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.mgz
INFO: could not find ...mat file for direction cosine infoINFO: 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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.