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
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
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
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
External Email - Use Caution
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*
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
External Email - Use Caution
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
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:
External Email - Use Caution
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
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
External Email - Use Caution
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 CautionAre 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Perfect, thanks Tim.
On 17/06/2020 10:50, Tim Schäfer wrote:
External Email - Use CautionTo 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 CautionAre 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
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@nmr.mgh.harvard.edu