Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Freesurfer surfaces in the original space
by Douglas N Greve 31 Aug '11

31 Aug '11

You'll need to do this in steps. 1. Create a registration matrix R between your axial and conformed data: tkregister2 --mov axial.nii --targ orig.mgz --regheader --reg axial.reg.dat --noedit --s subjectname 2. Get the tkreg vox2ras matrix T from your axial: mri_info --vox2ras axial.nii 3. Compute a new matrix M = inv(T)*R. Put it into a file with the same format as axial.reg.dat (call it axia.crs.reg.dat). Just replace the 4x4 matrix. 4. Convert the surfaces with mri_surf2surf, something like mri_surf2surf ---hemi --subject subjectname --sval-xyz lh.white --reg axial.crs.reg.dat --tval lh.white.axial.crs --tval-xyz doug Navid Shiee wrote: > Hi, > > I need coordinates in col-row-slice space of my axial data. The reason > for this is that I have manually picked landmarks on the cortex in the > axial data space and I want to compute landmark errors for the > generated surface. I work with vtk files. I think after all it is a > simple scale+translation of coordinates, but not sure if freesurfer > provides such a tool. > > I know "mri_label2vol" does this for segmentation image. Is there an > equivalent command for surfaces? > > Thanks a lot for your help. > > > On Wed, Aug 31, 2011 at 12:03 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Navid, it is still not clear what you want. Each surface > coordinate has an xyz. This space that this xyz is in is a > peculiar space defined by FS. You want to use a different xyz > space. It could be scanner space. It could be col-row-slice of > your axial data. Or is it that you just want to visualize the > surfaces on the axial. In that case, you'll have to indicate what > tool you are going to use (you cannot use tkmedit for this -- it > will just conform it to 256^3). > > doug > > > Navid Shiee wrote: > > Hi, > Thanks for your reply. I make an examaple to clarify myself. I > have a 256x256x128 axial image which has 0.83^3 resolution. I > am intrested in generating the cortical surfaces and overlay > it on this image. Freesurfer first converts this image to > 256^3 voxels and 1^3 resolution and then generates the > surfaces. Thus if I want to intersect freesurfer surfaces with > my axial data, I can not because surface is in a different > space. Is there a way to transform the freesurfer surfaces to > 256x256x256 axial space? > Thanks a lot for your help. > > Navid > > / Connected by MOTOBLUR™ on T-Mobile > / > > -----Original message----- > > *From: *Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>* > To: *Navid Shiee <navid(a)jhu.edu <mailto:navid@jhu.edu>>* > Cc: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>* > Sent: *Tue, Aug 30, 2011 20:13:09 GMT+00:00* > Subject: *Re: [Freesurfer] Freesurfer surfaces in the > original space > > > Hi Navid, what do you mean by "the original image space"? > Ie, what > coordinates do you specifically want? Voxel? Scanner? > doug > > Navid Shiee wrote: > > Dear Freesurfer team, > > > > I have a question regarding Freesurfer surfaces. I > submitted this > > questions to the wiki but did not get any response and I was > wondering > > if you can help me on this issue. > > I am doing some experiments with Freesurfer and would > like to have > > surfaces in the original image space. FS converts > everything to > 1mm^3 > > 256x256x256 grid in the coronal space. I have axial > images which > does > > not have homogenous grid (although it has isotropic > resolution). I > > know there is a command to convert the volumetric structural > > segmentation into the original space but could not find > the command > > for surfaces. I would be very grateful if you can provide me > with some > > information for doing this. > > > > I appreciate your kind help in advance. > > > > Regards, > > > > -- > > Navid Shiee > > Ph.D. Candidate > > Laboratory of MEDical Image Computing (MEDIC) > > Image Analysis and Communication Laboratory (IACL) > > Johns Hopkins University > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Navid -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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mri_surf2vol
by Antonella Cappelletti 31 Aug '11

31 Aug '11

Hi all, I don't understand what's wrong with this command line: mri_surf2vol --surfval .curv --hemi lh --fillribbon --template orig.mgz --outvol curv-orig.mgz I tried also to use: mri_surf2vol --surfval .curv --hemi lh --fillribbon --template orig.mgz --outvol curv-orig.mgz the error is always the same: cannot recognize the type .curv (or curv). Where is the problem? Thanks, -- Antonella

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Re: [Freesurfer] Freesurfer surfaces in the original space
by Douglas N Greve 31 Aug '11

31 Aug '11

Hi Navid, it is still not clear what you want. Each surface coordinate has an xyz. This space that this xyz is in is a peculiar space defined by FS. You want to use a different xyz space. It could be scanner space. It could be col-row-slice of your axial data. Or is it that you just want to visualize the surfaces on the axial. In that case, you'll have to indicate what tool you are going to use (you cannot use tkmedit for this -- it will just conform it to 256^3). doug Navid Shiee wrote: > Hi, > Thanks for your reply. I make an examaple to clarify myself. I have a > 256x256x128 axial image which has 0.83^3 resolution. I am intrested in > generating the cortical surfaces and overlay it on this image. > Freesurfer first converts this image to 256^3 voxels and 1^3 > resolution and then generates the surfaces. Thus if I want to > intersect freesurfer surfaces with my axial data, I can not because > surface is in a different space. Is there a way to transform the > freesurfer surfaces to 256x256x256 axial space? > Thanks a lot for your help. > > Navid > > / Connected by MOTOBLUR™ on T-Mobile > / > > -----Original message----- > > *From: *Douglas N Greve <greve(a)nmr.mgh.harvard.edu>* > To: *Navid Shiee <navid(a)jhu.edu>* > Cc: *freesurfer(a)nmr.mgh.harvard.edu* > Sent: *Tue, Aug 30, 2011 20:13:09 GMT+00:00* > Subject: *Re: [Freesurfer] Freesurfer surfaces in the original space > > > Hi Navid, what do you mean by "the original image space"? Ie, what > coordinates do you specifically want? Voxel? Scanner? > doug > > Navid Shiee wrote: > > Dear Freesurfer team, > > > > I have a question regarding Freesurfer surfaces. I submitted this > > questions to the wiki but did not get any response and I was > wondering > > if you can help me on this issue. > > I am doing some experiments with Freesurfer and would like to have > > surfaces in the original image space. FS converts everything to > 1mm^3 > > 256x256x256 grid in the coronal space. I have axial images which > does > > not have homogenous grid (although it has isotropic resolution). I > > know there is a command to convert the volumetric structural > > segmentation into the original space but could not find the command > > for surfaces. I would be very grateful if you can provide me > with some > > information for doing this. > > > > I appreciate your kind help in advance. > > > > Regards, > > > > -- > > Navid Shiee > > Ph.D. Candidate > > Laboratory of MEDical Image Computing (MEDIC) > > Image Analysis and Communication Laboratory (IACL) > > Johns Hopkins University > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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how to threshold a sig.mgh file and binarize?
by Burzynska, Aga 31 Aug '11

31 Aug '11

Dear experts, I cannot find a simple way to threshold my sig.mgh file from a functional group analysis (the file is in the fsaverage space). I would like to binarize it and save as a mask to use it with the --mask flag in the mri_glmfit command (to restrict other analyses to these parts of the cortex. I will be very grateful for your help! Cheers, Aga

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Re: [Freesurfer] mris_ca_label
by Haitao Ge 31 Aug '11

31 Aug '11

Hi Bruce, I want to check the results and do some edit if possible. What is the possible reason? Thanks, Haitao

1 0

mris_ca_label
by Haitao Ge 30 Aug '11

30 Aug '11

2 1

Periaqueductal gray ROI
by Ritobrato Datta 30 Aug '11

30 Aug '11

Hi All, Is there a Periaqueductal Gray ROI generated by freesurfer recon ? Please let me know. Thanks Ri

1 0

bad pial surfaces
by Reza Farivar 30 Aug '11

30 Aug '11

Hello, I've been banging my head against the wall and keyboard to get mris_make_surfaces generate correct pial surfaces. While the white matter surface looks okay for the most part, the pial matter surfaces almost never actually reach the pial surface, but rather stop very close to the white matter surface. I was able to get it pushed out a bit by setting MIN_GRAY_AT_CSF_BORDER and MAX of that same parameter to really low numbers, but then it makes the error of putting the pial surface somewhere in the csf. Is there a list of parameters that I can play with to correct this problem? I should note that I'm working with macaque MRI's acquired at 0.35mm iso that have been made to look like they were acquired at 1mm in order to make freesurfer happy. If there is a thickness limit to gray matter, then this may fail at some locations because of the incorrect voxel size. Is there such a limit set in mris_make_surfaces? Many thanks in advance for your help, Reza

1 0

Freesurfer surfaces in the original space
by Navid Shiee 30 Aug '11

30 Aug '11

Dear Freesurfer team, I have a question regarding Freesurfer surfaces. I submitted this questions to the wiki but did not get any response and I was wondering if you can help me on this issue. I am doing some experiments with Freesurfer and would like to have surfaces in the original image space. FS converts everything to 1mm^3 256x256x256 grid in the coronal space. I have axial images which does not have homogenous grid (although it has isotropic resolution). I know there is a command to convert the volumetric structural segmentation into the original space but could not find the command for surfaces. I would be very grateful if you can provide me with some information for doing this. I appreciate your kind help in advance. Regards, -- Navid Shiee Ph.D. Candidate Laboratory of MEDical Image Computing (MEDIC) Image Analysis and Communication Laboratory (IACL) Johns Hopkins University

2 1

Error with dt_recon
by Antonella Kis 30 Aug '11

30 Aug '11

Dear All: I am running the dt_recon:# setenv FREESURFER_HOME /usr/local/freesurfer # setenv SUBJECTS_DIR $FREESURFER_HOME # cd /usr/local/freesurfer/NPI001 # dt_recon --i /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti and I am getting the following error: ERROR: cannot extract sDiffusion.alBValue[1] from /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat Can someone help, please? Thank you. AK

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Freesurfer