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 FLOAT32dim1
212dim2 320dim3 320dim4 1datatype
16pixdim1 0.800000pixdim2 0.800000pixdim3 0.800000pixdim4
0.011000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+
fslinfo Right_Thalamus.nii.gz data_type INT32dim1 256dim2
256dim3 256dim4 1datatype 8pixdim1
1.000000pixdim2 1.000000pixdim3 1.000000pixdim4
0.011000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+
fslinfo dtifit_FA.nii.gz data_type FLOAT32dim1 128dim2
128dim3 60dim4 1datatype 16pixdim1
1.750000pixdim2 1.750000pixdim3 2.000001pixdim4
1.000000cal_max 1.0000cal_min 0.0000file_type NIFTI-1+
Specifically I have
1. Registered FreeSurfer conformed structural space to diffusion spacenet della
T1 e rinominarla come struct_brain
struct<->freesufertkregister2 --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<-->freesurferflirt -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 --lobesStrictmri_annotation2label --subject Control02
--annotation lobesStrict --hemi rh --outdir
$SUBJECTS_DIR/labelproducerh.frontal.labelrh.occipital.labelrh.parietal.labelrh.temporal.label
cd $SUBJECTS_DIR/surfmris_convert rh.white rh.white.giimris_convert lh.white
lh.white.giiecho $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.txtlabel2surf -s rh.white.gii -o rh.frontal.gii -l
listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.occipital.gii -l
listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.parietal.gii -l
listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.temporal.gii -l
listOfAreas_right.txtlabel2surf -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.txtlabel2surf -s lh.white.gii -o lh.frontal.gii -l
listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.occipital.gii -l
listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.parietal.gii -l
listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.temporal.gii -l
listOfAreas_right.txtlabel2surf -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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/
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The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
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recipient, be advised that any unauthorized use, disclosure, copying or the
taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone
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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.
