I highlighted some difference.
frontal_rh.nii.gz
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+
T1.nii.gz
data_type UINT8
dim1 256
dim2 256
dim3 256
dim4 1
datatype 2
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 0.0109999999
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
----Messaggio originale----
Da: greve@nmr.mgh.harvard.edu
Data: 5-set-2013 1.25
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Mask from cortical parcellation
The orientation looks right to me, ie, the little letters on the side
that indicate direction are correct. The odd orientation that it is
displayed in is an fslview issue
On 09/04/2013 07:16 PM, stdp82@virgilio.it wrote:
> 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
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> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > 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
>
>
--
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/