How to draw streamlines and their corresponding ROIs using freeview

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Zhiyuan Yu

26 Sep 2020 26 Sep '20

2:46 p.m.

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Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

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Wang, Ruopeng

28 Sep 28 Sep

9:17 a.m.

New subject: How to draw streamlines and their corresponding ROIs using freeview

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels.

Best, Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

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Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

Zhiyuan Yu

10:21 p.m.

New subject: How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

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Hi Ruopeng,

Thanks for your answer! My streamlines are in mat and trk file formats and I cannot load the fiber tracts as way points in Freeview. Could you please tell me why?

Best,

Zhiyuan Yu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@mgh.harvard.edu Sent: Monday, September 28, 2020 9:17 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels.

Best, Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Epnw_ITfSMW4!98uxD_oNguourixaZyWb-q_Wt-ACetsFENfDyzZdcgFGnSpI2N8FbMuRFPGeEMcKhg$

Wang, Ruopeng

29 Sep 29 Sep

11:20 a.m.

New subject: How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

Hi Zhiyuan,

You can load .trk file from “Load Tract” menu in freeview. Mat format is not supported unfortunately.

Best, Ruopeng

On Sep 28, 2020, at 10:21 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi Ruopeng,

Thanks for your answer! My streamlines are in mat and trk file formats and I cannot load the fiber tracts as way points in Freeview. Could you please tell me why?

Best, Zhiyuan Yu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Sent: Monday, September 28, 2020 9:17 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels.

Best, Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Epnw_ITfSMW4!98uxD_oNguourixaZyWb-q_Wt-ACetsFENfDyzZdcgFGnSpI2N8FbMuRFPGeEMcKhg$

Zhiyuan Yu

1 Oct 1 Oct

6:01 p.m.

New subject: How to draw streamlines and their corresponding ROIs using freeview {Disarmed} {Disarmed}

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Hi Ruopeng,

I am trying to load ROI file in freeview to display the ROIs. But I do not know what kind of ROI file I need. I try to use destrieux_dilated_labels.nii.gz but freeview cannot open this label file. Could you please tell me?

Best,

Zhiyuan Yu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@mgh.harvard.edu Sent: Tuesday, September 29, 2020 11:20 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

Hi Zhiyuan,

You can load .trk file from “Load Tract” menu in freeview. Mat format is not supported unfortunately.

Best, Ruopeng

On Sep 28, 2020, at 10:21 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi Ruopeng,

Thanks for your answer! My streamlines are in mat and trk file formats and I cannot load the fiber tracts as way points in Freeview. Could you please tell me why?

Best, Zhiyuan Yu

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels.

Best, Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Epnw_ITfSMW4!7PVy8IKv8ZnZKDRPtMeJsElbsBCVZ1u6vJ9FSbs5uPKWDqc6m3bWDg4dfGiDPBJkgQ$

Wang, Ruopeng

2 Oct 2 Oct

10:49 a.m.

New subject: How to draw streamlines and their corresponding ROIs using freeview {Disarmed} {Disarmed}

Hi Zhiyuan,

You can load the file as volume and select Lookup Table as the color map to show labels.

Best, Ruopeng

On Oct 1, 2020, at 6:01 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

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Hi Ruopeng,

Best, Zhiyuan Yu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Sent: Tuesday, September 29, 2020 11:20 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

Hi Zhiyuan,

You can load .trk file from “Load Tract” menu in freeview. Mat format is not supported unfortunately.

Best, Ruopeng

On Sep 28, 2020, at 10:21 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi Ruopeng,

Thanks for your answer! My streamlines are in mat and trk file formats and I cannot load the fiber tracts as way points in Freeview. Could you please tell me why?

Best, Zhiyuan Yu

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels.

Best, Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Epnw_ITfSMW4!7PVy8IKv8ZnZKDRPtMeJsElbsBCVZ1u6vJ9FSbs5uPKWDqc6m3bWDg4dfGiDPBJkgQ$

Zhiyuan Yu

4 Oct 4 Oct

3:33 p.m.

New subject: How to draw streamlines and their corresponding ROIs using freeview {Disarmed} {Disarmed} {Disarmed}

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Hi Ruopeng,

Thanks for your answer! Now I have loaded destrieux_dilated_labels.nii.gz and use freesurfercolorLUT as lookup table. However, Left-Putamen (12) and Right-Insula (55) are not existed. Only cortical section is existed. Could you please tell me why?

Best,

Zhiyuan Yu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@mgh.harvard.edu Sent: Friday, October 2, 2020 10:49 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed} {Disarmed}

Hi Zhiyuan,

You can load the file as volume and select Lookup Table as the color map to show labels.

Best, Ruopeng

On Oct 1, 2020, at 6:01 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi Ruopeng,

Best, Zhiyuan Yu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Sent: Tuesday, September 29, 2020 11:20 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

Hi Zhiyuan,

You can load .trk file from “Load Tract” menu in freeview. Mat format is not supported unfortunately.

Best, Ruopeng

On Sep 28, 2020, at 10:21 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi Ruopeng,

Thanks for your answer! My streamlines are in mat and trk file formats and I cannot load the fiber tracts as way points in Freeview. Could you please tell me why?

Best, Zhiyuan Yu

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels.

Best, Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu <zy16@my.fsu.edumailto:zy16@my.fsu.edu> wrote:

External Email - Use Caution

Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview.

Thank you, Zhiyuan

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Epnw_ITfSMW4!7PVy8IKv8ZnZKDRPtMeJsElbsBCVZ1u6vJ9FSbs5uPKWDqc6m3bWDg4dfGiDPBJkgQ$

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Epnw_ITfSMW4!_ucGAQEarPe93yo7n-BQR1d7YOv4XGRx-orKo3BklPAAFgo_BqyxWhJVZaUUhKY1Zg$

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Wang, Ruopeng
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