[Freesurfer] Fwd: Improved segmentation using 3D FLAIR

External Email - Use Caution Hello freesurfer users. I am a radiologist, who is trying to setup a protocol for freesurfer segmentation. I came to know that with 3D T2 weighted images, or 3D FLAIR images, I can get better surface segmentations, and based on search of previous archiv

[Freesurfer] Postdoctoral Position at the University of Zurich in Switzerland

External Email - Use Caution Description of the lab: The Methods of Plasticity Lab in the Department of Psychology (http://www.psychology.uzh.ch/en/chairs/plafor.html) is focussed on creating novel methods to advance the understanding about neuronal plasticity, and the mechanism

[Freesurfer] Options to decrease computation time

External Email - Use Caution I'm curious if there are options to decrease computation time, even at the expense of quality? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

Re: [Freesurfer] Fwd: Improved segmentation using 3D FLAIR

Hi Ho-Joon I'll cc Andre van der Kouwe who created the protocol. You generally need to match bandwidth and readout direction to match distortions. The bandwidth of the 3D FLAIR sequences if typically quite high, so for the T1 we usually go to multiple echoes like MEMPRAGE. I don't think we typ

Re: [Freesurfer] Options to decrease computation time

Hi Gregory I guess, although we don't recommend it. You could use expert opts to do this (increase the tolerance in the mri_ca_register step for example would decrease it). Many of the steps take a -tol switch that can be used to terminate the numerical minimization earlier. You can alwo ru

Re: [Freesurfer] Options to decrease computation time

External Email - Use Caution Hey, Not really reducing the computation time, but if you have enough ram and a good processor, you can run it in parallel. I have a mac with 6 Core Intel Xeon processor and 64 GB RAM. I can run up to 10 iterations on parallel and it works fine with

Re: [Freesurfer] Segmentation fault

Hi Jon – This log file also has output only from trac-all –path, and not from trac-all –prep. I’ll have to see the output from all steps. Thanks! a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Whitney, Jon" mailto:jon.whit...@ert.com>> Reply-To: Freesurfer support list

Re: [Freesurfer] Segmentation fault

External Email - Use Caution I probably deleted the log file prior to running the path step so I could focus on what was going on. I'll re-run it and give you the results when it finishes. Thanks! -- Notice: This e-mail message, together with any attachments, contains informat

Re: [Freesurfer] Freesurfer cortical parcellation not covering gray matter in depth

Hi Yixin it is pretty hard to parse these screen shots. Maybe you can just upload your entire subject dir to our ftp site and we can take a look? Did you do anything special to create the volumetric parcellation, or is it the standard one created by recon-all (e.g. aparc+aseg.mgz)? cheers Bru

[Freesurfer] preproc-sess not passing custom instem to rawfunc2surf-sess

External Email - Use Caution Hi FS Team, We've tried running preproc-sess using a custom instem, but it fails at rawfunc2surf-sess. From parsing the code a bit, it appears that while most of the x-sess scripts called in preproc-sess pass their respective outstem's as the instem t

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Hi Bruce Can confirm that both files (rh.area & rh.volume) load fine in freeview Thanks for the help! James From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 29 October 2018 15:

Re: [Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution Hi there, Thank you for directing me to the CMake fswiki. I was able to install the third party packages and execute the command `cmake . -DFS_PACKAGES_DIR="path/to/pkgs"`. However, when I run `make -j4` (after adjusting a few bash files in variou