Re: [Freesurfer] non-brain region

Hi Ramesh, Unless these non-brain regions affect the surfaces then it is fine to leave it as is. Your image looks fine to me. Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging

Re: [Freesurfer] PET partial volume correction:mri_gtmpvc error

Hi  Elena, it looks like the aseg.mgz has several unexpected segments in it. The aseg.auto.mgz looks ok, so I think FS is working properly. It looks like you made some changes to the aseg. What did you do? On 12/06/2017 03:51 PM, Douglas N Greve wrote: > Did you run this through the standard FS

[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess

Thanks once again for all the help on this. I am running the GLM in native space, typically so that I can get the beta values to use in an MVPA analysis. So it sounds like if you specify per-run motion-correction and registration, and don't tell it to resample to anything (e.g., the MNI brain or th

Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess

yes and yes On 12/07/2017 02:23 PM, Taylor, Johnmark wrote: > Thanks once again for all the help on this. I am running the GLM in > native space, typically so that I can get the beta values to use in an > MVPA analysis. So it sounds like if you specify per-run > motion-correction and registrat

Re: [Freesurfer] Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors

Dear all, We are seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and brain tumors. Our team includes full-time faculty from Ps

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, Have you take a look at our data? Have you find any possible cause? We need to continue with our analysis and it is now stopped. Thanks you in advance, M del Mar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harva

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, I think I’ve found the cause - it’s due to a small bug in make_average_surface. I should have a fix for you soon (today or tomorrow). best, Andrew > On Dec 7, 2017, at 3:47 PM, M del Mar Velasco wrote: > > Hi, > > Have you take a look at our data? Have you find any possible caus

Re: [Freesurfer] mri_vol2surf wrong hemisphere

Hi Doug, FSLView gives a label of L and R and the parcels on the LH in fslview match the LH parcels in their included Excel spreadsheet. That's really all the verification I have for it right now. It's possible they switched the hemispheres when they made the original parcellation volume befor

Re: [Freesurfer] A note about the Freesurfer license file

I am getting this same glibc message with Freesurfer 6. Unfortunately I have tried twice now to re-register and updated the license file to the new file that gets emailed to me, but I am still getting the same error. Any ideas what else I can try to troubleshoot this issue? -Mike __

[Freesurfer] [Re] Infant Atlas {Disarmed}

Hi Emma Thanks for your reply~ As I am not major in neuroscience, maybe it is quite hard for me to label the image. But thanks a lot and I will try. Would you please help me: 1. The link you provided mentions a new pipeline for infants. Is it integrated with specific infant .gcs atlas file

[Freesurfer] IndexError: list index out of range

Hello everyone, I am trying to run a cortical thickness analysis in QDEC. I have recon-all and qcache but while trying to run asegstats2table, I keep getting the error-list index out of range. asegstats2table --subjects 101 102 103 INSP104 INSP105 INSP107 INSP108 INSP109 112 113 114-S 115-S 116-S