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.
thanks,
Mara
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
|