If I not change the output orientation the .nii.gz is wrong (please see attached file).

mri_convert --in_type mgz --out_type nii T1.mgz T1.nii.gz


----Messaggio originale----
Da: greve@nmr.mgh.harvard.edu
Data: 5-set-2013 1.09
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Mask from cortical parcellation

Don't change the output orientation in mri_convert

On 09/04/2013 07:05 PM, stdp82@virgilio.it wrote:
> T1.mgz is corrected in tkmedit.
>
> When I added also frontal_rh.nii.gz
>
> tkmedit Diff01 orig.mgz frontal_rh.nii.gz
>
> Error: Loading Surface frontal_rh.nii.gz
> Couldn't load the surface.
> Tkmedit couldn't read the surface you specified. This could be because
> the file wasn't a surface type that tkmedit recognizes or the file was
> unreadable due to permissions.
>
> This is the command lines that I used for mri_binarize:
> mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1018 1019 1020
> 1026 1027 1028 1032 --o frontal_rh.nii.gz
>
> and for mri_convert:
> mri_convert --in_type mgz --out_type nii --out_orientation RAS T1.mgz
> T1.nii.gz
>
> Thanks,
>
>
> Stefano
>
> ----Messaggio originale----
> Da: greve@nmr.mgh.harvard.edu
> Data: 5-set-2013 0.49
> A: <stdp82@virgilio.it>
> Cc: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Mask from cortical
> parcellation
>
>
> first, display it in tkmedit and verify that it is incorrect there. If
> it is correct, then the problem is in your viewer
> If it is incorrect, send me the command lines you used for mri_binarize
> and mri_convert
>
>
> On 09/04/2013 06:46 PM, stdp82@virgilio.it wrote:
> > I have used mri_convert to obtain T1.nii.gz from T1.mgz.
> > I attached the image that shows what's happened when I have overlayed
> > the frontal mask (obtained by mri_binarize) on T1.nii.gz.
> >
> > Thanks,
> >
> >
> > Stefano
> >
> > ----Messaggio originale----
> > Da: greve@nmr.mgh.harvard.edu
> > Data: 5-set-2013 0.07
> > A: <stdp82@virgilio.it>
> > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > Ogg: Re: [Freesurfer] R: Re: R: R: Re: Mask from cortical parcellation
> >
> >
> > use the orig.mgz or any of the other FS volumes
> >
> > On 09/04/2013 05:48 PM, stdp82@virgilio.it wrote:
> > >
> > > I'd like to perform probtrackx (FSL) from seed (subcortical) to target
> > > (cortical) masks.
> > >
> > > To this aim, I should trasform all cortical and subcortical masks
> > > obtained by FS on MNI space.
> > >
> > > Therefore, firstly,  I'd like to overlay the masks that I obtained by
> > > mri_binarize on the structural image to check the masks.
> > >
> > > Next, I'd like to apply FLIRT to trasform all masks in a common
> > > MNI152_1mm space.
> > >
> > > My problem is " which is the T1.nii.gz that can I use to overlay the
> > > cortical masks created by mri_binarize?"
> > >
> > >
> > > Thanks,
> > >
> > >
> > > Stefano
> > >
> > >
> > >
> > > ----Messaggio originale----
> > > Da: greve@nmr.mgh.harvard.edu
> > > Data: 4-set-2013 23.28
> > > A: <stdp82@virgilio.it>
> > > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > > Ogg: Re: [Freesurfer] R:  R: Re:  Mask from cortical parcellation
> > >
> > > I don't understand your question. Can you elaborate?
> > > On 09/04/2013 05:27 PM, stdp82@virgilio.it wrote:
> > > > I mean anatomical.nii.gz with the same spatial features of the
> masks.
> > > >
> > > > Thanks,
> > > >
> > > >
> > > > Stefano
> > > >
> > > > ----Messaggio originale----
> > > > Da: stdp82@virgilio.it
> > > > Data: 4-set-2013 23.02
> > > > A: <greve@nmr.mgh.harvard.edu>, <freesurfer@nmr.mgh.harvard.edu>
> > > > Ogg: [Freesurfer] R: Re: Mask from cortical parcellation
> > > >
> > > > Thank you very much.
> > > >
> > > > A last help, please. How is the anatomical file that I can use to
> > > > overlay the masks. I'm noting that masks are characterized by:
> > > > data_type      INT32
> > > > dim1           256
> > > > dim2           256
> > > > dim3           256
> > > > dim4           1
> > > > datatype       8
> > > > pixdim1        1.0000000000
> > > > pixdim2        1.0000000000
> > > > pixdim3        1.0000000000
> > > > pixdim4        0.0109999999
> > > > cal_max        0.0000
> > > > cal_min        0.0000
> > > > file_type      NIFTI-1+
> > > >
> > > > Regards,
> > > >
> > > >
> > > > Stefano
> > > >
> > > > ----Messaggio originale----
> > > > Da: greve@nmr.mgh.harvard.edu
> > > > Data: 4-set-2013 17.10
> > > > A: <freesurfer@nmr.mgh.harvard.edu>
> > > > Ogg: Re: [Freesurfer] Mask from cortical parcellation
> > > >
> > > >
> > > >
> > > > you can use mri_binarize on aparc+aseg, eg, something like
> > > >
> > > > mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o
> > > > frontal.nii.gz
> > > >
> > > > those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt
> > > > That table has a lot of ROIs in it, and not all will be in the
> > > > aparc+aseg. You'll be interested in the ones between 1000-1035 and
> > > > 2000-2035
> > > >
> > > > doug
> > > >
> > > >
> > > >
> > > >
> > > > On 09/04/2013 08:46 AM, stdp82@virgilio.it wrote:
> > > > > Hi list,
> > > > >
> > > > > I need to create a mask of frontal, parietal, temporal and
> occipital
> > > > > lobes in a subject by using cortical parcellation output.
> > > > >
> > > > > Is it possible? Eventually, how can I transform these masks
> file to
> > > > > mii.gz (to import them in FSL analysis).
> > > > >
> > > > > Thank you very much.
> > > > >
> > > > > Regards,
> > > > >
> > > > >
> > > > > Stefano
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > > --
> > > > Douglas N. Greve, Ph.D.
> > > > MGH-NMR Center
> > > > greve@nmr.mgh.harvard.edu
> > > > Phone Number: 617-724-2358
> > > > Fax: 617-726-7422
> > > >
> > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > >
> > > > _______________________________________________
> > > > 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.
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer