Hi Thomas- On second thought is it valid to simply do if I want average time series of the cerebellum regions?
fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> avgCerebellum.txt
Is this correct?
Cheers, Sabin Khadka
On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka mr.sabinkhadka@gmail.com wrote:
Hi Thomas and Doug-
Thanks for you suggestions. Per your suggestions I performed following
recon-all -i $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz -subjid Yeo2011_MNI152_FS
recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS
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
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
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o cerebellum_mask_FSSub.nii.gz
fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz Buckner_atlas_FSSub
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz
mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf test.txt
However, I got the following error ERROR: must specify a segmentation volume
Am I doing anything wrong here. Do you have any suggestions/fixes?
Cheers, Sabin Khadka
On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Doug, thanks.
Hi Sabin, you can use the following steps to transform the Buckner cerebellum atlas to your subject's native anatomical space and then follow Doug's instructions (taken and adapted from another user Bronwyn's email):
- Run MNI152 1mm template through recon-all
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS
- Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
nonlinear volumetric space mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o BucknerAtlas1mm_FSI.nii.gz --nearest
- warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
volumetric space to each subject: mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
- Create a cerebellum gray matter mask in the native subject's space
by applying mri_binarize to aparc+aseg.mgz of the subject mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o cerebellum_mask_subjID.nii.gz
- Using this mask to mask the Buckner cerebellum parcellations
fslmaths Buckner2011_atlas_subjID.nii.gz -mas cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
Regards, Thomas
On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
yes
On 6/24/16 9:19 AM, Thomas Yeo wrote:
Hi Doug,
Would your mri_segstats command work if instead of aseg.mgz, Sabin passed in the cerbellum parcellation in the same anatomical space as aseg?
--Thomas
On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
After you run preproc-sess, there will be a file called register.dof6.dat. Map fmri into the anatomical space, something like
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz
Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
However, I don't think that the aseg has those cerebellum
parcellations.
On 6/21/16 5:52 PM, Sabin Khadka wrote:
Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I process my fmri data with
preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
-fwhm 6
-per-run -stc odd and then to extract ROI time series values I did
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
Now I am not sure as how to extract cerebellum ROIs (time series as described in Buckner et.al 2011)? If there are any other additional
steps
I need to perform ? or if I have to use some other scripts commands
(other
than mri_segstats).
Cheers, Sabin Khadka
On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Sabin,
The structures 601-628 FreeSurferCololLUT.txt correspond to
anatomical
substructures of the cerebellum (e.g., Crus I, etc). Is that what you want? Or are you looking to use the functional parcels defined in Buckner 2011?
In addition, I do not know how mri_segstats works, so I cannot verify how you call the command is correct. Maybe others can provide
feedback
here.
However, the Buckner cerebellar parcellations in $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152 space. From your command, I assume your data is in MNI305 space. So you might need to transform the parcellation from MNI152 to MNI305.
Thanks, Thomas
On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka <
mr.sabinkhadka@gmail.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 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. > > Cheers, > Sabin Khadka > > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer