Hi Paul
if you run mri_info on the orig.mgz and your new brainmask.mgz they should give you the same thing in terms of ras2vox and such
cheers
Bruce
On Mon, 28 Nov 2016, miracle ozzoude wrote:
This was the info from mri_convert when i converted my skull stripped volume to mgz
before replacing it with the brainmask from FS
mri_convert --in_type analyze --in_orientation LAS --out_type mgz --out_orientation LAS
brainmask.img brainmask.mgz
cp foldername/subjid/brainmask.mgz foldername/subjd/mri/brainmask INFO: could not find ...mat file for direction cosine infoINFO: use ANALYZE 7.5 hdr ->.mgz
hist.orient value: 0, transverse unflipped (default
INFO : if not valid, please provide the information ....... .mat file
analyzeRead() roi_scale 0.00000000
TR= 1000.00, TE = 0.00, TI = 0.00, flip angle = 0.00
setting input orientation to LAS
i_ras = (-1, 0, 0)
j_ras = (0,1,0)
k_ras = (0,0,1)
setting output orientation to LAS
writing to brainmask.mgz
why do i need the orig.mgz? I thought I only had to replace the brainmask.mgz (from FS)
with mine brainmask,mgz( from lesion explorer after i have renamed it to brainmask.mgz).
Also, I didn't use the "noskullstrip" flag like you suggested.
Best,
paul
On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
I mean after you have converted it
On Mon, 28 Nov 2016, miracle ozzoude wrote:
Thanks Bruce for the response. mri_info? do you mean when i
converted it from analyze to
mgz or when I ran recon-all autorecon2 after inserting it to
freesurfer.
On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
what is the output of mri_info on your new brainmask.mgz
and on say the
orig.mgz? You may need to conform you brainmask
On Mon, 28 Nov 2016, miracle ozzoude wrote:
Hello Freesurfer, I ran recon-all -autorecon 1 -s
subjID on T1
(T1_nii) image and after
that, I replaced the skull stripped volume generated
from FS with
the skull stripped
volume from lesion explorer ( using mri_convert
in_type analyze
in_orientation LAS
out-type img out_orientation LAS mgz; cp
folder/brainmask.mgz
folder/subjID/mri/brainmask.mgz). Then, I ran
recon-all
-autorecon2 -autorecon2 -s
subjID. My recon-all is stucked at
CORRECTION DEFECT 0 (vertices=49378, convex
hull=3422, v0 =0)
XL defect detected....
Please how do I resolve this problem?
I am running freesurfer-6 development. I have
attached the
recon-all/recon-all status to
the email.
Thank you very much
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