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
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 CautionDear 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:
- Coil element is wrong. 'HE2,4;NE2'.
- 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).
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
- Platform: Linux 5.10.0-28-amd64
- uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux
- recon-all.log: see attached
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Chen Yang -
Douglas N. Greve