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
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.
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
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 http://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 mailto: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 <mailto: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 <http://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 <mailto: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 <mailto: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
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
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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.
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.
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):
1. Run MNI152 1mm template through recon-all recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS
2. 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
3. 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
4. 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
5. 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
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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.
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
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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
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
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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.
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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 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
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
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
Hi Sabin,
You can try to combine with FreeSurfer's segmentation of left and right cerebellum.
--Thomas
On Thu, Jun 30, 2016 at 7:59 PM, Sabin Khadka mr.sabinkhadka@gmail.com wrote:
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
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
Hi Doug, As you suggested I mapped fmri into the anatomical space using
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz
The orientation of fmcpr.anat.nii.gz seem to have some problem (see below). However the label seems to be correct. I am a bit confused here. Do I need to tranform the file somehow?
fmcpr.nii.gz
[image: Inline image 1]
fmcpr.anat.nii.gz
[image: Inline image 2]
Cheers, Sabin Khadka
On Thu, Jun 23, 2016 at 11:28 AM, 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.commr.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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
What is the problem with the orientation? The little letters indicate that the orientation is correct. fslview ignores the orientation when displaying so it might come out upside down.
On 07/05/2016 01:35 PM, Sabin Khadka wrote:
Hi Doug, As you suggested I mapped fmri into the anatomical space using
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz
The orientation of fmcpr.anat.nii.gz seem to have some problem (see below). However the label seems to be correct. I am a bit confused here. Do I need to tranform the file somehow?
fmcpr.nii.gz
Inline image 1
fmcpr.anat.nii.gz
Inline image 2
Cheers, Sabin Khadka
On Thu, Jun 23, 2016 at 11:28 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto: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 <http://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 <mailto: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 <mailto: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 <http://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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Sabin Khadka -
Thomas Yeo