Hi Joe,
On 07/12/2013 06:51 PM, Joseph Dien wrote:
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)
No, that is fine.
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
When you made the analysis (mkanalysis-sess), do you specify the subject as "self" or "fsaverage"? doug
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: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
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