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
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
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