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Hi Freesurfer experts:
I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal from are close to the cerebral white matter that some voxels at the boundary may not contain any signals. Is there any arguments in mri_segstats that I can use to only extract voxels that has non-zero time-series?
Best, Renxi
I don't understand why WM was cropped out. What command were you trying to use?
On 11/18/2020 2:39 AM, RENXI LI wrote:
External Email - Use CautionHi Freesurfer experts:
I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal from are close to the cerebral white matter that some voxels at the boundary may not contain any signals. Is there any arguments in mri_segstats that I can use to only extract voxels that has non-zero time-series?
Best, Renxi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The WM was cropped out by applying a grey-matter mask in SPM, and I am trying to extract non-zero voxels with mri_segstats.
Best, Renxi
On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
I don't understand why WM was cropped out. What command were you trying to use?
On 11/18/2020 2:39 AM, RENXI LI wrote:
External Email - Use CautionHi Freesurfer experts:
I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal from are close to the cerebral white matter that some voxels at the boundary may not contain any signals. Is there any arguments in mri_segstats that I can use to only extract voxels that has non-zero time-series?
Best, Renxi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HcpQrOwsWp30a5Byx8SjDy-0mjvPRwBF9sIjXTumq5hy1Y...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HcpQrOwsWp30a5Byx8SjDy-0mjvPRwBF9sIjXTumq5hy1Y...
what is your command line?
On 11/29/2020 2:55 PM, RENXI LI wrote:
External Email - Use CautionThe WM was cropped out by applying a grey-matter mask in SPM, and I am trying to extract non-zero voxels with mri_segstats.
Best, Renxi
On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
I don't understand why WM was cropped out. What command were you trying to use?
On 11/18/2020 2:39 AM, RENXI LI wrote:
External Email - Use CautionHi Freesurfer experts:
I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal from are close to the cerebral white matter that some voxels at the boundary may not contain any signals. Is there any arguments in mri_segstats that I can use to only extract voxels that has non-zero time-series?
Best, Renxi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HcpQrOwsWp30a5Byx8SjDy-0mjvPRwBF9sIjXTumq5hy1Y...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HcpQrOwsWp30a5Byx8SjDy-0mjvPRwBF9sIjXTumq5hy1Y...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
RENXI LI