Hi,
If flirt is taking a long time then it is probably because the structural image has very high resolution and the segmentation is taking a long time.
You have a few options:
(i) pre-calculate your segmentations and save the white matter result with the same name as your brain-extracted structural image, but with "_wmseg" appended;
(ii) downsample your structural image a little (e.g. making the resolution 1mm);
(iii) be patient.
If your structural images are not very high resolution then let us know.
All the best,
Mark
On 7 May 2014, at 04:38, soft.join Huang <[log in to unmask]> wrote:
> Dear experts,
>
> I'm analyzing my fMRI data with FEAT using FSL 5.0. The FLIRT with BBR cost is used in the registration o EPI to structural image. For most of my data/sbjects, the processing is done successfully. However, for few subjects, the FLIRT step costs too much time (about 24 hours).
>
> And I check the log, it only shows following information:
>
> Initialisation
> /usr/local/neurosoft/fsl5/bin/fslmaths /nfs/h2/fmricenter/volume/S0029/obj/002/func prefiltered_func_data -odt float
> Total original volumes = 99
> /usr/local/neurosoft/fsl5/bin/fslroi prefiltered_func_data example_func 49 1
> /usr/local/neurosoft/fsl5/bin/mainfeatreg -d /nfs/h2/fmricenter/volume/S0029/obj/002/func.feat -l /nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/logs/feat5_reg -R /nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/report_unwarp.html -r /nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/report_reg.html -i /nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/example_func.nii.gz -h /nfs/h2/fmricenter/volume/S0029/3danat/reg/T1_brain -w BBR -x 90
> Option -d ( output directory ) selected with argument "/nfs/h2/fmricenter/volume/S0029/obj/002/func.feat"
> Option -l ( logfile )input with argument "/nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/logs/feat5_reg"
> Option -R ( html unwarping report ) selected with argument "/nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/report_unwarp.html"
> Option -r ( html registration report ) selected with argument "/nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/report_reg.html"
> Option -i ( main input ) input with argument "/nfs/h2/fmricenter/volume/S0029/obj/002/func.feat/example_func.nii.gz"
> Option -h ( high-res structural image ) selected with argument "/nfs/h2/fmricenter/volume/S0029/3danat/reg/T1_brain"
> Option -w ( highres dof ) selected with argument "BBR"
> Option -x ( highres search ) selected with argument "90"
>
> I don't know what's wrong with this processing, it it normal?
>
> Hope for help.
>
> Thanks in advance.
>
> Best,
> Lijie Huang
> Beijing Normal University
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