I'm using Freesurfer 5.3.0

(well, actually I ran the original analyses with 5.2.0 and then am running this ROI follow-up with 5.2.0, could that be a problem?  From the release notes, it didn't look like it would be an issue)

Anyway, I've run the following set of commands:

funcroi-config -roi /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg -annot /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot cluster-001 -analysis CPA.sm05.lh

funcroi-sess -roi /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg -s CPA003 -d .

I get the following output.

When I checked the results with:

tksurfer fsaverage lh inflated -overlay roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz -fthresh .5 

sure enough, it didn't look right.  Instead of the cluster, I got speckles all over the surface.

I used the Matlab command:

[vertex_coords, faces] = read_surf('lh.white');

and found sure enough that the size of the vertex array was only 143827 whereas mri_info indicates that the ocn file has 163842

Any suggestions what I might be doing wrong?

Thanks!

Joe

-------------------------------------------
/Volumes/Data/CP1/fsfast/CPA003 
Fri Jul 12 18:23:28 EDT 2013
mri_annotation2label --subject CPA003 --hemi lh --annotation /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot --outdir /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
subject = CPA003
annotation = /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
hemi = lh
outdir = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
surface   = white

Reading surface 
 /Volumes/Data/CP1/freesurfer/CPA003/surf/lh.white
Loading annotations from /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143827 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143828 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143829 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143830 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143831 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143832 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143833 i=00000000, in_array_size=143827

…

MRISreadAnnotationIntoArray: vertex index out of range: 163838 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163839 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163840 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=00000000, in_array_size=143827
    annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
reading colortable from annotation file...
colortable with 3 entries read (originally none)
Seg base 0
max index = 2
  1    952 /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label
  2    532 /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster2.label
mri_label2label --hemi lh --srclabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label --srcsubject CPA003 --trglabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label --trgsubject fsaverage --regmethod surface

srclabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label
srcsubject = CPA003
trgsubject = fsaverage
trglabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /Volumes/Data/CP1/freesurfer
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 952 points in source label.
Starting surface-based mapping
Reading source registration 
 /Volumes/Data/CP1/freesurfer/CPA003/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.white
Reading target registration 
 /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  952 nlabel points
Performing mapping from target back to the source label 163842
Number of reverse mapping hits = 415
Checking for and removing duplicates
Writing label file /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label 1367
mri_label2label: Done

mri_label2label --hemi lh --srclabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label --outmask /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz --regmethod surface --trglabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label --s fsaverage

srclabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label
srcsubject = fsaverage
trgsubject = fsaverage
trglabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /Volumes/Data/CP1/freesurfer
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 1311 points in source label.
Starting surface-based mapping
Reading source registration 
 /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.white
Reading target registration 
 /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1311 nlabel points
Performing mapping from target back to the source label 163842
Number of reverse mapping hits = 0
Checking for and removing duplicates
Creating output /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz
Writing label file /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label 1311
mri_label2label: Done

Ended   at Fri Jul 12 18:23:48 EDT 2013
funcroi-sess completed


--------------------------------------------------------------------------------

Joseph Dien,
Senior Research Scientist
University of Maryland 

Phone: 202-297-8117