You still have not indicated teh full filename. Your target is: $SUBJECTS_DIR/cvs_avg35_inMNI152 You need to indicate the full path (to the norm.mgz file) as I mentioned in my previous email.

Lilla

On Wed, 7 Aug 2013, Barron, Daniel S wrote:

Hi Lilla,

Thanks for your reply. I'm working off a network server and so copied the cvs_avg35_inMNI152 folder (and all contents) into my $SUBJECTS_DIR

My script is:

mri_vol2vol --targ $SUBJECTS_DIR/cvs_avg35_inMNI152 --m3z $SUBJECTS_DIR/NC001/cvs_avg35_inMNI152/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.m3z --noDefM3zPath --mov $SUBJECTS_DIR/NC001/labels/lh.hipp.nii.gz --o $SUBJECTS_DIR/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz --interp nearest --no-save-reg Using the m3z file as it is; no assumed location. movvol /media/users/barrond/NYU/Freesurfer/NC001/labels/lh.hipp.nii.gz targvol /media/users/barrond/NYU/Freesurfer/cvs_avg35_inMNI152 outvol /media/users/barrond/NYU/Freesurfer/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1375992019 corRead(): can't open file /media/users/barrond/NYU/Freesurfer/cvs_avg35_inMNI152/COR-.info

This still gives me the same error. I looked in the original cvs_avg35_inMNI152 folder downloaded from freesurfer and COR-.info is not there either. Where does this COR-.info file come in?

Cheers, Daniel

On Aug 6, 2013, at 6:46 PM, Lilla Zollei lzollei@nmr.mgh.harvard.edu wrote:

...

Hi Daniel,

You need to specify the full path to the target volume, the subject id is not sufficient. It should be somthing like this: $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz

Lilla

On Tue, 6 Aug 2013, Barron, Daniel S wrote:

...

Hi Freesurfers (Lilla),

I'm running v5.1.0 on a Mac trying to apply a cvs morph via the following function:

mri_vol2vol --targ cvs_avg35_inMNI152 --m3z $SUBJECTS_DIR/NC001/cvs_avg35_inMNI152/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.m3z --noDefM3zPath --mov $SUBJECTS_DIR/NC001/labels/lh.hipp.nii.gz --o $SUBJECTS_DIR/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz --interp nearest --no-save-reg Using the m3z file as it is; no assumed location. movvol /media/users/barrond/NYU/Freesurfer/NC001/labels/lh.hipp.nii.gz targvol cvs_avg35_inMNI152 outvol /media/users/barrond/NYU/Freesurfer/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1375994175 corRead(): can't open file /media/users/barrond/NYU/Freesurfer/cvs_avg35_inMNI152/COR-.info

I don't know what "COR-.info" is or how to make it. Could someone please point me in the right direction?

Cheers, Daniel

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.