thanks bruce for your response. You only answered question 4. :) Cheers, Pascal
On Mon, Feb 6, 2017 at 12:27 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it should just be:
mri_normalize -b 25
On Mon, 6 Feb 2017, Pascal Goodman wrote:
Thanks bruce, like creating expert.opts text file in the scripts directory
and inserting the command "mri_normalize -norm-b 25". Right? This is the modified script 1 #!bin/bash -eux 2 set -e 3 echo -e "EntireFreeSurferpipelinewithAutocontrolpoints" 4 5 SubjectID="$1" 6 SubjectDIR="$2" 7 T1="$3" #T1 FreeSurfer Input 8 T2="$4" #T2 FreeSurfer Input 9 10 recon-all -autorecon-all -i $T1 $T2 T2pial -s $SubjectID -parallel -hires
11 #we need to get aseg, brainmask, norm, brain 12 aseg=$SubjectDIR/$SubjectID/mri/aseg.presurf.mgz 13 brainmask=$SubjectDIR/$SubjectID/mri/brainmask.mgz 14 norm=$SubjectDIR/$SubjectID/mri/norm.mgz 15 brain=$SubjectDIR/$SubjectID/mri/brain.mgz 16 17 #make sure to create an expert.opts text file in the SubjectID/scriptsdirectory like this (SubjectID/scripts/expert.opts) and write down the command line "mri_normalize -norm2-b 25 18 echo "mri_normalize -norm2-b 25" > x.opts 19 20 #include T2pial since you are rerun -autorecon3 21 recon-all -s $SubjectID -autorecon2-cp -autorecon3 -expert x.opts 22 23 echo -e "done"
- Since I am rerun -autorecon2-cp and -autorecon3 then, do I need the
T2pial flag. 3) I named the expert option file expert.opts, shouldn't I replace the "x.opts" with the name of the file (please see lines 18 and 21) 4) For line 18, any reason why you suggested I remove "mri_normalize -mprage -norm2-b 25 -aseg $aseg -mask $brainmask $norm $brain"? 5) Do I need to specify the path to the expert.opts files? Cheers, Pascal
On Mon, Feb 6, 2017 at 9:42 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Pascal
I think you need to put it in an xopts file as the command linecalls -mprage after -b 20 and so will reset it. BTW: I used all the way up to -b 25 and things improved, so you might try that. At some point you will start eroding the gray/white boundary as you increase the -b threshold, but 25 looked ok to me Bruce
On Fri, 3 Feb 2017, Pascal Goodman wrote: Thanks bruce. That's Line 1 recon-all -all -i T2 T2pial -s subjectID -parallel Line 2 mri_normalize -mprage -norm2-b 20 -asegaseg.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 inrecon-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. Idon't know if you will need more 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 lineis where control points starts (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, BruceFischl fischl@nmr.mgh.harvard.edu wrote: HI Pascal
I got significantly improvedresults using -b 20 on the mri_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, PascalGoodman wrote:
Hello Bruce, I sent it. Pascal On Fri, Feb 3, 2017 at11:26 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
tar and gzip anexample subject directory and 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 entire file? Also,where can I find the link? Pascal
On Fri, Feb3, 2017 at 10:35 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Pascal
I don'tthink tissue priors will 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, Pascal Goodman wrote:
Hello Bruce, Thanks for replying. 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 at 10:22 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu>
wrote:
Hi Pascal what are you trying to achieve? Internally we have multiple prior maps ofthis 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: Hello Freesurfer, I do have a question. Can FS take probabilitymaps
of tissue
segmentation as prior? Thanks, Pascal ______________________________
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