I highlighted some difference. frontal_rh.nii.gz data_type INT32dim1 256dim2 256dim3 256dim4 1datatype 8pixdim1 1.0000000000pixdim2 1.0000000000pixdim3 1.0000000000pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ T1.nii.gz data_type UINT8dim1 256dim2 256dim3 256dim4 1datatype 2pixdim1 1.0000000000pixdim2 1.0000000000pixdim3 1.0000000000pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_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
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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:
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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/
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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/
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