Freesurfer

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30132 discussions

Multi Modality Data Orientation
by Barron, Daniel S 11 Jul '13

11 Jul '13

Dear Freesurfers, I am trying to perform probabilistic tractography (FSL Probtrackx) between seed and target VOIs made with Freesurfer's recon-all (T1) and dt_recon (DW) pipelines. I have the original T1 DICOMs, however, I only have the DW NIFTI image volumes. I do not know how the DW DICOMS were converted to NIFTI and am worried about L-R flipping. Within Mango, I have found the T1 images converted with mri_convert are (X+,Y-,Z+). The DW NIFTI is (Y-,Z-,X-). mri_info gives me a lot of information that, unfortunately, I do not entirely understand. Can you recommend a way for me to verify consistent orientation in both my T1 and DW images? Thank you! Cheers, Daniel

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How to fix grey matter boundary
by Giusy Chinnici 11 Jul '13

11 Jul '13

Dear developers, I'm working with patients affected by cortical focal dysplasia; images of these patients often show thickening in some areas of the cortex. In many cases the reconstruction of the pial boundary is not accurate. I have been trying to correct this boundary but I couldn't understand the procedure. I have already checked accuracy and intensity of white matter and have found no issues. I have attached a self explanatory picture. I wonder if you can help me to fix grey matter boundary errors. Thanks a lot in advance for your help! Best regards! -- Giusy Chinnici

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Pial surface missing parts of the brain
by ye tian 11 Jul '13

11 Jul '13

Dear Freesurfers, Is it true that a small piece of the brain is missing in the attached (all three views)? How do I correct this problem? Thank you very much! Sincerely, Ye

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Editing multiple sources of error in freesurfer
by ye tian 11 Jul '13

11 Jul '13

Dear freesurfers, I have a subject for which I need to delete some dura in brainmask.mgz and to add some control points. I wonder whether I can do it the following way (to save time): 1. Manually delete extra dura in brainmask.mgz 2. recon-all autoreon1 3. Add control points 4. recon-all -autoreon2-cp -autorecon3 Thank you very much! Sincerely, Ye

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Re: [Freesurfer] (no subject)
by Douglas N Greve 11 Jul '13

11 Jul '13

Hi Nick, please remember to post to the list and not to us personally. To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work. doug On 07/11/2013 02:57 PM, Nicholas Paul Denisuk wrote: > Thanks Doug, > > This is actually a retinotopy analysis and the paradigm files are > phase encoded. Is there any possible way to regress out the activity > associated with the button presses. > > Thanks for your assistance, > > Nick > > On 7/9/13, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >> Why not include it as a condition in your paradigm file? >> doug >> >> >> On 07/09/2013 03:47 PM, Nicholas Paul Denisuk wrote: >>> Dear Freesurfer Users, >>> >>> I am trying to regress out the activity associated with button presses >>> in my GLM analysis. How do I generate a nuisance regressor file >>> analogous to a white matter regressor generated in functional >>> connectivity (a one column time course file)? >>> >>> Thanks you, >>> >>> Nick >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 41
by Maria Kharitonova 11 Jul '13

11 Jul '13

Hi, sorry I must have missed the response to this a few weeks back. Yes, I'm doing an identical analysis: comparing 2 groups of kids (controls and ADHD) in cortical thickness, controlling for age and demeaned ICV (nuisance). So all the parameters are the same. I'm attaching 3 screen shots: group differences using 5.0 before using Monte Carlo correction (lots of clusters), group differences before correction using 5.3 (few small clusters), and group differences using 5.0 after correction (frontal cluster). there was nothing sig. remaining after correcting for multi. comparisons using 5.3. I'm puzzled about why the differences are so large. I selected DODS in 5.0, so everything should be the same? I triple-checked to make sure the other differences (e.g. FWHM, etc.) were identical (left at default). Thanks! Maria ****** Message: 10 Date: Tue, 18 Jun 2013 23:34:10 -0700 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <51C150E2.1080604(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Maria, can you elaborate on exactly what you have done? Is the data the same and you are only changing the version of QDEC? What is the nature of the difference? Can you send pics or stats? doug On 6/18/13 6:06 AM, Maria Kharitonova wrote: > Hi, > > I'm learning how to use QDEC and was comparing results that it produces under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS method of producing a design matrix, while the 5.3 only has DODS. This suggests that results should be identical (or at least similar) across versions if I select DODS. However, I'm getting very different results based on the version I select: complete lack of differences across groups in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like to understand where the differences are stemming from -- any ideas? > > Thanks in advance! > Maria > > ******************************* > > Maria Kharitonova, Ph.D. > Postdoctoral Research Fellow > Laboratories of Cognitive Neuroscience > Boston Children's Hospital > > >

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mris_curvature_stats
by Harms, Michael 11 Jul '13

11 Jul '13

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bugs with expert-options and clean flags
by Harms, Michael 11 Jul '13

11 Jul '13

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Fwd: How to use read_curv?
by fatma zribi 11 Jul '13

11 Jul '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/7/11 Subject: Re: How to use read_curv? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> i have used read_surf to read ?h.white data. Now i would like to use curv and sulc file of FreeSurfer and extract the variance compared two one template of the average of 80subjects. We hav'ent a method to go from curv file to plot a mesh with matlab. 2013/7/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > sorry, I still don't understand what the issue is. read_surf will give you > the surface geometry/topology, and read_curv will give you the scalar > fields to display over them. You can use mri_surf2surf to map them into a > common space (the fsaverage surface for example) > > > cheers > Bruce > On Thu, 11 Jul 2013, fatma zribi wrote: > > Hi Bruce, >> >> I would like to use information about curv and sulc of a population and >> plot >> the variance with plot_mesh (variance presented in one brain) >> >> With best regards, >> >> Fatma >> >> >> 2013/7/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Fatma >> >> I don't understand your question. read_curv returns a scalar >> field over the surface, not the surface itself, which is why it >> is nvertices x 1. Use read_surf to read the surface topology in >> >> cheers >> Bruce >> On Thu, 11 Jul 2013, fatma zribi wrote: >> >> Dear Bruce, >> Now i would like to use the function read_curv but I >> have a problem of >> dimension .. curv is a vector of [143704,1] and >> vertices must be a matrix of >> [3, 143704] >> >> Would you mind help me and send an exemple of the >> use of the function wiht >> the visualisation of the brain >> >> [curv, fnum] = >> read_curv([SD_atlas.parms.**SUBJECTS_DIR '/' >> SD_atlas.parms.SUBJECT '/surf/' SD_atlas.parms.hemi >> '.curv']); >> >> white_sbjMesh.vertices = curv'; >> white_sbjMesh.faces=(fnum+1)'**; >> >> SD_white_remeshed{j}.vertices = >> MARS_linearInterpolate(max_**mesh.vertices, >> SD_sphere_sbjMesh, white_sbjMesh.vertices); >> >> SD_avg_mesh.vertices = >> SD_avg_mesh.vertices+SD_white_**remeshed{j}.vertices; >> >> Thank you very much for your help >> >> with best regards, >> >> Fatma >> >> >> >> >> 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<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. >> >> >> >>

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How to use read_curv?
by fatma zribi 11 Jul '13

11 Jul '13

Dear Bruce, Now i would like to use the function read_curv but I have a problem of dimension .. curv is a vector of [143704,1] and vertices must be a matrix of [3, 143704] Would you mind help me and send an exemple of the use of the function wiht the visualisation of the brain [curv, fnum] = read_curv([SD_atlas.parms.SUBJECTS_DIR '/' SD_atlas.parms.SUBJECT '/surf/' SD_atlas.parms.hemi '.curv']); white_sbjMesh.vertices = curv'; white_sbjMesh.faces=(fnum+1)'; SD_white_remeshed{j}.vertices = MARS_linearInterpolate(max_mesh.vertices, SD_sphere_sbjMesh, white_sbjMesh.vertices); SD_avg_mesh.vertices = SD_avg_mesh.vertices+SD_white_remeshed{j}.vertices; Thank you very much for your help with best regards, Fatma

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