The output has to be a volume (eg, nii or mgh), not a label. If you need a label, run mri_cor2label on the output.
doug Massieh Moayedi wrote: > Hi Doug, > > I tried it, and it seems that it's working until the very last step. > > Here's the output I get: > > > $ mri_label2vol --seg > '/storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped.nii.gz' > --temp > '/storage/AllUsers/Massih/FreeSurferData_TMD/fsaverage/mri/orig.mgz' > --reg $FREESURFER_HOME/average/mni152.register.dat --invertmtx > --fillthresh 0.5 --o > /storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label > > Number of labels: 0 > Annot File: (null) > Template Volume: > /storage/AllUsers/Massih/FreeSurferData_TMD/fsaverage/mri/orig.mgz > Outut Volume: > /storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label > > Registration File: > /scratch/freesurfer_43/freesurfer/average/mni152.register.dat > Fill Threshold: 0.5 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.25.2.1 2008/12/19 23:18:26 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0.5 > RegMat: -------- > 1.000 -0.004 -0.001 1.195; > 0.001 0.018 1.000 -19.147; > -0.004 -1.000 0.018 -16.617; > 0.000 0.000 0.000 1.000; > Inverting matrix > RegMat: -------- > 1.000 0.001 -0.004 -1.227; > -0.004 0.018 -1.000 -16.266; > -0.001 1.000 0.018 19.444; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -1.000 -0.001 0.004 129.227; > 0.001 -1.000 -0.018 108.556; > -0.004 0.018 -1.000 111.734; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > ASeg2Vol: Sorting > ASeg2Vol: Mapping > ASeg2Vol: Reverse Map > nmisses = 9558488 (2727 filled) > ASeg2Vol: done > unknown file type for file > (/storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label) > > > > Any ideas? > > Thanks, > Massih > On 09/29/2010 11:37 AM, Douglas N Greve wrote: >> I assume the label is a binary mask in MNI152? If so, use >> mri_label2vol and spec the label as a segmenation, use >> $FREESURFER_HOME/average/mni152.register.dat as the registration, >> specify --invertmtx, and use the orig.mgz in fsaverage as the >> template. I *think* this should work. >> >> doug >> >> mmoayedi wrote: >>> Hi everyone, >>> >>> I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to >>> FreeSurfer's fsaverage brain inflated surface. >>> >>> Does anyone know how to do this? >>> >>> Thanks, >>> >>> Massih >>> >>> _______________________________________________ >>> 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 gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
