Marco

bash-3.2$ /usr/local/freesurfer/stable/bin/epidewarp.fsl --mag

$dirpath/$subjdir/fieldmap/fieldmap1.nii --dph

$dirpath/$subjdir/fieldmap/fieldmap2.nii --epi bold.nii --tediff 2.54

--esp .48 --sigma 2 --vsm shiftmap --epidw bold_dw.nii

FSLVersion 4.1.5

FSLVerMaj 4

Logfile is shiftmap.log

FSLOUTPUTTYPE NIFTI

Extension is nii

nframes = 180, nmidframe = 90

fslroi /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/6min_rest/bold.nii

./tmp-epidewarp.26204.fsl/exf.nii 90 1

fslroi /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/fieldmap/fieldmap1.nii

./tmp-epidewarp.26204.fsl/mag 0 1

bet ./tmp-epidewarp.26204.fsl/mag.nii ./tmp-epidewarp.26204.fsl/brain.nii

fslmaths ./tmp-epidewarp.26204.fsl/brain.nii -bin

./tmp-epidewarp.26204.fsl/brain.nii

fslmaths ./tmp-epidewarp.26204.fsl/brain.nii -dilM

./tmp-epidewarp.26204.fsl/head.nii

fslmaths ./tmp-epidewarp.26204.fsl/head.nii -dilM

./tmp-epidewarp.26204.fsl/head.nii

fslmaths ./tmp-epidewarp.26204.fsl/head.nii -dilM

./tmp-epidewarp.26204.fsl/head.nii

fslmaths

/autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/fieldmap/fieldmap2.nii -sub

2047.5 -mul 0.00153435539 ./tmp-epidewarp.26204.fsl/dph -odt float

prelude -p ./tmp-epidewarp.26204.fsl/dph -a

./tmp-epidewarp.26204.fsl/mag.nii -o ./tmp-epidewarp.26204.fsl/dph -f -v

-m ./tmp-epidewarp.26204.fsl/head.nii

Loading volumes

Phase loaded

Magnitude loaded

Mask loaded

Number of phase splits = 8

Calculating starting matrices (5173 by 5173)

Finished connection_matrices

13289 constraints left

7990 constraints left

6210 constraints left

4125 constraints left

2042 constraints left

174 constraints left

Did while loop 5172 times

fslmaths ./tmp-epidewarp.26204.fsl/dph -mul 0

./tmp-epidewarp.26204.fsl/ph.zeros.nii

fslmerge -t ./tmp-epidewarp.26204.fsl/ph.nii

./tmp-epidewarp.26204.fsl/ph.zeros.nii ./tmp-epidewarp.26204.fsl/dph

Masking with ./tmp-epidewarp.26204.fsl/brain.nii

fugue -i ./tmp-epidewarp.26204.fsl/mag.nii -u

./tmp-epidewarp.26204.fsl/magdw.nii -p ./tmp-epidewarp.26204.fsl/ph.nii

--dwell=.48 --asym=2.54 --mask=./tmp-epidewarp.26204.fsl/brain.nii

--saveshift=./tmp-epidewarp.26204.fsl/vsmmag.nii --smooth2=2

VSM Mean is -0.110589

fslmaths ./tmp-epidewarp.26204.fsl/vsmmag.nii -sub -0.110589

./tmp-epidewarp.26204.fsl/vsmmag.nii

fslmaths ./tmp-epidewarp.26204.fsl/vsmmag.nii -mul

./tmp-epidewarp.26204.fsl/brain.nii ./tmp-epidewarp.26204.fsl/vsmmag.nii

fugue -i ./tmp-epidewarp.26204.fsl/mag.nii -w

./tmp-epidewarp.26204.fsl/magfw.nii

--loadshift=./tmp-epidewarp.26204.fsl/vsmmag.nii

--mask=./tmp-epidewarp.26204.fsl/brain.nii

flirt.fsl -in ./tmp-epidewarp.26204.fsl/magfw.nii -ref

./tmp-epidewarp.26204.fsl/exf.nii -out

./tmp-epidewarp.26204.fsl/magfw-in-exf.nii -omat

./tmp-epidewarp.26204.fsl/magfw-in-exf.fsl.mat -bins 256 -cost corratio

-searchrx -10 10 -searchry -10 10 -searchrz -10 10 -dof 6 -interp

trilinear

flirt.fsl -in ./tmp-epidewarp.26204.fsl/vsmmag.nii -ref

./tmp-epidewarp.26204.fsl/exf.nii -out shiftmap -init

./tmp-epidewarp.26204.fsl/magfw-in-exf.fsl.mat -applyxfm

vsm-smooth --fwhm 10 --i shiftmap --o shiftmap

vsm-smooth: Command not found.

______________________

Marco L. Loggia, PhD

Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital

Harvard Medical School

Psychiatric Neuroimaging Research Program

CNY Building 120, suite 100

Charlestown, Massachusetts 02129

Phone:  (617) 643-7267

Fax:  (617) 643-7340

marco@nmr.mgh.harvard.edu