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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 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
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.
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 :
- *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
MNI152.dat --tw --init-coreg*
- *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
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 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 :
- *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
MNI152.dat --tw --init-coreg*
- *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 doesnot
> 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 Iam
> probably doing someting wrong. All my files come from an Atlas andI
> 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
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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <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/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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 <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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <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/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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 <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>
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 <(617)%20724-2358> Fax: 617-726-7422 <(617)%20726-7422>
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
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 :
- bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
MNI152.dat --t1 --init-coreg
- mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
--hemi lh --o ./multidem.mgh
- 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 mailto: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> > <mailto: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>> > > <mailto: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>> > > <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto: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>> > <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/>>> > > > > _______________________________________________ > > 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>> > <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <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 <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <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/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > 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:%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/ <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>
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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 :
- bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152.dat
--t1 --init-coreg
- mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
--hemi lh --o ./multidem.mgh
- 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 fileto
> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <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/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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 <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>
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 <%28617%29%20724-2358> Fax: 617-726-7422 <%28617%29%20726-7422>
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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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.
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 mailto: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 <mailto: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> > <mailto: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>> > > <mailto: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>> > > <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto: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>> > <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/>>> > > > > _______________________________________________ > > 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>> > <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <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 <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <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/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > 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:%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/ <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> _______________________________________________ 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>_______________________________________________ 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.
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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 :
- bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
MNI152.dat --t1 --init-coreg
- mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
--hemi lh --o ./multidem.mgh
- 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 thereg,
> 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 usingbbregister
> 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 fileto
> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <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/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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 <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>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 <%28617%29%20724-2358> Fax: 617-726-7422 <%28617%29%20726-7422>
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e du/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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Redwan Maatoug