Re: [Freesurfer] Freesurfer Digest, Vol 156, Issue 27

o exit code causing recon-all to stop? cheers Bruce On Mon, 13 Feb 2017, Gronenschild Ed (NP) wrote: Hi, All datasets that I've processed sofar with v6 resulted in exactly the same error during running the command: mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.

Re: [Freesurfer] System crash by extremely much generated output v6 beta

h that big a defect. You should try down the source of it and fix it then rerun. cheers Bruce On Thu, 10 Mar 2016, Gronenschild Ed (NP) wrote: Hi Bruce, Here it is Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

Re: [Freesurfer] System crash by extremely much generated output v6 beta

th d PS it may be worth pointing out that beta 6 was withdrawn for more development. On 3/10/16 5:09 AM, Gronenschild Ed (NP) wrote: Hi, I'm using a MacPro with 32 GByte RAM. The output of FreeSurfer is written to a disk with 1.5 TByte free space. At the time I ran into trouble the free disk spa

Re: [Freesurfer] System crash by extremely much generated output v6 beta

mris-topo-fixer. Cheers, Ed On 10 Mar 2016, at 10:41, mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: 20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc. hth d On Wed, Mar 9, 2016 at 12:09 PM, Gro

[Freesurfer] System crash by extremely much generated output v6 beta-Repost

Hi developers, Could you please help me out on this problem. Should I upload the data? Cheers, Ed Begin forwarded message: From: Ed Gronenschild mailto:ed.gronensch...@maastrichtuniversity.nl>> Subject: System crash by extremely much generated output v6 beta Date: 7 March 2016 12:57:57 CET To:

[Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi, I have made some manual skullstrip adjustments and added a number of control points in the white matter. How should I proceed with recon-all to incorporate both adjustments? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

[Freesurfer] Meaning of resample type in mri_convert - Repost

Hi FreeSurfer developers, Can you please provide information on the resample types "interpolate" and "weighted" which can be specified with option -rt in mri_convert? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] Meaning of resample type in mri_convert

Hi FreeSurfer developers, Can you please provide information on the resample types "interpolate" and "weighted" which can be specified with option -rt in mri_convert? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] Advice for FreeSurfer developers

;> Content-Type: text/plain; charset=windows-1252; format=flowed Do you know what command was looking for matlab? On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where th

[Freesurfer] Problem with hippocampal subfields segmentation FS v6 - Solved

Hi, It seemed to be a problem with Java Runtime which I installed because it is required to do the hippocampal subfields segmentation. After starting the Matlab R2012a application itself the problem was gone. Cheers, Ed Begin forwarded message: From: "Gronenschild Ed (NP)" mailto:ed

[Freesurfer] Problem with hippocampal subfields segmentation FS v6

Hi, At the very beginning of the hippocampal subfields segmentation the following message window popped up: segmentSubjectT1_autoEstimateAlveusML cannot be opened because of a problem. Check with the developer to make sure segmentSubjectT1_autoEstimateAlveusML works with this version of Mac OS X.

Re: [Freesurfer] Advice for FreeSurfer developers

charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: Dear developers, Is it possible to check the presence of Matlab r

[Freesurfer] Advice for FreeSurfer developers

Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed ___

Re: [Freesurfer] finding local extrema in surface data

Hi Sabine, Perhaps you can transform ?h.sphere and corresponding surface data into a polar image in which you can try to find the local extrema. Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

[Freesurfer] Interesting paper

Hi, This may be of interest to all of you: http://benthamscience.com/journal/abstracts.php?journalID=car&articleID=129744 Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf