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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 > 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 > addressed. If you believe this e-mail was sent to you in error and the > 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. > > > > > _______________________________________________ > 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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. |
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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.
