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: jdie...@mac.com <mailto:jdie...@mac.com>
> Phone: 202-297-8117
> http://joedien.com//
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
