[Freesurfer] Search angle limitation in the flirt registration

search. But I still don't quite understand how rx,ry and rz are defined and how negative and positive angles affect the result. Because sometimes I find the result after the angle limitation does not align well with my expectation of rotation angle. Thank you for your help, Yixin Ma Brain Image

[Freesurfer] co-registration between slab of DTI image

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about coregistration between a thin oblique coronal slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size anatomical image (volume size is 256x256x256), with additional whole brain low-resolution

[Freesurfer] Hippocampus subfield division error

External Email - Use Caution Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an error message as attached, could you please help me with which part might have gone wrong? This subject's other recon-all worked but not

Re: [Freesurfer] Hippocampus subfield division error

regards, Yixin -- Forwarded message - From: Yixin Ma Date: Fri, Jan 18, 2019 at 11:04 AM Subject: Hippocampus subfield division error To: Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an error message as attached

Re: [Freesurfer] Hippocampus subfield division error

e. I'm not sure what kinds of file do you want, so I uploaded the folder of the FreeSurfer reconstruction results, as attached. Thank you again for your help. Best regards, Yixin On Fri, Jan 18, 2019 at 12:28 PM Yixin Ma wrote: > Hi, > > The hippocampus subfields division problem happe

[Freesurfer] DKT40 classifier atlas

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask how can I reconstruct the DKT40 classifier atlas. Is it included in recon -all? Thank you for your help. Best regards, Yixin Ma ___ Freesurfer mailing list

[Freesurfer] Hippocampus cortical layers division

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cortical regions with the help of freesurfer. When generating cortical layers for other neocortex brain region, the surface

[Freesurfer] hippocampus cortex surface

External Email - Use Caution Hi Freesurfer experts, After running the segmentation of hippocampus subfields, I'm wondering if I can get the surface of the gray matter and white matter of hippocampus in addition to subfields. My goal is to divide the hippocampus cortex into

[Freesurfer] hippocampus subfield division

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about the hippocampus subfield division again. Last time, I gave you an example of the subject that I failed to run the hippocampal subfield division, and you told me that you were able to run the hippocampus

[Freesurfer] Run FreeSurfer recon-all on isoDWI

Message-ID: <14b89d9d-130f-08f0-d593-71f2cdef3...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" you are trying to run a DWI image through recon-all? Sorry, it can only take T1w right now On 3/12/2020 3:28 PM, Yixin Ma wrote: > > External Email - Use C

[Freesurfer] mri_surf2vol method one

External Email - Use Caution Hi Freesurfer experts, I'm trying to write the normals of the GM/WM meshes to the entire ribbon. We usually do it by: 1) Generate normal files from rh.white and lh.white mris_convert rh.white rh.white.gii mris_convert -n rh.white

[Freesurfer] Transform a surface (e.g., lh.white) with a register.dat (12 dof)

External Email - Use Caution Hi FreeSurfer developer, I want to transform surfaces files (lh.white, lh.pial, rh.white, and rh.pial) with a registration matrix that has 12 degrees of freedom. Is there a function in FreeSurfer that can do so? Very best, Yixin Ma