Re: [Freesurfer] FSFAST- Cerebellum

[Douglas N Greve]

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 
> > 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
>> > 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
>> >
>> wrote:
>> > Hi all,
>> >
>> > I am trying to extract mean time series BOLD data using
>> FSFAST from Cortical
>> > ROIs + sub cortical ROIs and cerebellum.
>> >
>> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh
>> -mni305 -fwhm 6
>> > -per-run -stc oddmri_segstats --annot fsaverage lh
>> aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz
>> --excludeid 1000
>> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
>> > mri_segstats --annot fsaverage rh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz
>> --excludeid 2000
>> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >
>> > and for cortical time series
>> >
>> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id
>> 12 --id 13 --id
>> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53
>> --id 54 --id 58
>> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> > subCorticalTimeSeries.txt
>> >
>> > But I am not sure on how exactly to extract time series
>> from cerebellar
>> > regions. So if I want to extract time series from regions
>> 

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

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  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 
> 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  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):
>>>
>>> 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
>>>  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
>>> >>  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
>>> >>> 

Re: [Freesurfer] FSFAST- Cerebellum

[Sabin Khadka]

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 
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  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):
>>
>> 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
>>  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
>> >>  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

Re: [Freesurfer] FSFAST- Cerebellum

[Sabin Khadka]

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  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):
>
> 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
>  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
> >>  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 
> >>> wrote:
> 
>  Hi Sabin,
> 
>  The structures 601-628 

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

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
 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
>>  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 
>>> 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 
 wrote:
>
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from
> Cortical
> ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm
> 6
> -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
> --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> /opt/freesurfer/FreeSurferColorLUT.txt 

Re: [Freesurfer] FSFAST- Cerebellum

[Douglas Greve]

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
>  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  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 
>>> wrote:
 Hi all,

 I am trying to extract mean time series BOLD data using FSFAST from
 Cortical
 ROIs + sub cortical ROIs and cerebellum.

 preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm
 6
 -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
 rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
 mri_segstats --annot fsaverage rh aparc --i
 rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt

 and for cortical time series

 mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
 /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
 --id
 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
 58
 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
 subCorticalTimeSeries.txt

 But I am not sure on how exactly to extract time series from cerebellar
 regions. So if I want to extract time series from regions as described
 in
 Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628
 in
 FreeSurferCololLUT.txt? If not could you please direct me to processes
 that
 I can use.

 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
>>
>>
>>
>> ___
>> 

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

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

Re: [Freesurfer] FSFAST- Cerebellum

[Douglas Greve]

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




___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list

Re: [Freesurfer] FSFAST- Cerebellum

[Sabin Khadka]

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

[Thomas Yeo]

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