Thanks bruce. That's
Line 1 recon-all -all -i T2 T2pial -s subjectID -parallel Line 2 mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz This is in visual studio code
Cheers, Pascal
On Fri, Feb 3, 2017 at 3:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Pascal
you can put the
mri_normalize -b 20
line in a file, and use it as the expert options in recon-all to rerun autorecon2-cp and autorecon3 with it
cheers Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote:
Thanks bruce. After running mri_normalize -mprage -b 20 -aseg
aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz, do I need to run recon-all -autorecon2 -autorecon3 again? Cheer., Pascal
On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Pascal
yes, that is the right command line. I don't know if you will needmore control points, but that helped a lot. -a specifies the intensity threshold above 110 and -g specifies the spatial gradient for the 1d normalization cheers Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote: Hello Bruce, Thank you very much. a) The mri_normalization command line is where control pointsstarts (normalization2). Right? b) Also, is this right command " mri_normalize -mprage -b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz"? c) Do I need any other flag besides -b? d) I don't need to make the manual control point edits right? e) Lastly, what does -a (float a) and -g (float g) mean? Cheers, Pascal
On Fri, Feb 3, 2017 at 2:14 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: HI Pascal
I got significantly improved results using -b 20 on themri_normalize command line. Note that this has to come after the mprage. I think you can do it with an expert options file with:
mri_normalize -b 20 cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Hello Bruce, I sent it. Pascal On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
tar and gzip an example subject directoryand send us the voxel coords of points you want us to look at
cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Thanks bruce. Do I upload the entirefile? Also,where can I find the link? Pascal
On Fri, Feb 3, 2017 at 10:35 AM,Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Pascal
I don't think tissue priorswill help due to the complexity and variability of the folding patterns. There may be other interventions though - can you send us some examples of where things don't look accurate to you?
cheers Bruce On Fri, 3 Feb 2017, PascalGoodman wrote:
Hello Bruce, Thanks forreplying. I am trying find ways to improve white matter surface (to reduce manual intervention by control points) with the probability map. Also, how do I extract the multiple prior maps you mentioned. Thank you. Best, Pascal
On Fri, Feb 3, 2017 at10:22 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Pascal
what are you tryingto achieve? Internally we have multiple prior maps of this type, but I don't think we are setup for a user to supply a different one
cheers Bruce On Fri, 3 Feb 2017,Pascal Goodman wrote:
HelloFreesurfer, I do have a question. Can FS take probability maps of tissue segmentation as prior? Thanks, Pascal
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