Re: [Freesurfer] dt_recon issue

External Email - Use Caution Here it is. [hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon set echo = 1 ; breaksw breaksw end

Re: [Freesurfer] dt_recon issue

what happens when you run ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm On 2/13/19 6:27 PM, Daniel Callow wrote: > > External Email - Use Caution > > The error output that accompanies the command. > > > administrator% dt_recon --debug --i > /Volumes/DANIEL/tutor

Re: [Freesurfer] dt_recon issue

Yes. Can you run it with --debug with the slash in front of "Volumes"? On 2/13/19 6:25 PM, Daniel Callow wrote: > > External Email - Use Caution > > > Is this what you mean by no variables?? > > dt_recon --debug --i > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s

Re: [Freesurfer] dt_recon issue

External Email - Use Caution The error output that accompanies the command. administrator% dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon set echo = 1 ; breaksw breaksw end end w

Re: [Freesurfer] dt_recon issue

External Email - Use Caution Is this what you mean by no variables?? dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Ex

Re: [Freesurfer] dt_recon issue

can you send the command line without the variables? On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > External Email - Use Caution > > Thanks for pointing that out! Unfortunately after making the change > > dt_recon --debug --i > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj

[Freesurfer] dt_recon issue

External Email - Use Caution Thanks for pointing that out! Unfortunately after making the change dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon I still get the error. ./

Re: [Freesurfer] License Registration Error "Spammer, go away!"

Are you using some sort of form auto-fill plugin when you're accessing the registration page? Our spam filter checks if a hidden parameter has been supplied. If there's a way for you to turn auto-fill off temporarily - I would try that first. Let me know how that goes. best Andrew On 2/13/19

Re: [Freesurfer] License Registration Error "Spammer, go away!"

it would be helpful if you were to tell us exactly what you were doing (eg, URL, which text box, etc) On 2/13/19 3:49 PM, Peng Wang wrote: > > External Email - Use Caution > > Please help! > > Repost with a better title. > > ___ > Freesurfer mai

[Freesurfer] License Registration Error "Spammer, go away!"

External Email - Use Caution Please help! Repost with a better title. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] dt_recon issue

External Email - Use Caution Hello Daniel. It looks like you need a slash in front of Volumes for the path after —I/Volumes - R. On Feb 13, 2019, at 14:44, Daniel Davidson Callow wrote:External Email - Use CautionHello,I am trying to run dt_rec

[Freesurfer] dt_recon issue

External Email - Use Caution Hello, I am trying to run dt_recon on my dti data using the following script. dt_recon --debug --i Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon with the followi

[Freesurfer] Registrations with freesurfer voxel space and posterior map of thalamic nuclei segmentation results

External Email - Use Caution Hello Freesurfer Developers, I got the posterior map of thalamic nuclei segmentation by setting the environment parameter: export WRITE_POSTERIORS=1 I found the posterior map is of different dimension. In my case, posterior map is of [173, 117,11

Re: [Freesurfer] FreeSurfer Registration Error

External Email - Use Caution The freesurfer license. https://surfer.nmr.mgh.harvard.edu/registration.html On Wed, Feb 13, 2019 at 1:38 PM Hoopes, Andrew wrote: > Hi, what are you trying to register for? A wiki account? > > Andrew > > > > > > *From: * on behalf of Peng Wang < >

Re: [Freesurfer] FreeSurfer Registration Error

Hi, what are you trying to register for? A wiki account? Andrew From: on behalf of Peng Wang Reply-To: FS Help Date: Wednesday, February 13, 2019 at 12:54 PM To: FS Help Subject: [Freesurfer] FreeSurfer Registration Error External Email - Use Caution Whatever I filled the form I go

[Freesurfer] Missing files after recon-all

External Email - Use Caution Hello FreeSurfer experts, I am trying recon-all in a SGE cluster. However, the size of of the results was smaller than that executed in a local CentOs system. I did not found error in the recon-all log file which ended with "recon-all -s sub001 finishe

[Freesurfer] FreeSurfer Registration Error

External Email - Use Caution Whatever I filled the form I got "Spammer. Go away!" message. Please help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

Hi Shachar, the patch will not fix this. You’ll probably need to disable SIP - http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ - which prevents access to libraries in /usr. This bug has been fixed in the dev version. best Andrew From: on behalf of Shacha

[Freesurfer] neuroimaging quality control survey

External Email - Use Caution Hello all, Forward this here as it seems relevant to this mailing list. Do not hesitate to circulate this on your institute mailing lists, and ask your collaborators and friends. Thanks Remi The neuroimaging quality control (niQC) special interest

Re: [Freesurfer] Fix topology correcting defect

Hi Milène a couple of things. First, to view a surface in freeview you have to specify that it is a surface with -f before the surface file name. So, from the mri dir you could do: freeview -v norm.mgz -f ../surf/lh.orig.nofix ../surf/lh.inflated.nofix Second, how long did you wait? Big defe

Re: [Freesurfer] MRISalloc error during automatic reconstruction

Hi Julia I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram che

Re: [Freesurfer] Different aseg and aparc stats with Freesurfer 5.3 and 6.0

Hi Ranila the different versions contain slightly different algorithms, so why would you expect them to be the same? With 20 subjects you may be at the edge of having enough power to see a significant effect. cheers Bruce On Wed, 13 Feb 2019, Ranila Bhoyroo wrote: External Email

[Freesurfer] Postdoctoral position (EEG-MRI) available at NORMENT (Oslo, Norway)

External Email - Use Caution Dear FreeSurfer users! A three-year position as postdoctoral fellow is now available at the Norwegian Centre for Mental Disorders Research (NORMENT) in Oslo, Norway. NORMENT is a Center of Excellence (CoE) funded by the Research Council of

Re: [Freesurfer] problem using recon-all

External Email - Use Caution I am not sure that the issue is with the SIP, because the message says this - *"freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"* does not exist in the patches directory, and in fact, it does not exist here - https://surfer.nmr.mgh.harvard.edu/pub/dist/

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Hey Tim, I tried to run the “-E fs_update”, and got this message: rsync -zbrlv --progress --suffix=.1550066275_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesur

Re: [Freesurfer] problem using recon-all

External Email - Use Caution That being said, this did not help in my case. I had to disable System Integrity Protection. > On February 13, 2019 at 2:08 PM Tim Schäfer wrote: > > > External Email - Use Caution > > The release notes mention this message: > >

Re: [Freesurfer] problem using recon-all

External Email - Use Caution The release notes mention this message: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes under 'Known issues' and recommend you run 'sudo -E fs_update'. > On February 13, 2019 at 1:45 PM Shachar Gal wrote: > > > External Email - U

Re: [Freesurfer] problem using recon-all

External Email - Use Caution ok, so I tried doing what I mentioned above (I used the hcp recon-all version), and when trying to run the FreeSurfer Pipeline, I received this error: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applica

[Freesurfer] talairach.m3z question

External Email - Use Caution Dear FreeSurfer experts, I have 2 questions on the talairach.m3z file generated by recon-all. 1) What exactly does it contain? I read its the displacement field for a non-linear transform from native space to some freesurfer space. But from which in

[Freesurfer] Fix topology correcting defect

External Email - Use CautionHi Freesurfers,   I tried to run the recon-all command for several subjects of my study. It worked out for all of them except for one. This one froze at fixing topology „Correcting defect“ 11 out of 140 defects.  I looked for advises in the mailing list

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Hey Douglas, A couple of question about the patch In order to use it, I need to download the regular Freesurfer version-6, and replace only the scripts that are in the patch? (i.e Make_average_surface, recon_all, conf2hires, longmc) Which recon-all to