Re: [Freesurfer] lopsided hemisphere
Hello Bruce, Thank you for your advice! I really appreciate it! Happy 4th July. 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: 04 July 2017 20:09:10 To: Freesurfer support list Subject: Re: [Freesurfer] lopsided hemisphere Hi Michael I don't think there is really a problem here - it is just that either the brain is oriented strangely or it indeed asymmetric. In any case the segmentations and surfaces look accurate cheers Bruce On Tue, 4 Jul 2017, Michael Davies wrote: > > Hello, I have encountered a lopsided hemisphere when analysing the data. > What procedure do i need to employ to fix the problem? Any advice would be > greatly appreciated! > > > 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] lopsided hemisphere
Hello, I have encountered a lopsided hemisphere when analysing the data. What procedure do i need to employ to fix the problem? Any advice would be greatly appreciated! 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] bad file conversion
Hi Bruce, i used a T1.nii file at the beginning and performed the standard recon-all to convert the file just like i did with the rest of them. I deleted the file and run it again but it still produced the same results using this method. Kind regards, Michael > On 3 Jul 2017, at 15:05, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Michael > > if it loaeds in freeview upside down then everything else will fail. What > format did it start as? Best to use dicoms directly if you can, and avoid > analyze. In any case, make sure that the directions are correct at the > beginning (that is, for the file that you give to recon-all as the input). > > cheers > Bruce > > > On Mon, 3 Jul 2017, Michael Davies wrote: > >> >> Hello, i was wondering if you could possibly help me with a subjects file >> that has loaded badly. It not only loaded up-side down but looks as though >> there are additional deficits that need correcting. Any tips or advice would >> be greatly appreciated! >> >> >> Kind regard, 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Surface Problem
Hello, i have been trying to regenerate the surface on one of my subjects but keep having a problem where the terminal is saying there is a missing file name. Do you have any suggestions please? 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/Subj5/Subj5 bash-4.1$ recon-all -autorecon-pial -s Subj5 if: Missing file name. bash-4.1$ ___ 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] Regenerating Surface problems
Hello, i have been trying to regenerate the surface on one of my subjects but keep having a problem where the terminal is saying there is a missing file name. Do you have any suggestions please? 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/Subj5/Subj5 bash-4.1$ recon-all -autorecon-pial -s Subj5 if: Missing file name. bash-4.1$ ___ 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] Regenerating the WM Volume surface
Hi Bruce, i tried your suggestion but it is saying Missing file name. Do i need to include wm.mgz in the command line? 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/Subj2/Subj2 bash-4.1$ recon-all -autorecon2-wm -autorecon3 -s Subj2 if: Missing file name. 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: 20 June 2017 19:10:10 To: Freesurfer support list Subject: Re: [Freesurfer] Regenerating the WM Volume surface can you include your full command line? It looks like you typed: recon-all -autorecon2-wm -autorecon3 -Subj2 when probably what you wanted was recon-all -autorecon2-wm -autorecon3 -s Subj2 cheers Bruce On Tue, 20 Jun 2017, Michael Davies wrote: > > Hello, i am currently having problems with the code required to regenerate > the surface when editing the WM Volume. I was wondering if you could provide > any tips or advice as > to where i am going wrong please? > > 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/Subj2/Subj2 > bash-4.1$ recon-all -autorecon2-wm -autorecon3 -Subj2 > ERROR: Flag -Subj2 unrecognized. > -autorecon2-wm -autorecon3 -Subj2 > Linux pbic.bham.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 > UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s exited with ERRORS at Tue Jun 20 19:58:38 BST 2017 > > For more details, see the log file > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > ___ 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] Regenerating the WM Volume surface
Hello, i am currently having problems with the code required to regenerate the surface when editing the WM Volume. I was wondering if you could provide any tips or advice as to where i am going wrong please? 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/Subj2/Subj2 bash-4.1$ recon-all -autorecon2-wm -autorecon3 -Subj2 ERROR: Flag -Subj2 unrecognized. -autorecon2-wm -autorecon3 -Subj2 Linux pbic.bham.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 20 19:58:38 BST 2017 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] WM Volume
Hello, i am currently looking at the WM Volume in heat mode and am curious as to if i need to fill in all the small missing voxels located within the boundary as well as the bigger holes? 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
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 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> 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 > <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=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 > > <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=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$ > > > > > > > > > > >>__ &
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 <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/fsave
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 <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
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 <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=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 > <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=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/complian
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 <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=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.
[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.
[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.
Re: [Freesurfer] viewing surfaces in 3D using freeview
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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang > <rpw...@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 > <rpw...@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.davie...@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 > > > ___ > 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 surfaces in 3D using freeview
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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpw...@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 <rpw...@nmr.mgh.harvard.edu><mailto:rpw...@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.davie...@hotmail.com<mailto:michael.davie...@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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<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.
Re: [Freesurfer] viewing surfaces in 3D using freeview
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 <rpw...@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.davie...@hotmail.com<mailto:michael.davie...@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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] viewing surfaces in 3D using freeview
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 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.
