Hi Antonella, the argument to --annot has to be an annotation file
(something.annot). mri_glmfit-sim should generate an annot file. If you
are running mri_surfcluster to get ocn.mgh, it will also generate an
annot file.
doug
On 8/27/12 8:31 PM, Antonella Kis wrote:
Hi,
I am trying to run the mri_label2vol but I am getting the following
error. I am not sure which annot file I should use for my QDEC
clusters. I tried to use my annot file from mri_glmfit-sim but it
didn't work. I was running:
mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg
$FREESURFER_HOME/average/mni152.register.dat --fillthresh 0 --subject
fsaverage --hemi lh --annot
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh
--o
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/sig2MNI.nii
and my error:
Number of labels: 0
Annot File:
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh
Template Volume: MNI152_T1_1mm_brain.nii.gz
Outut Volume:
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/sig2MNI.nii
Registration File: /usr/local/freesurfer//average/mni152.register.dat
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: fsaverage
Hemi: lh
UseNewASeg2Vol: 1
DoLabelStatVol 0
$Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $
Template RAS-to-Vox: --------
-1.000 0.000 0.000 91.000;
-0.000 -0.000 -1.000 109.000;
-0.000 1.000 -0.000 91.000;
0.000 0.000 0.000 1.000;
Template Voxel Volume: 1
nHits Thresh: 0
Loading registration from
/usr/local/freesurfer//average/mni152.register.dat
RegMat: --------
0.998 -0.007 0.018 0.957;
-0.013 -0.009 0.997 -17.816;
-0.015 -1.001 0.002 -18.550;
0.000 0.000 0.000 1.000;
Label RAS-to-Vox: --------
-0.998 0.007 -0.018 90.043;
0.015 1.001 -0.002 127.550;
-0.013 -0.009 0.997 73.184;
0.000 0.000 0.000 1.000;
INFO: loading surface
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/fsaverage/surf/lh.white
nvertices = 163842
Reading thickness
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/fsaverage/surf/lh.thickness
Loading annotations from
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh
MRISreadAnnotationIntoArray: vertex index out of range: 163842
i=00000001, in_array_size=163842
annot file:
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh
reading colortable from annotation file...
colortable with 1 entries read (originally )
annotidmax = 0
ERROR: load annot file
/media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh
Thanks,
AK
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