Freesurfer

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30132 discussions

Functional ROI in whole brain
by Tomer Livne 12 Apr '12

12 Apr '12

Hi, I'll appreciate some help with the following issue. I need to define an ROI in a whole brain volume to be used as a mask in PyMVPA. That means having a whole brain .nii file with '1' within the ROI and '0' in every other voxel. Is there a way to define a functional ROI in a whole brain volume, in a similar way to what I get when running funcroi with an annotation from aparc for a specific hemi? Or alternatively, is there a way to convert the aparc based ROI for a single hemi surface into a whole brain volume? Best, Tomer

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Manual editing of segmentation
by Cynthia Elisabeth Krafft 12 Apr '12

12 Apr '12

Hello, Sorry for a newbie question. If we have to edit the segmentation (and all that we are interested in investigating is the volumetric data), what step should I run after that? Is it necessary to run "recon-all -autorecon2 -autorecon3" or is there some less time-consuming processing that will be sufficient? Thanks, Cindy

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Re: [Freesurfer] Resampling volumes from functional to anatomical space
by Lingqiang Kong 12 Apr '12

12 Apr '12

Thanks Bruce. I used mri_info to verify. And there seems to be a small mismatch. I have an original contrast overlay file 'sig.nii', then I used mri_vol2vol --mov sig.nii --targ $SUBJECTS_DIR/$subj/mri/T1.mgz --reg register.dat --o sig-aligned.nii to get a new overlay sig-aligned.nii which is aligned with T1.mgz. >From mri_info, 'sig.nii' is 64*64*42 'sig-aligned.nii' and 'T1.mgz' both 256*256*256 however, the voxel to ras transform for 'sig-aligned': -1 0 0 130.5 0 0 1 -111.6 0 -1 0 115.8 0 0 0 1.0 and voxel to ras transform for 'T1.mgz': -1 0 0 129.9 0 0 1 -105.6 0 -1 0 129.2 0 0 0 1.0 So the two matrices are different from one another. Is that OK? Lingqiang > you can use mri_info to verify that the geometry is the same > On Thu, 12 Apr > 2012, Lingqiang Kong wrote: > >> Hi Bruce, >> >> Yes that's what I wanted! The --fstarg flag uses the >> $SUBJECTS_DIR/$subj/mri/orig.mgz as the targ so in my case it would be >> the >> same as using --targ $SUBJECTS_DIR/$subj/mri/T1.mgz. >> >> So I guessed it had worked from the beginning but I had mistakenly >> thought >> that it didn't. It just looked different to my eyes because the >> functional >> contrast sig.nii looked one size bigger than the T1 structural and a lot >> of stuff seems to be outside the brain (now I take it that it's normal >> to >> look this way?). >> >> >> Thank you so much for your clarification. I was really confused about >> what >> mri_vol2vol was doing. >> >> Lingqiang >> >>> Hi Lingqiang >>> >>> do you mean in voxel register with the anatomy, with the same voxel >>> dimensions, etc...? If so I think you can specify --targ \ >>> $SUBJECTS_DIR/$subject/mri/T1.mgz >>> >>> or you mri_convert with -rl <path to T1.mgz> >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 12 Apr 2012, Lingqiang Kong wrote: >>> >>>> Hi Surfers, >>>> >>>> I am trying to resample a GLM analysis contrast overalay ('sig.nii') >>>> back >>>> to individual subject anatomical space (T1.mgz). The functional scans >>>> and >>>> the anatomical scans were acquired on two different days and were >>>> co-registered with register.dat. The T1.mgz has high resolution and >>>> the >>>> sig.nii has low resolution. >>>> >>>> I used >>>> mri_vol2vol --mov sig.nii --fstarg --reg register.dat --o sig_high.nii >>>> >>>> trying to generate a new overlay 'sig_high.nii' which is aligned with >>>> T1.mgz. >>>> >>>> However, this only generated the appropriate tranformation but did not >>>> really "MOVE" the sig_high.nii to align with the T1.mgz. (I checked >>>> using >>>> tkregister2 and also with loading all three files in Matlab using >>>> MRIread()). The sig_high.nii is aligned with sig.nii instead of >>>> T1.mgz. >>>> >>>> In the end, I want to load them in Matlab by MRIread and have the new >>>> sig_high.nii aligned with T1.mgz. How do I do that? >>>> >>>> >>>> Thank you. >>>> >>>> Lingqiang >>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > > -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

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Re: [Freesurfer] Clarification on centos version/updates/patches
by Watson, Christopher 12 Apr '12

12 Apr '12

Hi Nick, So would you recommend I install Centos 6 on the new workstation? In addition, I've run recon-all on a large study group (>100); I take it I'll have to re-run all of them? Thanks, Chris -------------------- Chris, yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it in-house). when the v5.2 release of freesurfer is ready (hopefully at the end of may) you will want to use the centos6 build, as it will get a bit better performance because of the compiler and some openmp options. n. On Wed, 2012-04-11 at 10:48 -0400, Chris Watson wrote: > H i Nick, > Will the centos5 build of v5.1 work with centos6? I'm getting a new > workstation and want to know which version of centos is better to install. > > On 04/10/2012 10:08 AM, Nick Schmansky wrote: > > Wil, > > > > Hi, the contents of that 'misc' directory is just a filedrop of sorts to > > supply fixes to individuals who need particular updates. We dont supply > > formal patches, as it gets too unwieldy to track versions. Rather bug > > fixes are documented (mostly!) on the ReleaseNotes page with links to > > fixes. > > > > We have a centos6 build, but dont release it. We will for the next > > release, v5.2, hopefully by the end of May, as the centos6 build runs a > > little faster than the centos4/5 build because it uses a newer gcc, but > > this will mean it wont be possible to mix versions, and a centos6 platform > > (or kernel 2.6.32-220.7.1.el6.x86_6) will be needed. > > > > mri_info versioning wont affect the stream. i dont think it has any bug > > fixes outstanding. > > > > i think the trac-all script is the same, the versioning is different > > because our 'dev' tree version was committed to our 'stable' branch, and > > the two have different versions (but the file is the same). > > > > n. > > > > > > > >> Hi- > >> > >> It would appear the stable release for centos6 is ready for primetime > >> 'stable5.1-bin.tgz'; Is this correct? There is an updated version of > >> 'mri_info' based on file size > >> (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86…) > >> > >> > >> mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45 > >> mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32 > >> > >> Which version is the most current? > >> > >> Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin > >> to overwrite the extant files? > >> > >> Additionally, there is a versioning discrepancy between 'trac-all' located > >> in > >> (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/) > >> > >> '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a > >> > >> and the version packaged with the cenos6_x86_65 'stable5.1-bin.tgz' > >> > >> '$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $' > >> > >> I did not comprehensively look for any other discrepancies-these just > >> happened to stand out based on the work I was doing today. > >> > >> Thanks much, > >> Wil > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

group difference thickness map
by Miranka Wirth 12 Apr '12

12 Apr '12

Dear freesurfers, I am trying to create a map that shows the vertex-wise magnitude of thinning (f.e.) between two groups, similar to Fig5 in Dickerson et al., 2009. I know how to extract the group-average thickness map from the beta.mg (mri_convert beta.mgh group1.mgh --frame 0 etc.), assuming that this is the way to construct the figure. Is there an easy way in freesurfer to compute the difference between these to group-average maps? Thank you for sharing. Miranka

2 1

mri_label2vol
by Johnson 12 Apr '12

12 Apr '12

Hi Can someone tell me please in*_details_*what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz thanks -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

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Re: [Freesurfer] Resampling volumes from functional to anatomical space
by Lingqiang Kong 12 Apr '12

12 Apr '12

sorry. meant to sent to the list, too. L > Hi Bruce, > > Yes that's what I wanted! The --fstarg flag uses the > $SUBJECTS_DIR/$subj/mri/orig.mgz as the targ so in my case it would be the > same as using --targ $SUBJECTS_DIR/$subj/mri/T1.mgz. > > So I guessed it had worked from the beginning but I had mistakenly thought > that it didn't. It just looked different to my eyes because the functional > contrast sig.nii looked one size bigger than the T1 structural and a lot > of stuff seems to be outside the brain (now I take it that it's normal to > look this way?). > > > Thank you so much for your clarification. I was really confused about what > mri_vol2vol was doing. > > Lingqiang > >> Hi Lingqiang >> >> do you mean in voxel register with the anatomy, with the same voxel >> dimensions, etc...? If so I think you can specify --targ \ >> $SUBJECTS_DIR/$subject/mri/T1.mgz >> >> or you mri_convert with -rl <path to T1.mgz> >> >> cheers >> Bruce >> >> >> On Thu, 12 Apr 2012, Lingqiang Kong wrote: >> >>> Hi Surfers, >>> >>> I am trying to resample a GLM analysis contrast overalay ('sig.nii') >>> back >>> to individual subject anatomical space (T1.mgz). The functional scans >>> and >>> the anatomical scans were acquired on two different days and were >>> co-registered with register.dat. The T1.mgz has high resolution and the >>> sig.nii has low resolution. >>> >>> I used >>> mri_vol2vol --mov sig.nii --fstarg --reg register.dat --o sig_high.nii >>> >>> trying to generate a new overlay 'sig_high.nii' which is aligned with >>> T1.mgz. >>> >>> However, this only generated the appropriate tranformation but did not >>> really "MOVE" the sig_high.nii to align with the T1.mgz. (I checked >>> using >>> tkregister2 and also with loading all three files in Matlab using >>> MRIread()). The sig_high.nii is aligned with sig.nii instead of T1.mgz. >>> >>> In the end, I want to load them in Matlab by MRIread and have the new >>> sig_high.nii aligned with T1.mgz. How do I do that? >>> >>> >>> Thank you. >>> >>> Lingqiang >>> >>> >>> >>> >> >> >> > > > -- > Lingqiang Kong > Ph.D candidate > Auditory Neuroscience Laboratory > Perceptual Neuroimaging Laboratory > Boston University > > 677 Beacon St. > Boston, MA 02215 > http://www.cns.bu.edu/~shinn/ANL/index.html > http://people.bu.edu/fmri/ > -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

1 0

Re: [Freesurfer] Mapping pf fsaverage surface to native volume
by Douglas N Greve 12 Apr '12

12 Apr '12

The template specifies the output geometry. When you specify --identity, you specify a particular transformation between the volume and the surface, so you can't change the target volume without specifying a different transform. I'm at a bit of a loss as to why this is not working. What is your tkmedit command? doug On 04/05/2012 06:04 AM, René Besseling wrote: > Hi Doug, > > I'm using tksurfer to visualize the surface maps; this looks OK for > both the original map overlaid on fsaverage and the mapped surface > (generated using mri_surf2surf) overlaid on subj01. The mapping from > surface to cortical ribbon also works well for fsaverage but goes > haywire for subj01, see pics in attachment. > > I noticed that mri_surf2vol gives different results when using > different --template volumes. Why is that? I assumed that the > --template image essentially provides the range of voxel coordinates > to which the surface values can be mapped. In other words: when > providing a template with a bigger field of view, I'd expect the > center of the resulting output to look the same as the output > generating when using a small FOV template. Does it matter whether you > write your output as .mgz or .nii? > > Best regards, > > Rene > > On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > How are you visualizing the results? Can you send a pic? You should be > using tkmedit. > doug > > On 04/04/2012 09:59 AM, René Besseling wrote: > > Dear Freesurfer users, > > > > I've been trying to map a Qdec contrast sig.mgh to the native volume > > of a subject using mri_surf2surf (to get from Qdec fsaverage surface > > to native surface) and mri_surf2vol (to map from native surface to > > native volume cortical ribbon). However, the last step goes wrong: I > > get a nii with the same range of values as were in the surface, but > > the nonzero voxels are scattered all over, so I guess there is > > something wrong with the surface-to-voxel coordinate mapping. > Below is > > my code, any ideas on what goes wrong? > > > > Best regards, > > > > Rene > > > > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval > > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh > > > > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon > > --identity sub01 --template subj01/mri/orig.mgz --o > > sig_2subj01_volumetric.nii > > > > > > _______________________________________________ > > 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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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

2 2

How can I get the mean thickness of the significant cluster
by zhang mingxia 12 Apr '12

12 Apr '12

Dear Freesurfer experts, I have done the whole brain analysis and get some significant clusters. How can I get the mean thickness of these clusters of every subject? Thank you very much. Mingxia Zhang

2 1

Resampling volumes from functional to anatomical space
by Lingqiang Kong 12 Apr '12

12 Apr '12

Hi Surfers, I am trying to resample a GLM analysis contrast overalay ('sig.nii') back to individual subject anatomical space (T1.mgz). The functional scans and the anatomical scans were acquired on two different days and were co-registered with register.dat. The T1.mgz has high resolution and the sig.nii has low resolution. I used mri_vol2vol --mov sig.nii --fstarg --reg register.dat --o sig_high.nii trying to generate a new overlay 'sig_high.nii' which is aligned with T1.mgz. However, this only generated the appropriate tranformation but did not really "MOVE" the sig_high.nii to align with the T1.mgz. (I checked using tkregister2 and also with loading all three files in Matlab using MRIread()). The sig_high.nii is aligned with sig.nii instead of T1.mgz. In the end, I want to load them in Matlab by MRIread and have the new sig_high.nii aligned with T1.mgz. How do I do that? Thank you. Lingqiang -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

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