The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files
/usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
The former exists where it should, the latter does not exist at that location, although it can be downloaded from
http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e.
/usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
Could someone with the appropriate permissions please copy that file to where recon-all expects to find it?
Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?
Hi Steve
I think recon-all -deface only creates the orig_defaced.mgz which you can then use with mri_mask to remove facial features from whatever volumes you want.
I don't have write permissions to that directory, but I'll see if I can get help to copy it.
cheers Bruce
On Wed, 29 May 2013, slehar@nmr.mgh.harvard.edu wrote:
The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files
/usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
The former exists where it should, the latter does not exist at that location, although it can be downloaded from
http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e.
/usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
Could someone with the appropriate permissions please copy that file to where recon-all expects to find it?
Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
I see that somebody copied talairach_mixed_with_skull.gca to
/usr/local/freesurfer/stable5/average/
thank you, but FreeSurfer seems to be looking for it here:
/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca
Could you please have someone copy it there too?
Here is the error.log from the mri/ directory:
GCAread(/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca): could not open file
Steve
Hi Steve
I think recon-all -deface only creates the orig_defaced.mgz which you can then use with mri_mask to remove facial features from whatever volumes you want.
I don't have write permissions to that directory, but I'll see if I can get help to copy it.
cheers Bruce
On Wed, 29 May 2013, slehar@nmr.mgh.harvard.edu wrote:
The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files
/usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
The former exists where it should, the latter does not exist at that location, although it can be downloaded from
http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e.
/usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
Could someone with the appropriate permissions please copy that file to where recon-all expects to find it?
Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sure On Mon, 3 Jun 2013, slehar@nmr.mgh.harvard.edu wrote:
Hi Bruce,
I see that somebody copied talairach_mixed_with_skull.gca to
/usr/local/freesurfer/stable5/average/
thank you, but FreeSurfer seems to be looking for it here:
/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca
Could you please have someone copy it there too?
Here is the error.log from the mri/ directory:
GCAread(/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca): could not open file
Steve
Hi Steve
I think recon-all -deface only creates the orig_defaced.mgz which you can then use with mri_mask to remove facial features from whatever volumes you want.
I don't have write permissions to that directory, but I'll see if I can get help to copy it.
cheers Bruce
On Wed, 29 May 2013, slehar@nmr.mgh.harvard.edu wrote:
The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files
/usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
The former exists where it should, the latter does not exist at that location, although it can be downloaded from
http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e.
/usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
Could someone with the appropriate permissions please copy that file to where recon-all expects to find it?
Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
slehar＠nmr.mgh.harvard.edu