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 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> 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 > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <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=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 > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > > <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=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.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.
