was 0.001, and achieved tolerance was 0.02043
>> This may or may not be a problem in your application, but you should
>> look
>> into it
>>
>> What does this error indicate? In the registration report it
>> displays the
>> "Registration of example_func to highres" images but not the other
>> usual
>> output. The FLIRT registration from a previous analysis where FNIRT
>> was not
>> run seems to have been ok.
>
>Do you mean that when you see this warning FNIRT has not worked/
>finished? I would normally say that that warning is of no consequence
>(I have supressed it for the next version of fnirt). It is more a
>warning to the programmer who uses a particular library.
>
>Could you please check again if it means that fnirt hasn't fninshed,
>and if it hasn't get back to me again?
>
>Good Luck Jesper
>
>
>>
>>
>>
>>
>> On Wed, 17 Jun 2009 19:56:54 -0400, David V. Smith <[log in to unmask]
>> >
>> wrote:
>>
>>> Yeah, that should do the trick. Just make sure your skull-stripped
>>> anatomical scan has the same name as your raw anatomical but with
>>> "_brain"
>>> at the end of it. For example, if your raw anatomical is named
>>> anat.nii.gz,
>>> then your skull-stripped anatomical should be named
>>> anat_brain.nii.gz (and
>>> both images should be in the same directory).
>>>
>>> Cheers,
>>> David
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>> Behalf
>>> Of M Mather
>>> Sent: Wednesday, June 17, 2009 7:02 PM
>>> To: [log in to unmask]
>>> Subject: [FSL] FNIRT in FEAT
>>>
>>> Hi,
>>>
>>> Is FNIRT already implemented in FEAT?
>>>
>>> Is it as simple as setting this setting in the design.fsf file to 1?:
>>>
>>> # Do nonlinear registration from structural to standard space?
>>> set fmri(regstandard_nonlinear_yn) 0
>>>
>>> or is FNIRT something that must be run outside of feat?
>>>
>>>
>>>
>>>
>>> Here are the settings from one of my design.fsf files:
>>>
>>> # Registration?
>>> set fmri(reg_yn) 1
>>>
>>> # Registration to initial structural
>>> set fmri(reginitial_highres_yn) 0
>>>
>>> # Search space for registration to initial structural
>>> # 0 : No search
>>> # 90 : Normal search
>>> # 180 : Full search
>>> set fmri(reginitial_highres_search) 90
>>>
>>> # Degrees of Freedom for registration to initial structural
>>> set fmri(reginitial_highres_dof) 3
>>>
>>> # Registration to main structural
>>> set fmri(reghighres_yn) 1
>>>
>>> # Search space for registration to main structural
>>> # 0 : No search
>>> # 90 : Normal search
>>> # 180 : Full search
>>> set fmri(reghighres_search) 90
>>>
>>> # Degrees of Freedom for registration to main structural
>>> set fmri(reghighres_dof) 7
>>>
>>> # Registration to standard image?
>>> set fmri(regstandard_yn) 1
>>>
>>> # Standard image
>>> set fmri(regstandard) "/Users/mm/fsl/data/standard/
>>> MNI152_T1_2mm_brain"
>>>
>>> # Search space for registration to standard space
>>> # 0 : No search
>>> # 90 : Normal search
>>> # 180 : Full search
>>> set fmri(regstandard_search) 90
>>>
>>> # Degrees of Freedom for registration to standard space
>>> set fmri(regstandard_dof) 12
>>>
>>> # Do nonlinear registration from structural to standard space?
>>> set fmri(regstandard_nonlinear_yn) 0
>>>
>>> # Control nonlinear warp field resolution
>>> set fmri(regstandard_nonlinear_warpres) 10
>>>
>>>
>>> thanks,
>>> Mara
>>
>
>
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