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.mgz
INFO: could not find ...mat file for direction cosine info INFO: use ANALYZE 7.5 hdr -> 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 onT1 (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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