Re: [Freesurfer] Autorecon1 failure

2021-04-14 Thread Abdollahi, Shervin (NIH/NINDS) [C]
External Email - Use Caution Hi Douglas, Sure, here is the copy of recon-all.log From: "Douglas N. Greve" Reply-To: Freesurfer support list Date: Wednesday, April 14, 2021 at 10:32 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Autorecon1 failure Sorry, can

[Freesurfer] New York City-based Neuroimaging Postdoctoral Position Available

2021-04-14 Thread Sherry Simkovic
External Email - Use Caution The Psychiatry Research Institute at Montefiore Einstein (PRIME), a division of the Department of Psychiatry and Behavioral Sciences at Albert Einstein College of Medicine, is seeking a highly motivated postdoctoral scholar in the field of human

Re: [Freesurfer] Freeview does not open files through the Freeview window (Terminal only)

2021-04-14 Thread Max Korbmacher
External Email - Use Caution Hi Andrew, That fantastically did the trick! Thanks, Max > On 14 Apr 2021, at 20:29, Hoopes, Andrew wrote: > > Hi Max, > > You could try downloading an updated, standalone release of freeview >

Re: [Freesurfer] Freeview does not open files through the Freeview window (Terminal only)

2021-04-14 Thread Hoopes, Andrew
Hi Max, You could try downloading an updated, standalone release of freeview from https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Max Korbmacher Date: Wednesday, April 14, 2021 at 2:05 PM To:

[Freesurfer] Freeview does not open files through the Freeview window (Terminal only)

2021-04-14 Thread Max Korbmacher
External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to open files through Freeview v.2.0 (I’m using freesurfer-i386-apple-darwin11.4.2-stable6-20170119), but cannot do it “manually” but only through scripting / the terminal. The operating system is macOS

Re: [Freesurfer] addon question perl version needed for FS5.3

2021-04-14 Thread Hoopes, Andrew
Hi Phillip, Yes, 5.3 is getting to the point where some components are just too old to install correctly on modern system. I would read through this thread https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg69376.html that discusses this problem and a potential solution, similar to

Re: [Freesurfer] Install issue

2021-04-14 Thread Hoopes, Andrew
I’m not totally sure of the answer here. Could be filesystem limitations or a permissions issue. Have you tried untar’ing without the -p flag, or ensuring that you can write to /usr/local? Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Pål Gunnar Larsson Date:

Re: [Freesurfer] Autorecon1 failure

2021-04-14 Thread Douglas N. Greve
Sorry, can you resend the recon-all.log file? On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote: External Email - Use Caution *From: *"Abdollahi, Shervin (NIH/NINDS) [C]" *Date: *Thursday, March 18, 2021 at 12:42 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject:

Re: [Freesurfer] striatal parcellation

2021-04-14 Thread Douglas N. Greve
For the aseg.stats, you can run mri_segstats. Look in recon-all.cmd for the command that creates the aseg.stats file and change the input and output On 4/7/2021 8:24 AM, Marques Ana-raquel wrote: External Email - Use Caution Dear Freesurfer Team,  We would like to perform a striatal

Re: [Freesurfer] mris_label2annot - make all command exiting with errors

2021-04-14 Thread Douglas N. Greve
Sorry, there is not a good way in v7 On 4/7/2021 2:57 AM, Marion DURTESTE wrote: External Email - Use Caution Hi Douglas, Thank you very much for your answer! What would you suggest is therefore the best way to do this in V7? Best wishes, Marion D Le 2021-04-06 15:18, Douglas N.

Re: [Freesurfer] mris_average_surface fails

2021-04-14 Thread Douglas N. Greve
It looks like you do there, but downstream you might not. In general, macs don't like to give you permission in the apps folder. Try pointer your SUBJECTS_DIR to another location, eg, in your home directory On 4/6/2021 8:44 PM, バキット・ムダシル wrote: External Email - Use Caution I Think I

Re: [Freesurfer] Talairach Failed: Distorted T1

2021-04-14 Thread Douglas N. Greve
Sorry, what is the brainstem.dat file? Is that something we create? On 4/6/2021 7:53 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Douglas, Thanks again. Is this value in the brainstem.dat file accurate or is it subject to the same limitation in that the value will

Re: [Freesurfer] make_average_subject error

2021-04-14 Thread Douglas N. Greve
When I look at the README, this is the contents. Are you looking at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/README ? Download make_average_subject and the platform-specific version of mri_aparc2aseg from this directory and move them to your freesurfer bin directory

Re: [Freesurfer] recon-all transformations: raw nii to T1.mgz

2021-04-14 Thread Douglas N. Greve
If it is just visualization, you should be able to just load them in Freeview (assuming that  they share the RAS system) On 4/6/2021 3:01 PM, Fischl, Bruce wrote: Hi Noam You can always use the -rl switch in mri_convert (rl == “reslice like”). So for example mri_convert -rl rawavg.mgz

[Freesurfer] The cvs_avg35

2021-04-14 Thread バキット・ムダシル
External Email - Use Caution Hi, I was looking for any document describes how the cvs_avg35 and cvs_avg35_inMNI152 were made? Can you please send me a link or give me a brief about it please? I searched in the freesurfer wiki and here in the freesurfer folder but no success.

[Freesurfer] mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter

2021-04-14 Thread Camerino, I.L. (Ileana)
External Email - Use Caution Dear Freesurfer experts, I am running recon all as part of the tractography pipeline on a group of stroke patients. This is are the first lines of my log file: /opt/freesurfer/6.0/bin/recon-all -s sub-056 -i