[Freesurfer] FSFAST funcroi-sess problem

2013-07-12 Thread Joseph Dien 
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=, 
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=, 
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=, 
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=, 
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=, 
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=, 
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=, 
in_array_size=143827

…

MRISreadAnnotationIntoArray: vertex index out of range: 163838 i=, 
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=, 
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=, 
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=, 
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
  1952 
/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
  2532 
/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

Re: [Freesurfer] FSFAST funcroi-sess problem

2013-07-12 Thread Douglas N Greve 

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=, 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=, 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=, 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=, 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=, 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=, 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=, in_array_size=143827

 …

 MRISreadAnnotationIntoArray: vertex index out of range: 163838 
 i=, 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=, 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=, 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=, 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

Re: [Freesurfer] FSFAST funcroi-sess problem

2013-07-12 Thread Joseph Dien 
I followed the tutorial:

  mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh 
-fwhm 5 -event-related  -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 
-tpexclude tpexclude.dat




On Jul 12, 2013, at 7:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 
 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=, 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=, 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=, 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=, 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=, 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=, 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=, in_array_size=143827
 
 …
 
 MRISreadAnnotationIntoArray: vertex index out of range: 163838 
 i=, 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=, 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=, 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=, in_array_size=143827
 annot file: