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

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