[Freesurfer] Extract coordinates from .mgh file

Hi experts, I just want to know a way to extract the coordinates from a ROI mgh file. I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful. Thank you, Redwan

Re: [Freesurfer] Segmentation Violation problem in surface files

you can just mri_convert lh.template_angle.mgz lh.template_angle_MW.nii not, mri_convert, not mris_convert On 07/25/2017 04:16 PM, Yagmur Ozdemir 19 wrote: > mris_convert -c lh.template_angle.mgz lh.template_angle.mgz > lh.template_angle_MW.nii > > Thank you for the help, > Idil >

Re: [Freesurfer] Segmentation Violation problem in surface files

I just realized I needed lh.inflated in the command. I think it works now. Thank you for all the help! Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu]

Re: [Freesurfer] Segmentation Violation problem in surface files

mris_convert -c lh.template_angle.mgz lh.template_angle.mgz lh.template_angle_MW.nii Thank you for the help, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve

Re: [Freesurfer] Segmentation Violation problem in surface files

what is your command line? On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote: > When I do either of the conversions with mris_convert, the system gives > freadFloat: fread failed / No such file or directory then a Segmentation > fault error. > > Best, > Idil >

Re: [Freesurfer] Segmentation Violation problem in surface files

When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error. Best, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] reducing a matrix

Add another 0 after the register.lta On 07/25/2017 02:46 PM, Linda Eva Heidinger wrote: > The -gcam command requires 7 arguments. What would the seventh be? Please let > me know. I really appreciate all your help! > > From:

Re: [Freesurfer] Segmentation Violation problem in surface files

you can convert the overlays directly to nifti, but they aren't surfaces - they are scalar fields over the surface (that is, they are one value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti cheers Bruce On Tue, 25 Jul

Re: [Freesurfer] Segmentation Violation problem in surface files

I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert

Re: [Freesurfer] reducing a matrix

The -gcam command requires 7 arguments. What would the seventh be? Please let me know. I really appreciate all your help! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve

Re: [Freesurfer] How to create mask for Total Graymatter and White matter Volume

try --gm On 07/25/2017 08:33 AM, M Janani wrote: > > Hi Team, > > I would like to create mask for Total Gray matter and > white matter volume. > > I was able to get the total white matter volume using the below > mentioned command > > mri_binarize -i aparc+aseg.mgz --wm --o

Re: [Freesurfer] Freesurfer commands

you can do something like mri_cor2label --i aseg.mgz --id 17 --label left.hippo.label This will output tkregisterRAS coordinates which you can convert to voxel coords using https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems case #1 On 07/25/2017 02:02 AM, Aziz Nanthaamornphong

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

I would put the spm and fs analysis into the same space On 07/25/2017 10:19 AM, עדיאל חרבש wrote: > Hi Douglas, > Thank you, works perfectly. > But, I need to know first which structures id's are inside each file. > I preferred to extract all the brain map with Matlab, as Bruce commented. > >

Re: [Freesurfer] Segmentation Violation problem in surface files

Hi Idil I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote: > Bruce, > > Thank you so much for the help! I guess then the way to export these overlays > to other

Re: [Freesurfer] Segmentation Violation problem in surface files

Bruce, Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file. Best, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates

Thank you very much for this information!! Best, Li On Jul 24, 2017, at 4:06 PM, Douglas Greve > wrote: Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Hi Douglas, Thank you, works perfectly. But, I need to know first which structures id's are inside each file. I preferred to extract all the brain map with Matlab, as Bruce commented. Now I try to match the coordinates, according to the linked you posted. The brain space in results is of

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Hi Bruce, I had Matlab and freesurfer on separate machines. But for now I managed to have Matlab on both, so I can run it. It really helped, thanks! Adiel 2017-07-24 22:33 GMT+03:00 Bruce Fischl : > HI Adiel > > we distribute all our matlab scripts as part of

[Freesurfer] How to create mask for Total Graymatter and White matter Volume

Hi Team, I would like to create mask for Total Gray matter and white matter volume. I was able to get the total white matter volume using the below mentioned command mri_binarize -i aparc+aseg.mgz --wm --o wm.mgz But I couldn't find any option to create the mask for Total Gray

[Freesurfer] Freesurfer commands

Hi Freesurfer Experts, Currently, I am using these command excited in Matlab to extract the coordinates of volume. *mri = MRIread('aseg.mgz');pos = find(mri.vol == 17 | mri.vol == 53);* *[i,j,k] = ind2sub(mri.volsize,pos);* I would like to run these command in the Freesurfer itself rather than