Re: [Freesurfer] hippocampal subfield segmentation

External Email - Use Caution Hi Juan, Thank you for the quick reply. I tried unsetting my PATH and LD_LIBRARY_PATH, butI am still getting the kvlAutoCrop error:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlApplyTransform: line 3: kvlApplyTransform.bin: command

Re: [Freesurfer] Manually editing location of surface

External Email - Use Caution Thank you for getting back to me. I am attaching an example of one of the problems I am encountering. On Tue, Aug 21, 2018 at 8:57 AM Bruce Fischl wrote: > Hi Elena > > can you send us an image to show us what the issue is? The correct >

Re: [Freesurfer] hippocampal subfield segmentation

External Email - Use Caution Hi Ryan, Is it possible that you're mixing versions of FreeSurfer in your PATH and/or LD_LIBRARY_PATH? Maybe you could try unsetting them before you source FreeSurfer? Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical Image Computing

[Freesurfer] Calculating Gray Matter Density

External Email - Use Caution Hello, Does FreeSurfer have an option for calculating gray matter density during recon-all, or does one need to calculate it manually? In that case, what is the formula? The reason I would like to compute density is to replicate the effects show in

[Freesurfer] hippocampal subfield segmentation

External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory

Re: [Freesurfer] Lesion segmentation

External Email - Use Caution Thank you so much for your response, Bruce. Mo On Tue, Aug 21, 2018 at 12:04 PM, Bruce Fischl wrote: > Hi Mo > > lesion is basically anything that makes the tissue darker, so most of the > things you described. For jsut a straight T1 in recon-all

Re: [Freesurfer] Lesion segmentation

Hi Mo lesion is basically anything that makes the tissue darker, so most of the things you described. For jsut a straight T1 in recon-all the algorithm is just the standard aseg. If you have a T2 or flair and maybe a PD you can use the lesion segmentation algorithms that Emily Lindemer

Re: [Freesurfer] Manually editing location of surface

Hi Elena can you send us an image to show us what the issue is? The correct intervention depends on why the surface is not correct. cheers Bruce On Fri, 17 Aug 2018, Elena Nicole Dominguez wrote: External Email - Use Caution Hello FreeSurfer Developers, On the tutorial

Re: [Freesurfer] Fwd: vertex MNI305

External Email - Use Caution thanks Ruopeng for your speedy response! And this are indeed in MNI305? Bruce was fairly certain but I just wanted to confirm. best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Aug 21, 2018 at

Re: [Freesurfer] Flipped left to right hemisphere subjects

please include previous emails so that we know what your original question was On 08/21/2018 11:12 AM, Lutz,Olivia (BIDMC - Psychiatry) wrote: > > Hi Doug, > > > Yes the brainmask volume is left-right reversed as well. > > > Thanks! > > Olivia > > >

Re: [Freesurfer] Fwd: vertex MNI305

I think the coordinate circled in the picture is the exact coordinate of the vertex, also in surface ras. The coordinate under "SurfaceRAS" is the coordinate of the current cursor location in surface ras. The slight difference is because the cursor is not exactly on the vertex, but close

[Freesurfer] Flipped left to right hemisphere subjects

Hi Doug, Yes the brainmask volume is left-right reversed as well. Thanks! Olivia This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from

[Freesurfer] Fwd: vertex MNI305

External Email - Use Caution Hi there Doug can you please confirm? Bruce said you would be the best to answer and I've got revisions that are due. Please see the image attached. In my manuscript I report the x,y,z next to the vertex number in Freeview for MNI coordinates (MNI305)