Thank you very much Douglas,
I think that I probably miss something.
There is no error in the terminal but when i launch tksurfer, I have
the following screenshot (screen1). The overlay is loaded but the
coordinates are 0.00000 and the overlay is not in a different color
that the brain.
I have attached, in case, the brain file and the volumetric file.
As you can see, I have followed all the instructions :
1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
MNI152.dat --t1 --init-coreg
2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
--hemi lh --o ./multidem.mgh
3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1
Thank you,
Best,
Redwan Maatoug
Resident in psychiatry
Stanford University
Amit Etkin lab
On 13 March 2017 at 14:51, Douglas N Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>> wrote:
The file you created is not a label so don't try to load it with
-label.
Instead use -overlay file.mgh -fminmax .5 1
On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Sorry to bother you, again.
> Actually, my command was t1 and not t2 but even with t1 nothing
works.
> So if my command line is exact, do you think it is a problem with my
> files ?
>
> Thank you,
>
> Redwan Maatoug
> Resident in psychiatry
> Stanford University
> Amit Etkin lab
>
> On 13 March 2017 at 13:41, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>
> Use --t1 (I assume the --tw was supposed to be --t2, which is
> wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried to do, as you said.
> > I have used the brain image for the registration and then
I have
> > tried to convert my ROI nifti volumetric file into a
surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and I tried
> many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii
--reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> > <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>>> wrote:
> >
> > didn't I respond to this earlier this week? the images
> appear to be
> > binarized regions of interest and not whole (or ever
partial)
> > brain. To
> > run the registration, you will need an actual brain.
If you
> > created the
> > ROI from a brain image, then use that image to create
the reg,
> > then run
> > vol2surf using that reg with the ROI as input
> >
> >
> > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > Hi experts,
> > >
> > > I try to convert my volumetric nifti file to surface
files.
> > >
> > > My nifti volumetric file looks like : 1. screenshot
> > > I have first registered the volumetric file using
bbregister
> > with this
> > > command line :
> > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > segment_7.dat --t1
> > > --init-coreg*
> > >
> > > then I have used the following command line and the file
> looks like
> > > screenshot 1 attached :
> > > *tkregister2 --mov segment_7.nii --reg register7.dat
--surf*
> > >
> > > And after that, I have tried to convert my
volumetric file to
> > surface
> > > file with this command line :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> --hemi
> > lh --o
> > > ./segment_7-lh.nii --float2int round*
> > >
> > > But with this command when I load the file with freeview
> it does not
> > > work and with tkregister the file is empty.
> > >
> > > Or this one :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> --hemi
> > lh --o
> > > ./segment_7-lh.w --out_type paint --float2int
tkregister*
> > >
> > > But with this command I have this warning :
> > > Warning: all vertex values are zero
> > >
> > > Could you please help me to convert my volumetric files
> because I am
> > > probably doing someting wrong. All my files come from an
> Atlas and I
> > > just need to convert them to surfaces files.
> > >
> > > Thank you for your help,
> > > Redwan
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > >
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422>
> <tel:617-726-7422 <tel:617-726-7422>>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
> <https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
> <https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> >
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>
> > Outgoing:
> >
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>
> >
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> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> >
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>
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> >
> >
> > The information in this e-mail is intended only for the
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
> <https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
>
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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
Fax: 617-726-7422 <tel:%28617%29%20726-7422>
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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