Is that an MP2RAGE? The background may be messing things up. You can try masking it, eg, mri_synthstrip --i yourimage.mgz --o stripped.mgz Then pass stripped.mgz to recon-all
On 3/25/2024 6:33 AM, Chen Yang wrote: > External Email - Use Caution > > Dear FreeSurfer Developers, > > I am trying to do the processing for structural MRI data. I found that part > of brain is missing in one data (see Fig.1). Then I tried to change the > watershed parameter, but it didnt work at all (no matter which number I use), > the brainmask looks the same as before. So I did the manual editing, cloned > voxel from T1.mgz to brainmask.mgz. Then I run the -autorecon-pial, but it > froze in this step - fix topology. I checked 'wm.mgz', it contained a lot > skull and a lot of WM are missing (see Fig.2). > > I also tried to manually edit the brainmask.mgz and wm.mgz, then run > '-autorecon-wm' but it also froze in -fix topology. I put other might > relevant information in the end. > > I've searched in the mail archive but didn't find similar errors. I am not > sure if I did anything wrong. Does anyone have any thoughts on how to > trouble-shoot this problem? Also, Ive attached the recon-all.log in case it's > of any use. > > Thanks in advance! > > Best regards, > Chen > > > Other might relevant Information: > 1) Coil element is wrong. 'HE2,4;NE2'. > 2) I got an error message when I wad doing the recon-all first time: > watershed error: indices out of bounds. Then I added the command line > 'mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz > $mir/nu.mgz' based on this page > <https://secure-web.cisco.com/1uRXBiwoaszcFJpp3kKMMx2gS1DnuVTXjdvnMG63iVHxJH2XGF0dCvmMKVp2swPgw-Q5RowX74VPXTsaoKLSS2Rmu5Pd-SDQsw2BQzxF8osbt1Dakytp76YGXCvMDmbByZZeirztT2fl_whUrGTKUgdoSu8v36oB7Jyj8bSOGAbhlZX0rjXNPkKVaLjRmD90IdK-Do1bX3PACP5rlDCfAWcxs4o36dI_w8XeLl-s15fCghCVKm8OG6t6r95W8MVvikTff7rCZ7gvmOiJWvUYKVASGyL44tc-bDq3xyUcIMjKgkTZiorrroLXYMk0zhjH04eLy9f8kcogobac7caE1WQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg40730.html>. > Then I got another error message in recon-all: mri_em_register: could not > open brainmask.mgz so I added some cp to nu.mgz. It worked but the part of > brain is missing, as I mentioned in the beginning (Fig.1). > > > 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 > 2) Platform: Linux 5.10.0-28-amd64 > 3) uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 > (2024-01-31) x86_64 GNU/Linux > 4) recon-all.log: see attached > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
