Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Harms, Michael Tue, 29 Apr 2014 13:26:25 -0700

Yes, the S/I/A/P labels are all correct. (Can never tell with R/L).

So, FSLview is reading the orientation info correctly. Orientation, as coded in the NIFTI, is a completely separate issue from how a given viewing tool chooses to display the data. You may not like the manner in which FSLview displays the data, but it is respecting the orientation info.

cheers,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mha...@wustl.edu

From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 3:20 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Please, see the snapshot attached. A/P/S/I/L/R labels seem correct. What do you think about?

Thanks,

Stefano

----Messaggio originale----
Da: mha...@wustl.edu
Data: 29-apr-2014 21.13
A: "std...@virgilio.it"<std...@virgilio.it>, "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael"<mha...@wustl.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Yes, they need to be the same dimensions to overlay in FSLview.

Run 'mri_convert' on orig.mgz, and you should be able to underlay the orig.

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mha...@wustl.edu

From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 2:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no.

fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)

data_type FLOAT32

dim1 212

dim2 320

dim3 320

dim4 1

datatype 16

pixdim1 0.800000

pixdim2 0.800000

pixdim3 0.800000

pixdim4 0.011000

cal_max 0.0000

cal_min 0.0000

file_type NIFTI-1+

fslinfo Right_Thalamus.nii.gz

data_type INT32

dim1 256

dim2 256

dim3 256

dim4 1

datatype 8

pixdim1 1.000000

pixdim2 1.000000

pixdim3 1.000000

pixdim4 0.011000

cal_max 0.0000

cal_min 0.0000

file_type NIFTI-1+

fslinfo dtifit_FA.nii.gz

data_type FLOAT32

dim1 128

dim2 128

dim3 60

dim4 1

datatype 16

pixdim1 1.750000

pixdim2 1.750000

pixdim3 2.000001

pixdim4 1.000000

cal_max 1.0000

cal_min 0.0000

file_type NIFTI-1+

Specifically I have

1. Registered FreeSurfer conformed structural space to diffusion space

net della T1 e rinominarla come struct_brain

struct<->freesufer

tkregister2 --mov $SUBJECTS_DIR/mri/orig.mgz --targ $SUBJECTS_DIR/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit

convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat

fa<-->freesurfer

flirt -in $SUBJECTS_DIR/dmri/dtifit_FA.nii.gz -ref struct_brain -omat fa2struct.mat

convert_xfm -omat struct2fa.mat -inverse fa2struct.mat

convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat

convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat

convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat

2. Creating a label file from FreeSurfer

mri_binarize --i aparc+aseg.mgz --match 49 --o Right_Thalamus.nii.gz

mri_annotation2label --subject Control02 --hemi rh --outdir $SUBJECTS_DIR/label --lobesStrict --lobesStrict

mri_annotation2label --subject Control02 --annotation lobesStrict --hemi rh --outdir $SUBJECTS_DIR/label

produce

rh.frontal.label

rh.occipital.label

rh.parietal.label

rh.temporal.label

cd $SUBJECTS_DIR/surf

mris_convert rh.white rh.white.gii

mris_convert lh.white lh.white.gii

echo $SUBJECTS_DIR/label/rh.frontal.label $SUBJECTS_DIR/label/rh.occipital.label $SUBJECTS_DIR/label/rh.parietal.label $SUBJECTS_DIR/label/rh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt

label2surf -s rh.white.gii -o rh.frontal.gii -l listOfAreas_right.txt

label2surf -s rh.white.gii -o rh.occipital.gii -l listOfAreas_right.txt

label2surf -s rh.white.gii -o rh.parietal.gii -l listOfAreas_right.txt

label2surf -s rh.white.gii -o rh.temporal.gii -l listOfAreas_right.txt

label2surf -s rh.white.gii -o rh.Right_Thalamus.gii -l listOfAreas_right.txt

echo $SUBJECTS_DIR/label/lh.frontal.label $SUBJECTS_DIR/label/lh.occipital.label $SUBJECTS_DIR/label/lh.parietal.label $SUBJECTS_DIR/label/lh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt

label2surf -s lh.white.gii -o lh.frontal.gii -l listOfAreas_right.txt

label2surf -s lh.white.gii -o lh.occipital.gii -l listOfAreas_right.txt

label2surf -s lh.white.gii -o lh.parietal.gii -l listOfAreas_right.txt

label2surf -s lh.white.gii -o lh.temporal.gii -l listOfAreas_right.txt

label2surf -s lh.white.gii -o lh.Right_Thalamus.gii -l listOfAreas_right.txt

----Messaggio originale----
Da: mha...@wustl.edu
Data: 29-apr-2014 20.56
A: "std...@virgilio.it"<std...@virgilio.it>, "Harms, Michael"<mha...@wustl.edu>, "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy.

It is very unlikely that FSLview is ignoring the orientation information.

cheers,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mha...@wustl.edu

From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 1:52 PM
To: "Harms, Michael" <mha...@wustl.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Hi Michael,

please, see the file attached. They are reffered to FS and FSL visualization of the same file (R_thalamus overlapped on T1).

Thanks,

Stefano

----Messaggio originale----
Da: mha...@wustl.edu
Data: 29-apr-2014 20.32
A: "std...@virgilio.it"<std...@virgilio.it>, "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Is the brain merely shown "sideways" in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation.

cheers,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mha...@wustl.edu

From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 29, 2014 1:19 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Hi Bruce,

in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results.

Thanks,

Stefano

----Messaggio originale----
Da: gr...@nmr.mgh.harvard.edu
Data: 29-apr-2014 17.52
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

How do you know the orientation is wrong? Is it right in tkmedit?

On 04/29/2014 10:23 AM, std...@virgilio.it wrote:
> My apologies, how can I visualize mri_binarize output? I tried in
> fslview but orientation is wrong. Different orientation is a file's
> feature or swapdim is request?
>
> Thanks,
>
>
> Stefano
>
>
> ----Messaggio originale----
> Da: fis...@nmr.mgh.harvard.edu
> Data: 29-apr-2014 16.01
> A: <std...@virgilio.it>, "Freesurfer support
> list"<freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL
>
> Hi Stefano
>
> you can use either mri_binarize --match or mri_extract_label with labels
> 10 and 49 (which I got from FreeSurferColorLUT.txt)
>
> cheers
> Bruce
> On Tue, 29 Apr 2014,
> std...@virgilio.it wrote:
>
> > Hi list,
> > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it
> as seed
> > mask in probtrackx.
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >_______________________________________________
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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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
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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

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