Hi Sabin,
The idea is to use the freesurfer left and right cerebellar masks to make
the Buckner parcellation.
Your steps seem roughly correct but the names of your variables seem to
change from one section to another, so I can't be sure.
Regards,
Thomas
On Friday, 1 July 2016, Sabin Khadka <mr.sabinkhadka(a)gmail.com> wrote:
> Hi Thomas- Thanks for reply.
>
> Sorry for not being clear on the previous email. I want extract values
> from Buckner et al 2011 defined 7 regions (network) for left and right
> hemisphere separately. Wondering if I am in correct direction if I do
> ****
> 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
> *****
> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
> cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8 # For left
> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
> cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47 # For right
> *****
> and use
> mri_segstats --seg Buckner_atlas_FSSub_m8.nii.gz --ctab
> $FREESURFER_HOME/average/YeoJNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
> --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt
> mri_segstats --seg Buckner_atlas_FSSub_m47.nii.gz --ctab
> $FREESURFER_HOME/average/YeoJNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
> --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt
>
> to extract values.
>
> Again, thanks for all your help and input.
>
> Cheers,
> Sabin Khadka
>
> On Thu, Jun 30, 2016 at 3:40 PM, Thomas Yeo <ythomas(a)csail.mit.edu
> <javascript:_e(%7B%7D,'cvml','ythomas(a)csail.mit.edu');>> wrote:
>
>> 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(a)gmail.com
>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)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(a)csail.mit.edu
>>> <javascript:_e(%7B%7D,'cvml','ythomas(a)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(a)gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)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(a)gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)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(a)csail.mit.edu
>>>> <javascript:_e(%7B%7D,'cvml','ythomas(a)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):
>>>> >>>
>>>> >>> 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(a)nmr.mgh.harvard.edu
>>>> <javascript:_e(%7B%7D,'cvml','greve(a)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(a)nmr.mgh.harvard.edu
>>>> <javascript:_e(%7B%7D,'cvml','greve(a)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(a)csail.mit.edu
>>>> <javascript:_e(%7B%7D,'cvml','ythomas(a)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(a)gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)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
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>>>> <javascript:_e(%7B%7D,'cvml','Freesurfer(a)nmr.mgh.harvard.edu');>
>>>> >>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >>> >>>>>
>>>> >>> >>>>>
>>>> >>> >>>>> The information in this e-mail is intended only for the
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>>>> >>> >>>>> whom
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>>>> >>> >>>>> addressed. If you believe this e-mail was sent to you in
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>>>> >>> >>>>> contains patient information, please contact the Partners
>>>> >>> >>>>> Compliance
>>>> >>> >>>>> HelpLine at
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>>>> >>> >>>
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>>>> >>> >>>
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>>>> and
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>>>> >>
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>>>> >
>>>>
>>>
>>>
>>
>
Hello freesurfers,
I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have
the Recon edit button.
I saw that someone asked about this questions twice in the archive but was
never answered.
There was a note in the wiki page that reads "*Note*: Recon edit mode is
only available in the most recent release of freeview". I thought that the
most recent release of freeview comes with the most recent release of
freesurfer.
Can someone please let me know if there is a separate download link to the
recent release of freeview?
Thank you in advance,
Also If someone can answer my previous question regarding the Gyrification
i would really really appreciate it.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html
Thank you again,
Best regards,
Walid
