For the input,I try using this command:
# recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning
It returns the following error:
# ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force
...
that means the subject already exists, probably from a previous run that failed. Did you try running it with -force? On Wed, 14 Apr 2010, Christophe Chênes wrote:
For the input,I try using this command:
# recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning
It returns the following error:
# ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force
...
I try with -force and it works. But I want my parcelations have the same orientation as the input Nifti image...
Le 14 avril 2010 15:23, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :
that means the subject already exists, probably from a previous run that failed. Did you try running it with -force?
On Wed, 14 Apr 2010, Christophe Chênes wrote:
For the input,I try using this command:
# recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning
It returns the following error:
# ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force
...
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you mean the aseg+aparc.mgz? They should be in the same orientation as the input images, but if you want them to have the same voxel geometry you can use either mri_convert --reslice_like or mri_vol2vol.
cheers Bruce On Mon, 19 Apr 2010, Christophe Chênes wrote:
I try with -force and it works. But I want my parcelations have the same orientation as the input Nifti image...
Le 14 avril 2010 15:23, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :
that means the subject already exists, probably from a previous run that failed. Did you try running it with -force?
On Wed, 14 Apr 2010, Christophe Chênes wrote:
For the input,I try using this command:
# recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning
It returns the following error:
# ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force
...
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Christophe Chênes