That did it :) thank you so much for your help!!
Kind regards, Michael ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> 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> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu><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> > <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu><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.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<mailto: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 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.
