External Email - Use Caution
Dear,
The Freesurfer program generated the error after multiple comparison
corerction.
Thank you for your help.
Kind regards
Donatienne
Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:
> what program generated the error? What is the full command line for that
> program?
>
> On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear,
>
>
> I encountered a problem when going from pmod to freesurfer.
>
>
> I made Vt images in pmod using the logan plot, then I used the following
> commands to convert them to freesurfer space:
>
>
>
> #flirt -noresample -in
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
> -ref
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
> -applyxfm -init
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
> -out
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>
> #3dresample -master
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
> -inset
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
> -prefix
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>
>
>
> Then I did partial volume correction using this command:
>
> #mri_gtmpvc --i
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
> --reg Vt.reg.lta --psf 5 --seg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
> --default-seg-merge --auto-mask 5 0.01 --rbv --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
> --no-rescale --threads 8
>
>
>
>
>
> Then I did surface projection:
>
> #mri_vol2surf --mov
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
> --hemi lh --projfrac 0.5 --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
> #mri_vol2surf --mov
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
> --hemi rh --projfrac 0.5 --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
>
>
> followed by smoothing, concatening and then a group comparison. However
> then I obtained the following error:
>
> ERROR: cannot find
> /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd
>
>
> Kind regards
>
> Donatienne
>
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