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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