SAVE REG in tkregister2

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Hao wen

7 Jun 2016 7 Jun '16

4:46 a.m.

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output:

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

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Hao wen

7 Jun 7 Jun

4:55 a.m.

Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized.

I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration

FsTutorial/ManualRegistration - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration surfer.nmr.mgh.harvard.edu top | previous. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can ...

I think my FS version is the newest, but it seems that this errors are really a little silly...

Thanks

________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mardi 7 juin 2016 10:46:59 À : freesurfer@nmr.mgh.harvard.edu; Bruce Fischl Objet : [Freesurfer] SAVE REG in tkregister2

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output:

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

Douglas Greve

9:54 a.m.

That will work in version 6

On 6/7/16 4:55 AM, Hao wen wrote:

...

Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized.

I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration

FsTutorial/ManualRegistration - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration surfer.nmr.mgh.harvard.edu top | previous. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can ...

I think my FS version is the newest, but it seems that this errors are really a little silly...

Thanks

*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 7 juin 2016 10:46:59 *À :* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl *Objet :* [Freesurfer] SAVE REG in tkregister2 Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

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

Hao wen

8 Jun 8 Jun

4:02 a.m.

Sorry, I sent you the wrong site, I followed the multimodal registration with three ways to do the regi, Freeview, tkregister2, and bbregister, so with tkregister is not cmdline, its a GUI, but I can not save the result with SAVE REG button, here is the link

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_...

FsTutorial/MultiModalRegistration_freeview - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview surfer.nmr.mgh.harvard.edu 2. Basic Manual Registration. The purpose of this exercise is to: Familiarize you with the FreeView and/or tkregister2 command interface. Show you how to make manual ...

Thank you and the bbregister, the flag will work in version 6?

thanks

________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 7 juin 2016 15:54:46 À : Freesurfer support list Objet : Re: [Freesurfer] SAVE REG in tkregister2

That will work in version 6

On 6/7/16 4:55 AM, Hao wen wrote:

Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized.

I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration

I think my FS version is the newest, but it seems that this errors are really a little silly...

Thanks

________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com mailto:hao.freesurfer@hotmail.com Envoyé : mardi 7 juin 2016 10:46:59 À : freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; Bruce Fischl Objet : [Freesurfer] SAVE REG in tkregister2

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output:

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

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

Douglas Greve

9:39 a.m.

when you run tkregister, you have a command line. I want you to send me that command line

On 6/8/16 4:02 AM, Hao wen wrote:

...

Sorry, I sent you the wrong site, I followed the multimodal registration with three ways to do the regi, Freeview, tkregister2, and bbregister, so with tkregister is not cmdline, its a GUI, but I can not save the result with SAVE REG button, here is the link

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_...

FsTutorial/MultiModalRegistration_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview surfer.nmr.mgh.harvard.edu 2. Basic Manual Registration. The purpose of this exercise is to: Familiarize you with the FreeView and/or tkregister2 command interface. Show you how to make manual ...

Thank you and the bbregister, the flag will work in version 6?

thanks

*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 7 juin 2016 15:54:46 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] SAVE REG in tkregister2 That will work in version 6

On 6/7/16 4:55 AM, Hao wen wrote:

...
Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized.

I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration

FsTutorial/ManualRegistration - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration surfer.nmr.mgh.harvard.edu top | previous. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can ...

I think my FS version is the newest, but it seems that this errors are really a little silly...

Thanks

*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 7 juin 2016 10:46:59 *À :* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl *Objet :* [Freesurfer] SAVE REG in tkregister2 Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

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

Hao wen

10:05 a.m.

tkregister2 --mov template.nii --s fbirn-anat-101.v4 \ --regheader --reg myregister.dat --surf

ok, here it is

________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mercredi 8 juin 2016 10:02:16 À : Freesurfer support list Objet : Re: [Freesurfer] SAVE REG in tkregister2

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_...

Thank you and the bbregister, the flag will work in version 6?

thanks

That will work in version 6

On 6/7/16 4:55 AM, Hao wen wrote:

Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized.

I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration

I think my FS version is the newest, but it seems that this errors are really a little silly...

Thanks

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output:

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

Douglas Greve

14 Jun 14 Jun

11:32 a.m.

When you run that command, are you in a folder where you have write permission?

On 6/8/16 10:05 AM, Hao wen wrote:

...

tkregister2 --mov template.nii --s fbirn-anat-101.v4 \ --regheader --reg myregister.dat --surf ok, here it is

*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mercredi 8 juin 2016 10:02:16 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] SAVE REG in tkregister2

Sorry, I sent you the wrong site, I followed the multimodal registration with three ways to do the regi, Freeview, tkregister2, and bbregister, so with tkregister is not cmdline, its a GUI, but I can not save the result with SAVE REG button, here is the link

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_...

FsTutorial/MultiModalRegistration_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview surfer.nmr.mgh.harvard.edu 2. Basic Manual Registration. The purpose of this exercise is to: Familiarize you with the FreeView and/or tkregister2 command interface. Show you how to make manual ...

Thank you and the bbregister, the flag will work in version 6?

thanks

*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 7 juin 2016 15:54:46 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] SAVE REG in tkregister2 That will work in version 6

On 6/7/16 4:55 AM, Hao wen wrote:

...
Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized.

I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration

FsTutorial/ManualRegistration - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration surfer.nmr.mgh.harvard.edu top | previous. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can ...

I think my FS version is the newest, but it seems that this errors are really a little silly...

Thanks

*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 7 juin 2016 10:46:59 *À :* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl *Objet :* [Freesurfer] SAVE REG in tkregister2 Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

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

Douglas Greve

7 Jun 7 Jun

9:54 a.m.

what is your command line?

On 6/7/16 4:46 AM, Hao wen wrote:

...

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL

I think maybe this is a very stupid question:) But FS is really complicated...

Thanks in advance

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

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Douglas Greve
Hao wen