Can you send me the result of "which epidewarp.fsl" (no quotes)?
Marco Loggia wrote:
Hi Doug, Below are my paths:
FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 FSFAST_HOME /usr/local/freesurfer/stable5_0_0/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /autofs/cluster/randy/2/lbp/freesurfer/patients+controls MNI_DIR /usr/local/freesurfer/stable5_0_0/mni FSL_DIR /usr/pubsw/packages/fsl/current
Thanks, Marco
Marco, which version are you using? doug
Marco Loggia, PhD wrote:
Dear Surfers,
In the past couple of days epidewarp.fsl has been failing, reporting "vsm-smooth: Command not found" (see below). Epidewarp was run using the same parameters, and within the same script that I have been using with no problems for many months... Has there been a software update that I have missed?
Thanks, Marco
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 mailto:marco@nmr.mgh.harvard.edu
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 e-mail: marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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