[Freesurfer] Recall: freeview upgrade isn’t working/library issue

External Email - Use Caution Hoptman, Matthew (NKI) would like to recall the message, "freeview upgrade isn’t working/library issue". IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain co

[Freesurfer] freeview upgrade isn’t working/library issue

External Email - Use Caution TO: freesurfer@nmr.mgh.harvard.edu FROM: matthew.hopt...@nki.rfmh.org SUBJECT: freeview upgrade isn’t working/library issue Hello FreeSurfer Developers, I followed the instructions here to upgrade freeview: https

[Freesurfer] Freesurfer 6.0

Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me. I also tried to ftp to your ftp site, and unfortunately, I got the message 421 Proxy is closed (unknown user location). Could you please tell me how I could get the new version

Re: [Freesurfer] application of mri_cvs_register question

Thanks, Anastasia, That worked. Sorry I missed it!! --Mat -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 3:17 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] application of mri_cvs_register

Re: [Freesurfer] application of mri_cvs_register question

stuck at that point. Lilla Zollei told me she'd look into it, but maybe you've communicated with her? Thanks Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:30 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.h

Re: [Freesurfer] application of mri_cvs_register question

Message- From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu] Sent: Wednesday, July 10, 2013 6:07 PM To: Hoptman, Matthew Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt, As diff2anat.bbr.mat was created by bbregister, I believe you should be able to use --reg

[Freesurfer] application of mri_cvs_register question

Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I'm not clear on how to do so to DTI data processed in Tracula. The command in the "Multimodal integration and inter-subject registration" tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg

[Freesurfer] libboost_programs_options.so.5 problem solved, at least for me

Hi, I never got an answer to this problem, which affected numerous programs including mris_resample, but I solved it with help from my local sysadmin. I think the problem is that there is a versioning difference between Centos and other Linux "flavors" (I use Linux Mint 14). But anyway, I: 1)

Re: [Freesurfer] libboost_program_options.so.5 issue

Hi all, Any update on this issue? At present, I'm not able to use mri_cvs_register as a result of the problem (several other programs also require this library). Best, Matt From: Hoptman, Matthew Sent: Tuesday, June 18, 2013 9:01 AM To: freesurfer@nmr.mgh.harvard.edu Su

[Freesurfer] libboost_program_options.so.5 issue

Hi all, Any news on the libboost_program_options.so.5 issue, as relates to mri_cvs_register? I've encountered it using mris_resample (as part of mri_cvs_register) using. When I run: qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V ${FREESURFER_HOME}/bin/mri_cvs_register

[Freesurfer] averaging tracts?

Hi all, Thanks for tracula , which I think is a terrific tool. Is there any way to average tracts across subjects for viewing purposes? I have in mind somehting along the line of a group average merged_avg33_mni_bbi.mgz. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline

Re: [Freesurfer] Tracula problem

Gotcha, Thanks. -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, May 20, 2013 10:06 AM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem Hi Matt - Yes, the dcmroot variable can be used if you

Re: [Freesurfer] any way to parallelize Tracula?

: Friday, May 17, 2013 1:02 PM To: Susan Kuo Cc: Hoptman, Matthew; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] any way to parallelize Tracula? Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about

[Freesurfer] FW: Tracula problem

ily script the trac-all job to run in SGE, but I can't fiugre out how to pass it to the trac-all command. Is there any way to pass the subject number directly to the command? Does this make sense? Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]

Re: [Freesurfer] Tracula problem

Hi Anastasia, To follow up, yes, those files exist. -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 12:31 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem Hi Matt - Can you

[Freesurfer] any way to parallelize Tracula?

Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nath

[Freesurfer] Tracula problem

Hi all, I'm having a problem with tracula. I'm trying to run in version 5.3 beta (is that version very different from the newer 5.3?). If I run trac-preproc -c dmrirc -prep, I get: mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.ni

[Freesurfer] freeview crash

Hi Ruopeg, No, glxgears doesn't crash. I'm getting about 3929 FPS. Thanks, Matt Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwis

[Freesurfer] FW: freeview crash

Hi all, I've been using Freesurfer for several years. I just upgraded to v. 5.1, but when I try to run freeview it crashes. I am running it on a 64-bit Centos 5.4 server and am accessing the server with Xming. When I try to start freeview it crashes Xming and I have to restart it. The only

[Freesurfer] license file

Hi, I just registered my new installation of Freesurfer 5.1, but I've used 5.0 and 4.5 in the past. Can I just copy the ".license" file from the prior installation? My impression is I needed a new .license file for v. 5.1, but I haven't received it despite registering. --Matt Conserve Resour

[Freesurfer] version number

Hi, I have a relatively old version of Freesurfer, and I'm not sure how to get the version number. Could anyone please advise? It's from back in the day when we used csurf. Best, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Resear

[Freesurfer] how to?

Hi all, How do I apply a Talairach registration to a segmentation? I can apply the transformation to the main volume and auxiliary volume in tkmedit, but I am not sure how to apply it to a segmentation volume. It looks like I can't load an aseg.mgz file as a main or auxiliary vol

[Freesurfer] tksurfer woes

Hi all, I'm having trouble using freesurfer's tksurfer program (I only get a sliver of the brain). Here is the error info I get: [ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root su