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>> 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>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     <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>
>     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/>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     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
>     <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
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
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