Re: [Freesurfer] FSFAST time series extraction

2016-07-06 Thread Sabin Khadka 
Hi Doug,

Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from
Buckner 2011 7 Cerebellar network. Please see below for the steps I
performed to extract time series from Buckner 2011 7 Cerebellar networks.
If you could give your thoughts on the steps/process that'd be great.

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
Yeo2011_MNI152_FS
recon-all -all Yeo2011_MNI152_FS

*2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to
freesurfe nonlinear volumetric space*
mri_vol2vol --mov
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
\
--s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest

*3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear*
volumetric space to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph


*4. Create a cerebellum gray matter mask in the native subject's space by
applying mri_binarize to aparc2009s+aseg.mgz of the subject*

mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8  --o
cerebellum_mask_FSSub_m8.nii.gz #  For left
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o
cerebellum_mask_FSSub_m47.nii.gz #  FOr right


*5. Using this mask to mask the Buckner cerebellum parcellations*

fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8.nii.gz #  For
left
fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47.nii.gz #  For
right

*6. Functional data to anatomical space*

mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz #  functional into anatomical space

*7. Extract L/R Cerebellar ROIs time series*

 mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m8.nii.gz   --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt #
 extract Left Cerebellum time series
mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m47.nii.gz  --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt #
 extract right Cerebellum time series

Cheers,
Sabin Khadka

On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve 
wrote:

> has this question been answered?
>
> On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> > Hi all,
> >
> > I am trying to extract mean time series BOLD data using FSFAST from
> > Cortical ROIs + sub cortical ROIs and cerebellum.
> >
> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> > -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc
> > --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid
> > 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> > mri_segstats --annot fsaverage rh aparc --i
> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >
> > and for cortical time series
> >
> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> > --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id
> > 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz
> > --avgwf subCorticalTimeSeries.txt
> >
> > But I am not sure on how exactly to extract time series from
> > cerebellar regions. So if I want to extract time series from regions
> > as described in Buckner et.al 2011. Could I just use mri_segstats for
> > the labels 601-628 in FreeSurferCololLUT.txt? If not could you please
> > direct me to processes that I can use.
> >
> >
> >
> > Sent from Yahoo Mail. Get the ap 
> >
> >
> > ___
> > 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

Re: [Freesurfer] FSFAST time series extraction

2016-07-05 Thread Douglas N Greve 
has this question been answered?

On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from 
> Cortical ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 
> -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc 
> --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 
> 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i 
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab 
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 
> --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 
> 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz 
> --avgwf subCorticalTimeSeries.txt
>
> But I am not sure on how exactly to extract time series from 
> cerebellar regions. So if I want to extract time series from regions 
> as described in Buckner et.al 2011. Could I just use mri_segstats for 
> the labels 601-628 in FreeSurferCololLUT.txt? If not could you please 
> direct me to processes that I can use.
>
>
>
> Sent from Yahoo Mail. Get the ap 
>
>
> ___
> 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/

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[Freesurfer] FSFAST time series extraction

2016-06-17 Thread curry_sam77 
 Hi all,
I am trying to extract mean time series BOLD data using FSFAST from Cortical 
ROIs + sub cortical ROIs and cerebellum.
preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 
-per-run -stc odd    mri_segstats --annot fsaverage lh aparc --i 
rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 
1004 --avgwf CorticalTimeSeries_lh.txt     
mri_segstats --annot fsaverage rh aparc --i 
rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 
2004 --avgwf CorticalTimeSeries_rh.txt    
and for cortical time series
mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab 
/opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 
--id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i 
rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf 
subCorticalTimeSeries.txt    
But I am not sure on how exactly to extract time series from cerebellar 
regions. So if I want to extract time series from regions as described in 
Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in 
FreeSurferCololLUT.txt? If not could you please direct me to processes that I 
can use. 


Sent from Yahoo Mail. Get the ap___
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