Re: [Freesurfer] FSFAST funcroi-sess problem
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 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
>> MRISreadAnnotati
Re: [Freesurfer] FSFAST funcroi-sess problem
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
[Freesurfer] FSFAST funcroi-sess problem
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
/Volumes/Dat
