Hi Ruopeng, this is the command i ran and resulting error message;

bash-4.1$ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \

/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0 \ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \ projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ --viewport 3d

bash: /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file or directory

Kind regards, Michael

On 14 Jun 2017, at 15:05, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:

Please copy and paste the full command line you ran and the error message you got.

Thanks, Ruopeng

On Jun 14, 2017, at 9:26 AM, Michael Davies <Michael.davies30@hotmail.commailto:Michael.davies30@hotmail.com> wrote:

Hello i am trying to access the data files in 3D but i am having problems opening the files using the command syntax given on the website.

I have set my own pathway using my own data;

“/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/”

However, one i progress with the code past this point i am unable to load the data and get the error message No file or directory in the terminal even though this is the correct pathway to the data.

When i enter the rest as follows this is when the problems begin to occur lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \

Could you please advise me how to proceed?

Kind regards, Michael University of Birmingham _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

Hi, the server has been down and i currently cannot access my account. I did however try putting freeview -f at the beginning before without any luck but i will try again when possible.

Kind regards, Michael

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@nmr.mgh.harvard.edu Sent: 14 June 2017 15:54:15 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview

You didn't call freeview there... Try adding "freeview -f " at the beginning of the command.

On 06/14/2017 11:02 AM, Michael Davies wrote: Hi Ruopeng, this is the command i ran and resulting error message;

bash-4.1$ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \

/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0 \ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \ projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ --viewport 3d

bash: /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file or directory

Kind regards, Michael

On 14 Jun 2017, at 15:05, Ruopeng Wang rpwang@nmr.mgh.harvard.edumailto:rpwang@nmr.mgh.harvard.edu wrote:

Please copy and paste the full command line you ran and the error message you got.

Thanks, Ruopeng

On Jun 14, 2017, at 9:26 AM, Michael Davies <Michael.davies30@hotmail.commailto:Michael.davies30@hotmail.com> wrote:

Hello i am trying to access the data files in 3D but i am having problems opening the files using the command syntax given on the website.

I have set my own pathway using my own data;

“/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/”

However, one i progress with the code past this point i am unable to load the data and get the error message No file or directory in the terminal even though this is the correct pathway to the data.

When i enter the rest as follows this is when the problems begin to occur lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \

Could you please advise me how to proceed?

Kind regards, Michael University of Birmingham _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Hi Bruce this is the command i am attempting to run but having no luck as yet. Any help would be greatly appreciated.

bash-4.1$ freeview -f \

/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0 \ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \ /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ --viewport 3d

bash: freeview: command not found bash-4.1$

Kind regards, Michael

University of Birmingham

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 14 June 2017 18:46:00 To: Freesurfer support list Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview

Hi Michael

can you send us the full command line and screen output of any command that you ran that fails and you want our help with?

thanks Bruce On Wed, 14 Jun 2017, Michael Davies wrote:

Hi, the server has been down and i currently cannot access my account. I did however try putting freeview -f at the beginning before without any luck but i will try again when possible.

Kind regards, Michael

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@nmr.mgh.harvard.edu Sent: 14 June 2017 15:54:15 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] viewing surfaces in 3D using freeview You didn't call freeview there... Try adding "freeview -f " at the beginning of the command.

On 06/14/2017 11:02 AM, Michael Davies wrote: Hi Ruopeng, this is the command i ran and resulting error message;

bash-4.1$/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apar c.annot:name=pial_aparc:visible=0 \

...

/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla

y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \

...

projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible

=0 \

...

/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0

\

...

projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ --viewport 3d

bash:/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apar c.annot:name=pial_aparc:visible=0: No such file or directory

Kind regards, Michael

  On 14 Jun 2017, at 15:05, Ruopeng Wang
  <rpwang@nmr.mgh.harvard.edu> wrote:

Please copy and paste the full command line you ran and the error message you got.

Thanks, Ruopeng

  On Jun 14, 2017, at 9:26 AM, Michael Davies
  <Michael.davies30@hotmail.com> wrote:

Hello i am trying to access the data files in 3D but i am having problems opening the files using the command syntax given on the website. I have set my own pathway using my own data;

“/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/”

However, one i progress with the code past this point i am unable to load the data and get the error message No file or directory in the terminal even though this is the correct pathway to the data.

When i enter the rest as follows this is when the problems begin to occur lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \

Could you please advise me how to proceed?

Kind regards, Michael University of Birmingham _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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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