Re: [Freesurfer] FSFAST- Cerebellum

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
    >
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