Re: [Freesurfer] Defacing with mri_deface
sure On Mon, 3 Jun 2013, sle...@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, >> sle...@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 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.
Re: [Freesurfer] Defacing with mri_deface
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, > sle...@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 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.
Re: [Freesurfer] Defacing with mri_deface
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, sle...@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/$subjid/mri directory, or does it only > deface a copy of orig.mgz to orig_defaced.mgz? > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Defacing with mri_deface
The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that location, although it can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e. /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca Could someone with the appropriate permissions please copy that file to where recon-all expects to find it? Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$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 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.
