[Freesurfer] DEFECT 57
Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013 My question is this much edges normal and how much memory i need allocate to process this. Many Thanks Chikku ___ 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] Pial boundaries
Hello, I would like to ask if there are any commands or any manual edits I can use to fix the pial boundaries even if the white matter boundaries are fine. The white matter boundaries follow the white matter pretty good but there is some grey matter missing at some areas. Its not a massive problem though. Thank you in advance. Melina ___ 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] Generate mask from surface in diffusion space
Dear freesurfers I'm using bbregister and mri_surf2surf to transform intermediate cortical surfaces and mid surfaces normals to diffusion space. Next I'm trying to generate volumes from these surfaces (in the same diffusion space), however the generated volumes are much thicker then the generated surfaces. for example to generate surface normals I used the following: mri_surf2surf --s subjectid --hemi lh --sval-nxyz white_surface_in_diffusion --tval lhwhitediffusion_n.mgh mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white --reg mri/register.dat --outvol lh_white_n.img --template lowb.img Any idea what am I doing wrong? Thanks! Shani ___ 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] nb0 question
Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ 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] Registration segmentation with FSL - obtaining correlation matrix..
On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote: Hello I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat aseg2feat) When I extract the values (as per the matlab code below), I see NaNs in certain regions. Of the 19 datasets that I have analyzed I have see NaNs for the following labels 10061033200620132033 Is this a known problem? Is there a solution? Thanks, S On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote: Sorry, I don't think we have such a program. You could do it in matlab fairly easily, eg, f = MRIread('filtered_func_data'); fmat = fast_vol2mat(f); a = MRIread('aparc+aseg'); seglist = unique(a.vol(:)); seglist = seglist(2:end); % remove segid=0 (unkown) clear roimean for nthseg = 1:length(seglist) ind = find(a.vol == seglist(nthseg)); roimean(:,nthseg) = mean(fmat(:,ind),2); end m = roimean'*roimean; On 01/31/2013 01:29 PM, Sudhin A. Shah wrote: Hello, This worked perfectly 2 years ago :), but now I am having some trouble. I run reg-feat2anat aseg2feat with no problem. I now need a correlation matrix of every ROI (created by freesurfer) against every other ROI. For this I used @ROI_Corr_Mat (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html). Again - this worked fine in the past. Now I get an error (working with AFNI to see if it can be fixed). Question: Is there any alternative to getting this correlation matrix? i.e every ROI against every other ROI? Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Pial boundaries
Can you send us an image? On Feb 21, 2013, at 7:24 AM, melinaki p-t tritic...@gmail.com wrote: Hello, I would like to ask if there are any commands or any manual edits I can use to fix the pial boundaries even if the white matter boundaries are fine. The white matter boundaries follow the white matter pretty good but there is some grey matter missing at some areas. Its not a massive problem though. Thank you in advance. Melina ___ 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] DEFECT 57
Hi Chikku That is a giant defect - almost the size of an entire hemi. Something is badly wrong. Check the aseg and filled volumes to see what's going on, and the ?h.orig.nofix Bruce On Feb 21, 2013, at 5:35 AM, Varghese Chikku chik...@tcd.ie wrote: Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013 My question is this much edges normal and how much memory i need allocate to process this. Many Thanks Chikku ___ 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] Pial boundaries
I am afraid I can't... Can you give any advise without pictures? Thank you in advance. Melina 2013/2/21 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you send us an image? On Feb 21, 2013, at 7:24 AM, melinaki p-t tritic...@gmail.com wrote: Hello, I would like to ask if there are any commands or any manual edits I can use to fix the pial boundaries even if the white matter boundaries are fine. The white matter boundaries follow the white matter pretty good but there is some grey matter missing at some areas. Its not a massive problem though. Thank you in advance. Melina ___ 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 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] longitudinal sulci depth change
Hello, I was wondering if I could get some clarification regarding the longitudinal measure of rate of change in sulci depth. In our study we have a patient population that participated in an intervention and a similar group of wait list controls. We have scans for pre and post intervention timepoints. I have ran the longitudinal analysis in QDEC looking at the thickness change measures, however I was also interested in the sulc measures. I was able to get the analysis to run with the new measures long.sulc-rate etc. However I am having a hard time conceptualizing the meaning of the results. Does a negative rate change indicate either a deepening or a shallowing of the sulci? Is the opposite the case for gyral regions? Any advice would be greatly appreciated. -Andrew ___ 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] nb0 question
Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* ** - To be replaced with the actual number from the acquisition. On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] nb0 question
Hi Juan, The number of b0 images can be more than 1; it is specified when you acquire the image. Hth, Shantanu On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* ** - To be replaced with the actual number from the acquisition. On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ 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] nb0 question
Of course! But, if I understood correctly, Stefano only has one, either at the beginning of the end of the gradient table, and in both cases nb0=1 Cheers, /Eugenio On Thu, February 21, 2013 12:20 pm, Shantanu Ghosh wrote: Hi Juan, The number of b0 images can be more than 1; it is specified when you acquire the image. Hth, Shantanu On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* ** - To be replaced with the actual number from the acquisition. On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] dual installation question
If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh ___ 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] dual installation question
Hi Josh, you can modify the SetUpFreeSurfer.sh to source the correct version. Hth, Shantanu On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ 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] dual installation question
Or you may have multiple freesurfer versions within the freesurfer director, something like /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. and then export FREESURFER_HOME=freesurfer_installation_directory/freesurfer/5.1 etc Hth, S. On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: Hi Josh, you can modify the SetUpFreeSurfer.sh to source the correct version. Hth, Shantanu On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ 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] Tkregister2 / Tksurfer / Tkmedit Won't Open
Hello freesurfers, I just ran registration of my functional images and am trying to visualize the registration for assessment. However, when I use the commands tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f or tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov $FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS the command gets stuck on Opening window SUBJECT01. I've also tried just opening tksurfer and tkmedit but the terminal produces no output/windows opening and simply freezes. Any ideas to why this could be occurring? I've let it sit at this stage for multiple hours without anything popping up and without any errors. Thanks! Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu ___ 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] tkregister2 window error: Remote login
Hello, I am remotely logged in to my Ubuntu system(from Mac). I have previously run tkregister2 but am now having trouble; Opening window subj Window type not found register: tkoinitwindow(name) failed. Is there a solution to this? Thanks, S ___ 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] dual installation question
Thanks. Best, - Josh On Thu, Feb 21, 2013 at 10:05 AM, Shantanu Ghosh shant...@nmr.mgh.harvard.edu wrote: Or you may have multiple freesurfer versions within the freesurfer director, something like /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. and then export FREESURFER_HOME=freesurfer_installation_directory/freesurfer/5.1 etc Hth, S. On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: Hi Josh, you can modify the SetUpFreeSurfer.sh to source the correct version. Hth, Shantanu On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging 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.