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=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
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>
> --
> 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
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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--------------------------------------------------------------------------------
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
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