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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
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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
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I'm curious if there are options to decrease computation time, even at the
expense of quality?
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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
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
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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
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
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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!
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informat
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
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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
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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:
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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
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