trac-all using nifti

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segmentThalamicNuclei.sh do not...

Heidi Emmanuel Foo

17 Sep 2018 17 Sep '18

12:55 a.m.

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Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message:

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

Attachments:

attachment.html (text/html — 1.9 KB)
config.txt (text/plain — 1.7 KB)

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Yendiki, Anastasia

17 Sep 17 Sep

10:46 a.m.

Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <heidifoo92@gmail.commailto:heidifoo92@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] trac-all using nifti

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Hi Anastasia,

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

Heidi Emmanuel Foo

11:03 p.m.

External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

...

Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?

a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message:

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Yendiki, Anastasia

18 Sep 18 Sep

4:11 a.m.

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?

Best,

a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Sent: Monday, September 17, 2018 11:03:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti

External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?

a.y

External Email - Use Caution

Hi Anastasia,

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

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

Heidi Emmanuel Foo

19 Sep 19 Sep

11:06 p.m.

External Email - Use Caution

Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards, Heidi Foo

On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

...

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?

Best,

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < heidifoo92@gmail.com> *Sent:* Monday, September 17, 2018 11:03:47 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?

a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message:

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Yendiki, Anastasia

20 Sep 20 Sep

8:18 a.m.

What is the trac-all command line that you run?

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Sent: Wednesday, September 19, 2018 11:06:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti

External Email - Use Caution

Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards, Heidi Foo

On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?

Best,

a.y

________________________________ 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 Heidi Emmanuel Foo <heidifoo92@gmail.commailto:heidifoo92@gmail.com> Sent: Monday, September 17, 2018 11:03:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti

External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

a.y

External Email - Use Caution

Hi Anastasia,

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Heidi Emmanuel Foo

21 Sep 21 Sep

2:41 a.m.

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Hi Anastasia,

I think I ran trac-all -c config.txt.

Regards, Heidi

On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

...

What is the trac-all command line that you run?

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < heidifoo92@gmail.com> *Sent:* Wednesday, September 19, 2018 11:06:09 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards, Heidi Foo

On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?

Best,

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < heidifoo92@gmail.com> *Sent:* Monday, September 17, 2018 11:03:47 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?

a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message:

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Yendiki, Anastasia

2:48 a.m.

You need to specify one more option, like -prep, etc. Please follow the instructions on the tutorial and, if the problem persists, send the exact command line that you ran and the full text of the output that you got.

On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo heidifoo92@gmail.com wrote:

External Email - Use Caution

Hi Anastasia,

I think I ran trac-all -c config.txt.

Regards, Heidi

On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

What is the trac-all command line that you run?

________________________________ 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 Heidi Emmanuel Foo <heidifoo92@gmail.commailto:heidifoo92@gmail.com> Sent: Wednesday, September 19, 2018 11:06:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti

External Email - Use Caution

Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards, Heidi Foo

On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?

Best,

a.y

External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

a.y

External Email - Use Caution

Hi Anastasia,

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

Heidi Emmanuel Foo

2:50 a.m.

External Email - Use Caution

Hi Anastasia,

Sure, I will try that. Thanks for the advice!

Regards, Heidi

On Fri, Sep 21, 2018 at 4:49 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

...

You need to specify one more option, like -prep, etc. Please follow the instructions on the tutorial and, if the problem persists, send the exact command line that you ran and the full text of the output that you got.

On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo heidifoo92@gmail.com wrote:
    External Email - Use Caution
Hi Anastasia,

I think I ran trac-all -c config.txt.

Regards, Heidi

On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

...
What is the trac-all command line that you run?

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < heidifoo92@gmail.com> *Sent:* Wednesday, September 19, 2018 11:06:09 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards, Heidi Foo

On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)?

Best,

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < heidifoo92@gmail.com> *Sent:* Monday, September 17, 2018 11:03:47 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards, Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed?

a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo heidifoo92@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all using nifti
    External Email - Use Caution
Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message:

: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards, Heidi Foo

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Heidi Emmanuel Foo
Yendiki, Anastasia