Thank you very much Michael.
Now I'm running probtrackx, I will update you.

Stefano





----Messaggio originale----

Da: mha...@wustl.edu

Data: 29-apr-2014 22.25

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











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

> >

> >_______________________________________________

> Freesurfer mailing list

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> 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.

>

>

>

>

> _______________________________________________

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> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

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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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 
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immediately notify the sender via telephone
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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 
intended
 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
 or return mail.










 



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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taking of any action in reliance on the contents of this information is 
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immediately notify the sender via telephone
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