Thank you very much Douglas,

You made my day !

Have a good day,

Redwan

On 14 March 2017 at 10:48, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Yes, I see a spot on the medial wall. You can also look at it in the volume with

tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
On 3/14/17 1:45 PM, Redwan Maatoug wrote:
Hi Bruce,

Yes, I did.
Do you see something ?

Thank you,
Redwan
On 14 March 2017 at 09:19, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
did you look at the medial wall?
On 3/13/17 8:48 PM, Redwan Maatoug wrote:
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 <greve@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 <greve@nmr.mgh.harvard.edu

> <mailto:greve@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
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

> > <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@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
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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
> <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
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> 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/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
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