Hi Bruce, Yes, I did. Do you see something ?
Thank you, Redwan On 14 March 2017 at 09:19, Douglas Greve <gr...@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 <gr...@nmr.mgh.harvard.edu> > wrote: > >> The file you created is not a label so don't try to load it with -label. >> Instead use -overlay file.mgh -fminmax .5 1 >> >> >> >> On 03/13/2017 05:40 PM, Redwan Maatoug wrote: >> > Hi Douglas, >> > >> > Sorry to bother you, again. >> > Actually, my command was t1 and not t2 but even with t1 nothing works. >> > So if my command line is exact, do you think it is a problem with my >> > files ? >> > >> > Thank you, >> > >> > Redwan Maatoug >> > Resident in psychiatry >> > Stanford University >> > Amit Etkin lab >> > >> > On 13 March 2017 at 13:41, Douglas N Greve <gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > Use --t1 (I assume the --tw was supposed to be --t2, which is >> > wrong for >> > that mni152 volume) >> > >> > >> > On 03/09/2017 08:58 PM, Redwan Maatoug wrote: >> > > Hi Douglas, >> > > >> > > Indeed you have already helped me ! >> > > Thank you for your help and for your time. >> > > >> > > I have tried to do, as you said. >> > > I have used the brain image for the registration and then I have >> > > tried to convert my ROI nifti volumetric file into a surface file >> > > using this registration file. >> > > >> > > I do not know what is wrong with my command line and I tried >> > many many >> > > things. >> > > >> > > I have attached two files >> > > (MNI152_T1_2mm_brain.nii is the brain file, >> > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file). >> > > >> > > I have tried the following commands : >> > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg >> > > MNI152.dat --tw --init-coreg* >> > > >> > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg >> > > MNI152.dat --hemi lh --o ./multidem.mgh* >> > > >> > > I do not know if the output format .mgh is correct. >> > > Anyway when I launch it with : >> > > *tksurfer fsaverage lh inflated -label multidem.mgh* >> > > >> > > the multidem.mgh file does not appear. >> > > >> > > Thank you by advance for your advice, >> > > Best, >> > > Redwan >> > > >> > > On 9 March 2017 at 09:09, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> > > <mailto:gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>>> 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 >> > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu >> >> >> > > Phone Number: 617-724-2358 <tel:617-724-2358> >> > <tel:617-724-2358 <tel:617-724-2358>> >> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> > <tel:617-726-7422>> >> > > >> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > <https://gate.nmr.mgh.harvard.edu/filedrop2> >> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 >> > <https://gate.nmr.mgh.harvard.edu/filedrop2>> >> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> > > Outgoing: >> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/ >> > <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 >> > gr...@nmr.mgh.harvard.edu <mailto:gr...@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:freesur...@nmr.mgh.har >> vard.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 >> gr...@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 > listfreesur...@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 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.
