[Freesurfer] viewing 3D surfaces
Hello, i am having problems accessing the 3D surfaces of my data. Is there any advice you could provide for me please? 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 Kind regards, Michael ___ 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] Viewing 3D surfaces
Hello, i am having problems loading the 3D surface for my data. I was wondering if you could provide any advice please? This is the command code i put into the terminal; 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 ___ 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.
Re: [Freesurfer] viewing 3D surfaces
Hi Michael you need to have FreeSurfer in your path or nothing will work. Have you sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the environment? cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > Hello, i am having problems accessing the 3D surfaces of my data. Is there > any advice you could provide for me please? > bash-4.1$ freeview -f \ > >/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:visibl > e=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 > > Kind regards, Michael > > ___ 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.
Re: [Freesurfer] viewing 3D surfaces
Hi Bruce, i am still getting error messages. is there anything else i could try doing? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file or directory bash-4.1$ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 14:11 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces Hi Michael you need to have FreeSurfer in your path or nothing will work. Have you sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the environment? cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > Hello, i am having problems accessing the 3D surfaces of my data. Is there > any advice you could provide for me please? > bash-4.1$ freeview -f \ > >/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:visibl > e=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 > > Kind regards, Michael > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... 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.
Re: [Freesurfer] viewing 3D surfaces
you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote: Hi Bruce, i am still getting error messages. is there anything else i could try doing? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat ed_thickness:visible=0 \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file or directory bash-4.1$ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 14:11 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces Hi Michael you need to have FreeSurfer in your path or nothing will work. Have you sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the environment? cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > Hello, i am having problems accessing the 3D surfaces of my data. Is there > any advice you could provide for me please? > bash-4.1$ freeview -f \ >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa r > c.annot:name=pial_aparc:visible=0 \ >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl a > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib l > e=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 > > Kind regards, Michael > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... 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.
Re: [Freesurfer] viewing 3D surfaces
Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ freeview -f \ > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d MRISread(/surf/lh.pial): could not open file No such file or directory MRISread failed No such file or directory ould not open file bash-4.1$ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 15:19:21 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i am still getting error messages. is there anything else i could > try doing? > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > file or directory > bash-4.1$ > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 14:11 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > you need to have FreeSurfer in your path or nothing will work. Have you > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > environment? > > cheers > Bruce > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > Hello, i am having problems accessing the 3D surfaces of my data. Is there > > any advice you could provide for me please? > > bash-4.1$ freeview -f \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa > r > > c.annot:name=pial_aparc:visible=0 \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl > a > > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib > l > > e=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 > > > > Kind regards, Michael > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Freesurfer Info Page - Harvard University > mail.nmr.mgh.harvard.edu > To see the collection of prior postings to the list, visit the Freesurfer > Archives. A searchable archive which of messages PRIOR to March 2004 is at > ... > > > > 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 t
Re: [Freesurfer] viewing 3D surfaces
Remove the '/' in front of "surf". On 06/15/2017 11:45 AM, Michael Davies wrote: Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ freeview -f \ > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d MRISread(/surf/lh.pial): could not open file No such file or directory MRISread failed No such file or directory ould not open file bash-4.1$ *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl *Sent:* 15 June 2017 15:19:21 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] viewing 3D surfaces you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i am still getting error messages. is there anything else i could > try doing? > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > file or directory > bash-4.1$ > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 14:11 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > you need to have FreeSurfer in your path or nothing will work. Have you > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > environment? > > cheers > Bruce > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > Hello, i am having problems accessing the 3D surfaces of my data. Is there > > any advice you could provide for me please? > > bash-4.1$ freeview -f \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa > r > > c.annot:name=pial_aparc:visible=0 \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl > a > > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib > l > > e=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 > > > > Kind regards, Michael > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Freesurfer Info Page - Harvard University > mail.nmr.mgh.harvard.edu > To see the collection of prior postings to the list, visit the Freesurfer > Archives. A searchable archive which of messages PRIOR to March 2004 is at > ... > > > > 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 Partner
Re: [Freesurfer] viewing 3D surfaces
That did it :) thank you so much for your help!! Kind regards, Michael From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang Sent: 15 June 2017 15:48:31 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] viewing 3D surfaces Remove the '/' in front of "surf". On 06/15/2017 11:45 AM, Michael Davies wrote: Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ freeview -f \ > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d MRISread(/surf/lh.pial): could not open file No such file or directory MRISread failed No such file or directory ould not open file bash-4.1$ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <mailto:fis...@nmr.mgh.harvard.edu> Sent: 15 June 2017 15:19:21 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i am still getting error messages. is there anything else i could > try doing? > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > file or directory > bash-4.1$ > > > > > From: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Bruce Fischl > <mailto:fis...@nmr.mgh.harvard.edu> > Sent: 15 June 2017 14:11 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > you need to have FreeSurfer in your path or nothing will work. Have you > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > environment? > > cheers > Bruce > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > Hello, i am having problems accessing the 3D surfaces of my data. Is there > > any advice you could provide for me please? > > bash-4.1$ freeview -f \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa > r > > c.annot:name=pial_aparc:visible=0 \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl > a > > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ > >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib > l > > e=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 > > > > Kind regards, Michael > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.ed
Re: [Freesurfer] viewing 3D surfaces
Hi Michael I think you need to do a Unix tutorial. That path is wrong. cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions? Kind regards, Michael bash-4.1$ freesurfer_setup_freeview freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ freeview -f \ > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat ed_thickness:visible=0 \ > /surf/lh.inflated:visible=0 \ > /surf/lh.white:visible=0 \ > /surf/lh.pial \ > --viewport 3d MRISread(/surf/lh.pial): could not open file No such file or directory MRISread failed No such file or directory ould not open file bash-4.1$ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 15:19:21 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i am still getting error messages. is there anything else i could > try doing? > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla t > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > file or directory > bash-4.1$ > > > >___ _ > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 14:11 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > you need to have FreeSurfer in your path or nothing will work. Have you > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > environment? > > cheers > Bruce > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > Hello, i am having problems accessing the 3D surfaces of my data. Is there > > any advice you could provide for me please? > > bash-4.1$ freeview -f \ >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=ap a > r > > c.annot:name=pial_aparc:visible=0 \ >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:over l > a > > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > \ >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visi b > l > > e=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 > > > > Kind regards, Michael > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Freesurfer Info Page - Harvard University > mail.nmr.mgh.harvard.edu > To see the collection of prior postings to the list, visit the Freesurfer > Archives. A searchable archive which of messages PRIOR to March 2004 is at > ... > > > > 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.partner
Re: [Freesurfer] viewing 3D surfaces
Hello Bruce, how do you mean the path is wrong? I am curious as the data loaded just. Kind regards, Michael From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 16:11:53 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces Hi Michael I think you need to do a Unix tutorial. That path is wrong. cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i'm getting closer to opening it now. But the final command > /surf/lh.pial \ didnt work this time. Any further suggestions? > > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ freeview -f \ > > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > MRISread(/surf/lh.pial): could not open file > No such file or directory > MRISread failed > No such file or directory > ould not open file > bash-4.1$ > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 15:19:21 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > you are not calling freeview in this command. Try putting freeview at the > start > On Thu, 15 Jun 2017, Michael Davies wrote: > > > > > Hi Bruce, i am still getting error messages. is there anything else i > could > > try doing? > > > > Kind regards, Michael > > > > > > bash-4.1$ freesurfer_setup_freeview > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > > FSL_DIR /usr/local/fsl > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla > t > > ed_thickness:visible=0 \ > > > /surf/lh.inflated:visible=0 \ > > > /surf/lh.white:visible=0 \ > > > /surf/lh.pial \ > > > --viewport 3d > > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > > file or directory > > bash-4.1$ > > > > > > > >___ > _ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > on behalf of Bruce Fischl > > > > Sent: 15 June 2017 14:11 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] viewing 3D surfaces > > Hi Michael > > > > you need to have FreeSurfer in your path or nothing will work. Have you > > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > > environment? > > > > cheers > > Bruce > > > > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > > > Hello, i am having problems accessing the 3D surfaces of my data. Is > there > > > any advice you could provide for me please? > > > bash-4.1$ freeview -f \ > >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=ap > a > > r > > > c.annot:name=pial_aparc:visible=0 \ > >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:over > l > > a > > > > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > > \ > >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visi > b > > l > > > e=0 \ > >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible > = > > 0 > > > \ > > > > /projects/pbic1030/
Re: [Freesurfer] viewing 3D surfaces
I mean the /surf/lh.pial path has to be wrong, as that points to the root where you wouldn't be allowed to put data. I guess surf/ worked for you, but would only work if you were in the $SUBJECTS_DIR/$subject dir when you issued the freeview command. cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: Hello Bruce, how do you mean the path is wrong? I am curious as the data loaded just. Kind regards, Michael From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 16:11:53 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces Hi Michael I think you need to do a Unix tutorial. That path is wrong. cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > > Hi Bruce, i'm getting closer to opening it now. But the final command > /surf/lh.pial \ didnt work this time. Any further suggestions? > > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > bash-4.1$ freeview -f \ > > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla t > ed_thickness:visible=0 \ > > /surf/lh.inflated:visible=0 \ > > /surf/lh.white:visible=0 \ > > /surf/lh.pial \ > > --viewport 3d > MRISread(/surf/lh.pial): could not open file > No such file or directory > MRISread failed > No such file or directory > ould not open file > bash-4.1$ > >___ _ > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 15:19:21 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > you are not calling freeview in this command. Try putting freeview at the > start > On Thu, 15 Jun 2017, Michael Davies wrote: > > > > > Hi Bruce, i am still getting error messages. is there anything else i > could > > try doing? > > > > Kind regards, Michael > > > > > > bash-4.1$ freesurfer_setup_freeview > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > > FSL_DIR /usr/local/fsl > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infl a > t > > ed_thickness:visible=0 \ > > > /surf/lh.inflated:visible=0 \ > > > /surf/lh.white:visible=0 \ > > > /surf/lh.pial \ > > > --viewport 3d > > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > > file or directory > > bash-4.1$ > > > > > > >>__ _ > _ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > on behalf of Bruce Fischl > > > > Sent: 15 June 2017 14:11 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] viewing 3D surfaces > > Hi Michael > > > > you need to have FreeSurfer in your path or nothing will work. Have you > > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the > > environment? > > > > cheers > > Bruce > > > > > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > > > Hello, i am having problems accessing the 3D surfaces of my data. Is > there > > > any advice you could provide for me please? > > > bash-4.1$ freeview -f \ >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=a p > a > > r > > > c.annot:name=pial_aparc:visible=0 \ >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:ove r > l > > a > > > > y=lh.thickn
Re: [Freesurfer] viewing 3D surfaces
Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is there any others you could recommend? Michael From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 17:03:19 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces I mean the /surf/lh.pial path has to be wrong, as that points to the root where you wouldn't be allowed to put data. I guess surf/ worked for you, but would only work if you were in the $SUBJECTS_DIR/$subject dir when you issued the freeview command. cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > > Hello Bruce, how do you mean the path is wrong? I am curious as the data > loaded just. > > > Kind regards, Michael > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 16:11:53 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > I think you need to do a Unix tutorial. That path is wrong. > > cheers > Bruce > > > On Thu, 15 Jun > 2017, Michael Davies wrote: > > > > > Hi Bruce, i'm getting closer to opening it now. But the final command > > /surf/lh.pial \ didnt work this time. Any further suggestions? > > > > > > Kind regards, Michael > > > > > > bash-4.1$ freesurfer_setup_freeview > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > > FSL_DIR /usr/local/fsl > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > > bash-4.1$ freeview -f \ > > > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla > t > > ed_thickness:visible=0 \ > > > /surf/lh.inflated:visible=0 \ > > > /surf/lh.white:visible=0 \ > > > /surf/lh.pial \ > > > --viewport 3d > > MRISread(/surf/lh.pial): could not open file > > No such file or directory > > MRISread failed > > No such file or directory > > ould not open file > > bash-4.1$ > > > >___ > _ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > on behalf of Bruce Fischl > > > > Sent: 15 June 2017 15:19:21 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] viewing 3D surfaces > > you are not calling freeview in this command. Try putting freeview at the > > start > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > > > > > > Hi Bruce, i am still getting error messages. is there anything else i > > could > > > try doing? > > > > > > Kind regards, Michael > > > > > > > > > bash-4.1$ freesurfer_setup_freeview > > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > > > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > > > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > > > FSL_DIR /usr/local/fsl > > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > > > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > >>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infl > a > > t > > > ed_thickness:visible=0 \ > > > > /surf/lh.inflated:visible=0 \ > > > > /surf/lh.white:visible=0 \ > > > > /surf/lh.pial \ > > > > --viewport 3d > > > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > > > file or directory > > > bash-4.1$ > > > > > > > > > > >>__ > _ > > _ > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > > on behalf of Bruce Fischl > > > > > > Sent: 15 June 2017 14:11 > > > To: Freesurfer support list > >
Re: [Freesurfer] viewing 3D surfaces
seems like that is a good start On Thu, 15 Jun 2017, Michael Davies wrote: Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is there any others you could recommend? Michael From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 June 2017 17:03:19 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces I mean the /surf/lh.pial path has to be wrong, as that points to the root where you wouldn't be allowed to put data. I guess surf/ worked for you, but would only work if you were in the $SUBJECTS_DIR/$subject dir when you issued the freeview command. cheers Bruce On Thu, 15 Jun 2017, Michael Davies wrote: > > Hello Bruce, how do you mean the path is wrong? I am curious as the data > loaded just. > > > Kind regards, Michael > >___ _ > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 June 2017 16:11:53 > To: Freesurfer support list > Subject: Re: [Freesurfer] viewing 3D surfaces > Hi Michael > > I think you need to do a Unix tutorial. That path is wrong. > > cheers > Bruce > > > On Thu, 15 Jun > 2017, Michael Davies wrote: > > > > > Hi Bruce, i'm getting closer to opening it now. But the final command > > /surf/lh.pial \ didnt work this time. Any further suggestions? > > > > > > Kind regards, Michael > > > > > > bash-4.1$ freesurfer_setup_freeview > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > > FSL_DIR /usr/local/fsl > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > > bash-4.1$ freeview -f \ > > > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infl a > t > > ed_thickness:visible=0 \ > > > /surf/lh.inflated:visible=0 \ > > > /surf/lh.white:visible=0 \ > > > /surf/lh.pial \ > > > --viewport 3d > > MRISread(/surf/lh.pial): could not open file > > No such file or directory > > MRISread failed > > No such file or directory > > ould not open file > > bash-4.1$ > > >>__ _ > _ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > on behalf of Bruce Fischl > > > > Sent: 15 June 2017 15:19:21 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] viewing 3D surfaces > > you are not calling freeview in this command. Try putting freeview at the > > start > > On Thu, 15 Jun 2017, Michael Davies wrote: > > > > > > > > Hi Bruce, i am still getting error messages. is there anything else i > > could > > > try doing? > > > > > > Kind regards, Michael > > > > > > > > > bash-4.1$ freesurfer_setup_freeview > > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > > > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > > > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > > > FSL_DIR /usr/local/fsl > > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage > > > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ >>>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inf l > a > > t > > > ed_thickness:visible=0 \ > > > > /surf/lh.inflated:visible=0 \ > > > > /surf/lh.white:visible=0 \ > > > > /surf/lh.pial \ > > > > --viewport 3d > > > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such > > > file or directory > > > bash-4.1$ > > > > > > > > > >>>_ _ > _ > > _ > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > &g
