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Is this only in FSL 7 Doug? I can't find it in 6.

On 16/06/2020 14:59, Douglas N. Greve wrote:

Try  mri_segcentroids. Run it with --help to get docs

On 6/16/2020 8:39 AM, Ian wrote:

...

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Hi Freesurfers.

I'm looking to find the center of the various Ventricles. Are they included in the freesurfer segmentation images with a specific code?

If not, what approach would you use?

Thanks, Ian

--

*Ian Hardingham*

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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

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Thank you so much Doug.

Ian

On 16/06/2020 15:44, Douglas N. Greve wrote:

Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids

On 6/16/2020 10:32 AM, Ian Hardingham wrote:

...

External Email - Use Caution

Is this only in FSL 7 Doug? I can't find it in 6.

On 16/06/2020 14:59, Douglas N. Greve wrote:

...

Try  mri_segcentroids. Run it with --help to get docs

On 6/16/2020 8:39 AM, Ian wrote:

...

External Email - Use Caution

Hi Freesurfers.

I'm looking to find the center of the various Ventricles.  Are they included in the freesurfer segmentation images with a specific code?

If not, what approach would you use?

Thanks, Ian

--

*Ian Hardingham*

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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

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

you're not running it correctly. Run it with just --help to get info on how to set up the command line

On 6/17/2020 3:48 AM, Ian Hardingham wrote:

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Hi Doug, just an FYI that I think this requires extra recon-all files that are only output by v7 ?

./mri_segcentroids --i freesurfer/surf --o results.txt error: corRead(): can't open file freesurfer/surf/COR-.info

On 16/06/2020 15:44, Douglas N. Greve wrote:

...

Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids

On 6/16/2020 10:32 AM, Ian Hardingham wrote:

...

External Email - Use Caution

Is this only in FSL 7 Doug? I can't find it in 6.

On 16/06/2020 14:59, Douglas N. Greve wrote:

...

Try  mri_segcentroids. Run it with --help to get docs

On 6/16/2020 8:39 AM, Ian wrote:

...

External Email - Use Caution

Hi Freesurfers.

I'm looking to find the center of the various Ventricles.  Are they included in the freesurfer segmentation images with a specific code?

If not, what approach would you use?

Thanks, Ian

--

*Ian Hardingham*

---

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

---

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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To find the code, look at FreeSurferColorLUT.txt, e.g., you may be interested in a subset of these:

grep -i vent $FREESURFER_HOME/FreeSurferColorLUT.txt

The last 4 values on each line make up a color code (RGBA, in range 0-255 per channel). The first value is the region code, used in a segmentation file.

So the voxels with intensity 14 in the file <subject>/mri/aseg.mgz should belong to the 3rd ventricle.

I hope that is what you were asking?

Tim

On June 17, 2020 at 11:41 AM Ian Hardingham ian@mode7.games wrote:

    External Email - Use Caution        

Are the ventricles currently in V6 Surf directory as a set of vertices, or a labelled list of voxels, or anything like that?

Ian

On 16/06/2020 13:39, Ian wrote:

...

External Email - Use Caution

Hi Freesurfers.

I'm looking to find the center of the various Ventricles.  Are they included in the freesurfer segmentation images with a specific code?

If not, what approach would you use?

Thanks, Ian

--

*Ian Hardingham*

---

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