Thank you very much Douglas, You made my day ! Have a good day, Redwan
On 14 March 2017 at 10:48, Douglas Greve <gr...@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 <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/freesurf >>> er >>> > <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.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 > 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. > >
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