Hi Thomas,
Yes, I think I got it working. I forgot to put --seg in my command line which is my the ERROR: segmentation volume needed to be specified error. I did following and gave me average time series from each region (or Network) mri_segstats --seg Buckner_atlas_FSSub.nii.gz --ctab $FREESURFER_HOME/average/YeoJNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt --excludeid 0 --i fmcpr.anat.nii.gz --avgwf test.txt
Yes, I did overlay Buckner_atlas_FSSub.nii.gz over subject's aparc.a2009s+aseg.mgz and I assumed it looked fine. Please see below for freeview screenshot below (with and without overlay)
However, I have a followup question. If I want to get the network values separately for
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --o cerebellum_left_mask_FSSub.nii.gz : For left regions & mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o cerebellum_right_mask_FSSub.nii.gz : For right regions
and follow other steps for each mask?
without overlay
[image: Inline image 1] with overlay
[image: Inline image 2]
Thanks for your help.
Cheers, Sabin Khadka
On Thu, Jun 30, 2016 at 11:29 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Sabin,
I think fslmeants should work. But you might need to first run mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual ROIs.
Also can you tell us which step generated the error "ERROR: must specify a segmentation volume"? Is this the final step? Have you tried overlaying Buckner_atlas_FSSub.nii.gz onto your individual subject in freeview to check that the previous steps have worked?
Thanks, Thomas
On Mon, Jun 27, 2016 at 6:53 PM, Sabin Khadka mr.sabinkhadka@gmail.com wrote:
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
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