[Freesurfer] openmp/mkl support in tracula

hi a.y., is there any part of tracula that currently benefits from openmp or mkl availability? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] recon-all subject -qcache in a different version of freesurfer?

Hi Doug, To follow-up: I have been running recon-all subject -qcache but for some of my subjects it "exited with ERRORS" due to unmatched number of vertices. I read from previous threads that the general fix is to run -autorecon2 and -autorecon3 again. However, I hesitate to do that in my case due

Re: [Freesurfer] openmp/mkl support in tracula

Hi Satra - Sorry, no. a.y On Fri, 25 Apr 2014, Satrajit Ghosh wrote: > hi a.y., > is there any part of tracula that currently benefits from openmp or mkl > availability? > > cheers, > > satra > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

[Freesurfer] Coordinate transformation to average surface space

Hi All, I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject. By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_regis

[Freesurfer] Invalid license for recon-all

Dear FreeSurfer experts, I have FreeSurfer installed on an Ubuntu system and I got the following error: ERROR: Invalid FreeSurfer license key found in license file /media/datas/study_tools/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harva

Re: [Freesurfer] recon-all subject -qcache in a different version of freesurfer?

Run with those flags using the version of FS that you analyzed them with originally On 04/25/2014 09:55 AM, Yizhou Ma wrote: > Hi Doug, > > To follow-up: I have been running recon-all subject -qcache but for > some of my subjects it "exited with ERRORS" due to unmatched number of > vertices.

[Freesurfer] Segmentatoin fault using Freesurfer Functions Fedora 19 - Freesurfer 5.1

Hello. We are trying to get Freesurfer 5.1 to work on Fedora 19. The functions we have tried show the help menu successfully when asked, but run into a Segmentation Fault when trying to process anything. Both tkmedit and mri_convert have shown this behavior. Segmentation Faults are notorious

[Freesurfer] Multi-echo FLASH

Hi all, I'm building a scan protocol for what is primarily a MEG study, which needs T1 information for co-registration and T1/T2 information to construct an accurate BEM from the inner skull surface. It seems like the two multi-echo FLASH sequences at 5 and 30 degrees would give me all of the inf

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

Hi Joshua: Thanks for the input. Very helpful. Alan On Thu, Apr 24, 2014 at 8:10 PM, Joshua Lee wrote: > Hi Alan, > > Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x > 0.4 mm in-plane resolution). The thickness of a CA subfield typically range > between 0.5-1.00 mm, b

[Freesurfer] longitudinal recon-all -long error

Hello, I am on the recon-all -long step of the longitudinal processing stream and the final time point exits with errors at the mri_convert stage. mri_convert -at /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta -odt u

[Freesurfer] FreeSurfer on MacBook Pro

Dear Sir/Madame, I am trying to install and run Freesurfer on my new MacBook Pro 15.4" Retina 2880x1800 2.3GHZ Intel QC i7 Intel Iris Graphics 16GB RAM 512GB SSD ME294LL/A I am not sure why it's not running but I noticed that my OS is Mavericks and the download page says: Lion OX X 10.7 (64b In

[Freesurfer] aparc+aseg.mgz recovery

Hi all, I accidentally damaged my aparc+aseg.mgz file. Is there any way to recover this without rerunning recon-all? Thanks so much! Daria ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

Re: [Freesurfer] aparc+aseg.mgz recovery

Just run recon-all -s subject -aparc2aseg should only take about 10 min to run On 04/25/2014 06:33 PM, Daria Boratyn wrote: > Hi all, > > I accidentally damaged my aparc+aseg.mgz file. Is there any way to recover > this without rerunning recon-all? > > Thanks so much! > Daria > > > ___

Re: [Freesurfer] Catastrophic Surface Inaccuracies

Hi Jon that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want. cheers Bruce

Re: [Freesurfer] Catastrophic Surface Inaccuracies

Thanks Bruce, I’ll check for such wm connections. Is this the default method for correcting topology issues? jon On Apr 25, 2014, at 10:59 PM, Bruce Fischl wrote: > Hi Jon > > that is almost certainly a topology correction problem. Check to see if the > wm.mgz contains any spurious connectio

Re: [Freesurfer] Segmentatoin fault using Freesurfer Functions Fedora 19 - Freesurfer 5.1

Hi John we could give you a version with debugging info and source and you could run it in gdb and find out where it is crashing. Or you could send us the core fie from a version with debugging on cheers Bruce On Fri, 25 Apr 2014, West, John D. wrote: Hello. We are trying to get Frees

Re: [Freesurfer] Multi-echo FLASH

Hi Jon yes, that works fine. The mprage gives better CNR/unit time in the cortex, but if you are really only interested in MEG that is probably a secondary concern (it would be important if you were doing e.g. a thickness study) cheers Bruce On Fri, 25 Apr 2014, Jon Houck wrote: Hi all, I

Re: [Freesurfer] Catastrophic Surface Inaccuracies

Hi Jon in this kind of case the default method did the wrong thing (closing the hole instead of cutting the handle). You need to identify the incorrectly segmented voxels that cause the spurious correction and delete them from the wm.mgz, then run autorecon2-wm autorecon3 cheers Bruce On F