What is the full command line for that program?
On 3/29/19 11:01 AM, Donatienne Van Weehaeghe wrote:
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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<mailto: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:
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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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
