Hello all,
I have a related question as I am also a freesurfer beginner and
starting to use it on submilliter MP2RAGE 7T images.
After having had a quick look at the videos, tutos and the archives, I
found this: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
BTW on that page I guess that the line:
"recon-all -mprage -normalization -skulstrip -s $SUBJ"
should read
"recon-all -mprage -normalization *-skullstrip* -s $SUBJ"
For a test run and to familiarize mysef with freesurfer and the trouble
shooting steps, I ran the "basic" recon-all on one of the native images
which gave me results at a 1 mm res.
My question is: is there any reason why these steps should work
differently for a MP2RAGE compared to the MPRAGE described the
HiResRecon page?
For testing, I am currently running the steps in the page mentioned
above on one image for practice before running more subjects.
So far, so good but the following command:
mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o
$SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm
0.15 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm
issued the following warning:
"Use of ?PATTERN? without explicit operator is deprecated at
~/Program/freesurfer/mni/bin/sharpen_volume line 153."
Thanks
*Remi Gau
*
On 09/04/14 21:57, Torrisi, Sam (NIH/NIMH) [F] wrote:
Good afternoon gurus-
I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with
AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to
1mm. Now I have basically the same sentiment and question as this thread from
~2 years ago (i’m linking to the middle for simplicity):
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html
What’s the very latest on this? Thanks!
-Salvatore (Sam) Torrisi
Section on the Neurobiology of Fear and Anxiety
National Institute of Mental Health
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