Hello Freesurfers,
I am interested in taking a volume file that is in fsaverage MNI305 space and converting this volume to each subject's volume. How can this be done?
Thanks!
Best, Omar
mri_vol2vol should do the trick using the inverse (I think) of the mri/transforms/talairach.xfm file. Doug can confirm
cheers Bruce On Thu, 20 Mar 2014, Omar Singleton wrote:
Hello Freesurfers,
I am interested in taking a volume file that is in fsaverage MNI305 space and converting this volume to each subject's volume. How can this be done?
Thanks!
Best, Omar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, so I can use the following command to go from MNI305 to subject space?
mri_vol2vol --mov AL15/mri.2mm/orig.mgz --targ lh.AItou_fs_2mm.nii.gz --reg AL15/mri/transforms/talairach.xfm --invertmtx --inv --o lh.aitou.ac15.2mm.nii.gz
I ran that command and got this error:
regio_read_register(): Success Error reading inplaneres from AL15/mri/transforms/talairach.xfm
Matrix from regfile: MatrixPrint: mat = NULL!
I am also trying to convert from MNI152 to subject space. Can I use these commands below to convert from MNI305 to subject space as well by substituting the talairach.xfm file for the reg.mni152.2mm.dat file?
I tried to do what this previous question suggested:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-December/034722....
I tried to create a registration matrix from subject space to MNI152:
mni152reg --s AL15
However, this error appeared:
... mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345': Permission denied ... writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii
I would then have used this command:
mri_label2vol --seg lh.AItou.nii.gz --reg AL15/mri/transforms/reg.mni152.2mm.dat --invertmtx --o lh.aitou.AL15.2mm.nii.gz --temp AL15/mri/orig.mgz
How can I make the mni152reg command work?
Thanks!
Best, Omar
mri_vol2vol should do the trick using the inverse (I think) of the mri/transforms/talairach.xfm file. Doug can confirm
cheers Bruce On Thu, 20 Mar 2014, Omar Singleton wrote:
Hello Freesurfers,
I am interested in taking a volume file that is in fsaverage MNI305 space and converting this volume to each subject's volume. How can this be done?
Thanks!
Best, Omar _______________________________________________ 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
When you say the MNI305 space, do you mean the 2mm space that is the output of FSFAST? If so, then first run reg-mni305.2mm to create the appropriate registration file. Then use this registration file when running mri_vol2vol
doug
On 03/20/2014 02:39 PM, Omar Singleton wrote:
Hello Freesurfers,
I am interested in taking a volume file that is in fsaverage MNI305 space and converting this volume to each subject's volume. How can this be done?
Thanks!
Best, Omar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Omar Singleton