Hi, Yes my original data has 1x1x1mm voxel dimension but I prefer to work with the upsampled data. I am satisfied with the results I get from Freesurfer and the results actually look better than the results I get with the 1mm data, the only problem I have is that the thalamus mask does not keep the original dimensions in both cases. It is 256x256x256 ,so in terms of the thalamus position I do not know if it is at the right place. I will need to combine the STN that I have traced out in Analyze with the thalamus, thats why I need to make sure everything are in the correct position with respect to others.
Thank you Dorsa On Tue, Jul 26, 2016 at 1:58 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > sorry, I'm confused about what you are trying to do. Can you start from > the beginning and explain? If the data you have is 1mm but upsampled by the > scanner there is really nothing to be gained by processing the upsampled > data and it will waste lots of time > > > cheers > Bruce > > On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote: > > Yes I created it using the higher resolution and I think it looks fine. I >> attached the aseg.mgz. Is there any way to create the thalamus mask with >> the >> original properties ( same as the original mri) at the first place? I need >> to make sure the size and position of the thalamus corresponds to the >> original mri. >> >> Thank you! >> >> Dorsa >> >> On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Dorsa >> >> did you create the aseg.mgz from 1mm data (using the standard >> "conform" process), or higher res? The file you sent is higher: >> >> mri_info resliceduncoregtahalmus.nii.gz >> Volume information for resliceduncoregtahalmus.nii.gz >> type: nii >> dimensions: 512 x 512 x 288 >> voxel sizes: 0.488281, 0.488281, 0.625000 >> type: SHORT (4) >> fov: 250.000 >> dof: 0 >> xstart: -125.0, xend: 125.0 >> ystart: -125.0, yend: 125.0 >> zstart: -90.0, zend: 90.0 >> TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip >> angle: 0.00 degrees >> nframes: 1 >> PhEncDir: UNKNOWN >> FieldStrength: 0.000000 >> ras xform present >> >> >> it also has strange values in it (-32K and 32K, so probably >> things that can't be represented as a short). Does your aseg.mgz >> look right? >> >> cheers >> Bruce >> >> >> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote: >> >> Hi, This is the command line for reslicing: >> mri_convert -rl aseg.mgz thalamus.nii >> resliceduncoregtahalmus.nii >> >> thalamus.nii is the thalamus mask obtained by using >> the following command: >> mri_binarize --i aseg.mgz --match 10 --o >> thalamus.mask.nii.gz >> >> and I have attached the out put. >> >> Thank you! >> >> On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Dorsa >> >> you need to give us more details. What was >> your reslicing >> command line? And the screen output? >> >> Bruce >> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari >> wrote: >> >> >> Hi, >> >> I re-sliced my left thalamus so that the >> size and >> number of slices correspond with the >> original MRI, >> but when I open it in freeview, it shows >> an extra >> part( >> like a cube) on the bottom of the image >> ( I have >> attached the mask). do you have any >> idea how to >> solve that? >> Also how can I make sure that the >> position and size >> of the thalamus makes sense since the >> thalamus mask >> has a different slice size and number >> than the >> original mri? >> >> Thank you >> >> Dorsa >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > _______________________________________________ > 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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