Re: [Freesurfer] probability maps

thanks Doug! I will give this a shot! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, May 15, 2017 at 9:56 PM, Douglas Greve wrote: > you can do something like > > a = MRIread('map1.mgz'); > > b = MRIread('map2.mgz'); > > c = MRIread('map3.m

Re: [Freesurfer] probability maps

you can do something like a = MRIread('map1.mgz'); b = MRIread('map2.mgz'); c = MRIread('map3.mgz'); d = (a.vol > thresh + b.vol > thresh + d.vol> thresh)/3; [mm ii] = max(d); Then the vertex number will be ii-1 (need to convert from 1-based to 0-based) On 5/15/17 3:34 PM, Trisanna Spr

Re: [Freesurfer] probability maps

Hi Bruce The maps are .mgz format and are % overlap (across 40 subjects). They were generated using -labels turned into surface overlay using mri_vol2surf -then registered to fsaverage using mri_surf2surf -then averaged within fsaverage space using mri_concat and then mris_fwhm to smooth. Best T

Re: [Freesurfer] probability maps

what format is your map of p-values in? On Mon, 15 May 2017, Trisanna Sprung-Much wrote: > Hi Bruce > I would not know where to start (not an avid matlab user) - what input would > be needed to be fed into matlab? > > Trisanna > > -- > Ph.D. CandidateMcGill University > Integrated Program in Ne

Re: [Freesurfer] probability maps

Hi Bruce I would not know where to start (not an avid matlab user) - what input would be needed to be fed into matlab? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl wrote: > hmmm, should be pretty ea

Re: [Freesurfer] probability maps

hmmm, should be pretty easy in matlab, no? On Mon, 15 May 2017, Trisanna Sprung-Much wrote: > Hi there > I have generated some anatomical probabilistic maps as overlays on the > fsaverage pial surface. Is there a way to automatically find the vertex > coordinates of the vertex with the highest pr

[Freesurfer] probability maps

Hi there I have generated some anatomical probabilistic maps as overlays on the fsaverage pial surface. Is there a way to automatically find the vertex coordinates of the vertex with the highest probability of overlap? Or does this have to be done manually in Freeview? Many thanks Trisanna -- Ph

Re: [Freesurfer] Probability Maps

thanks bruce for your response. You only answered question 4. :) Cheers, Pascal On Mon, Feb 6, 2017 at 12:27 PM, Bruce Fischl 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 d

Re: [Freesurfer] Probability Maps

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 "EntireFr

Re: [Freesurfer] Probability Maps

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" #

Re: [Freesurfer] Probability Maps

p.s. you don't need the T2pial in the autorecon2-cp, just if you rerun autorecon3 I think On Mon, 6 Feb 2017, Pascal Goodman wrote: Thanks Bruce. Please can you confirm if this script is correctSubjectID="$1"SubjectDIR="$2" T1="$3" #T1 FreeSurfer Input T2="$4" #T2 FreeSurfer Input recon-all -

Re: [Freesurfer] Probability Maps

the x.opts doesn't need all that stuff, just mri_normalize -b 25 cheers Bruce On Mon, 6 Feb 2017, Pascal Goodman wrote: Thanks Bruce. Please can you confirm if this script is correctSubjectID="$1"SubjectDIR="$2" T1="$3" #T1 FreeSurfer Input T2="$4" #T2 FreeSurfer Input recon-all -autorecon-

Re: [Freesurfer] Probability Maps

Hi Pascal I think you need to put it in an xopts file as the command line calls -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 thresho

Re: [Freesurfer] Probability Maps

Thanks Bruce. Please can you confirm if this script is correct SubjectID="$1" SubjectDIR="$2" T1="$3" #T1 FreeSurfer Input T2="$4" #T2 FreeSurfer Input recon-all -autorecon-all -i $T1 $T2 T2pial -s $SubjectID -parallel -hires # we need to get aseg, brainmask, norm, brain aseg=$SubjectDIR/$Subject

Re: [Freesurfer] Probability Maps

no, more like: echo "mri_normalize -b 20" > x.opts recon-all -s subjectID -autorecon2-cp -autorecon3 -expert x.opts or if you ware starting from scratch, use your command with the -expert x.opts stuff at the end cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Thanks bruce. That's

Re: [Freesurfer] Probability Maps

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 wrote: > Hi Pascal

Re: [Freesurfer] Probability Maps

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

Re: [Freesurfer] Probability Maps

yes On Fri, 3 Feb 2017, Pascal Goodman wrote: Also Bruce, Can I use this command line for the new version of freesurfer "  mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz". ThanksPascal.  On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman wrote:

Re: [Freesurfer] Probability Maps

Also Bruce, Can I use this command line for the new version of freesurfer " mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz". Thanks Pascal. On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman wrote: > Thanks bruce. After running mri_normalize -mprage -

Re: [Freesurfer] Probability Maps

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 wrote: > Hi Pascal > > yes, that is the right command line.

Re: [Freesurfer] Probability Maps

Hi Pascal yes, that is the right command line. I don'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: Hel

Re: [Freesurfer] Probability Maps

Hello Bruce, Thank you very much. a) The mri_normalization command line is 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

Re: [Freesurfer] Probability Maps

HI Pascal I got significantly improved results 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, Pascal Goodman wrote: Hello Bruce, I sent

Re: [Freesurfer] Probability Maps

Hello Bruce, I sent it. Pascal On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl wrote: > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > tar and gzip an example subject directory and send us the voxel coords of > points you want us to look at > > > cheers > Bruce > On Fri, 3 Feb 2017,

Re: [Freesurfer] Probability Maps

Thanks bruce. Do I upload the entire file? Also,where can I find the link? Pascal On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl wrote: > Hi Pascal > > I don't think tissue priors will help due to the complexity and > variability of the folding patterns. There may be other interventions > though

Re: [Freesurfer] Probability Maps

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange tar and gzip an example 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

Re: [Freesurfer] Probability Maps

Hi Pascal I don't think 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: Hell

Re: [Freesurfer] Probability Maps

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 w

Re: [Freesurfer] Probability Maps

Hi Pascal what are you trying to 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: Hello Freesurfer, I do have a question. Can FS take probability maps of

[Freesurfer] Probability Maps

Hello Freesurfer, I do have a question. Can FS take probability maps of tissue segmentation as prior? Thanks, Pascal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information