Freesurfer

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30091 discussions

Re: [Freesurfer] Permutation doubts
by Douglas N Greve 08 Apr '13

08 Apr '13

On 04/04/2013 03:56 PM, Gabriel Gonzalez Escamilla wrote: > Dear Doug, > > > Thank you so much as always for your answer. > > When you said that the permutation test is done normally, do you mean > that does not take account of the nuisance variables, and only test > for the groups comparison? It creates the full matrix including nuisance, then it permutes the rows of the matrix. > > Now I'm wondering if you have something implemented on matlab or > anything that could do a correction for multiple comparisons? > different than the cluster-wise correction (of mri_surfcluster), and > without having to wait the long time that the mc-z simulations (of > mri_glmfit-sim) take. If you're doing whole hemisphere, then you can used the cached mc-z with mri_glmfit-sim. Run mri_glmfit-sim with --help to get more info. There's also stuff on the wiki. doug > > > Regards, > Gabriel. > > > > El 04/04/13, *Douglas N Greve * <greve(a)nmr.mgh.harvard.edu> escribió: >> Correct, you cannot do a permutation test with continuous variables (or >> with any non-orthogonal design matrix). If you use the --perm-force, it >> will do the permutation test as normal (by randomly swapping the rows), >> but technically the test is not legal. Having said that, I suspect that >> LOTS of people do exactly that. >> doug >> >> >> >> On 04/04/2013 10:03 AM, Gabriel Gonzalez Escamilla wrote: >> > >> > Dear Freesurfer experts, >> > >> > >> > I'm having troubles when setting a permutation test, I'm making group >> > comparisons, but I'm introducing the Age, and cortical thickness as >> > niusance variables (as previously recommended). >> > >> > It seems that permutations only work for orthogonal matrices, does >> > this means that I cannot set any niusance variable? >> > >> > >> > If so, this is telling me that I can run the command with the flag >> > "--perm-force", and I'm wondering, which would be the implications of >> > force to run the permutations with niusance variables? >> > >> > >> > Many thanks in advance, >> > Gabriel >> > >> > >> > _______________________________________________ >> > 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 >> 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. >> > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggonesc(a)upo.es > http://www.upo.es/neuroaging/es/ -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Confused with Coordinate System in FS
by ZhiLiangLong 07 Apr '13

07 Apr '13

Hi all: I am confused with coordinate systems in FS. I have several questions bellow. 1. when we run recon-all -s subjid -all, Is the individual native space transformed to talairach coordinate system?. when run recon-all -s subjid -qcache, does the talairach system go into MNI system (fsaverage space)? 2. what is the tranformation matrix within the file of <subjid>/mri/transforms/talairach.xfm?, what is it used for? 3. Does the coordinates within .label files under <subjid>/label/ belong to the MNI coordinate system? 4. In TkSurfer Tool, does the coordinate of "Vertex RAS" belong to MNI coordinate? Hope someone gives me suggestions. best

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Making mid-gray surfaces without mris_expand?
by Keith Jamison 06 Apr '13

06 Apr '13

I have seen that the official recommendation for making a mid-gray surface is to use mris_expand. This seems to be a very slow procedure on my machine. I have also tried just loading the ?h.white and ?h.pial surfaces into matlab, averaging their vertices, and exporting the result. This seems to result in a nearly identical surface as mris_expand. On a test subject, only 48 out of 127,998 (0.0375%) vertices differed by more than 0.1mm, and these were almost entirely around the edges of the corpus callosum. Is there a reason this alternative is a bad idea? I imagine mris_expand does additional topology checks along the way, but if the vertices vary so little, can that be a major problem? I'm inclined to go with the faster solution, but since I'm relatively new to this procedure, I wanted to see what the community's experience might be. Thanks! Keith _______________________________ Keith Jamison Graduate Research Assistant Department of Biomedical Engineering University of Minnesota 7-105 NHH, 312 Church St. SE Minneapolis, MN 55455 Office: 6-112 Nils Hasselmo Hall Mobile: 607-227-0696 kjamison(a)umn.edu

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Intensity Normalization
by Dan LaFreniere 06 Apr '13

06 Apr '13

Dear Experts, I've been working on cleaning up some 4T nifti images for cortical thickness analysis. Initially our images were quite dark inferiorly due to the nature of the RF coil used (it doesn't extend much further than the temples resulting in signal drop-off). I've managed to find what appears to be a decent fix for the problem by running a higher number of -nuiterations during -autorecon1; usually 20-50 does the trick. Because I'm quite new to this, I was wondering if this is an acceptable fix? Just wanted to double-check with the experts before moving forward. I've attached a screenshot contrasting image quality of default iterations, 10, 20, and 50 iterations. It's also worth mentioning that -surfs appear to be quite accurate especially after I lay down some control points after an initial autorecon2 run. Thank you very much for your help and patience, Dan

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fsaverage mappings
by Satrajit Ghosh 06 Apr '13

06 Apr '13

hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the vertices in fsaverage4. is there an easy way to map those to vertices on to fsaverage/fsaverage5/... without going through surf2surf? something perhaps implemented in matlab or python. e.g., 1->1, 2->1, 3->1, ... 10->2, 11->2, ... i believe fsaverage 6/5/4/3 are icosahedral subsampling of fsaverage -- can i find this mapping somewhere or create it somehow? cheers, satra

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Re: [Freesurfer] mri_aparc2aseg issue
by Paul Beach 06 Apr '13

06 Apr '13

Hi Freesurfers, I'm currently trying to take manually made ROIs (label files) that have been incorporated into new annotation files (one for each hemisphere - rh.aug_aparc.annot & lh.aug_aparc.annot) and turn them into a new (augmented) annotation into a aseg file (an aug_aparc+aseg.mgz file). To do so I've been using the mri_aparc2aseg command and, at face value, it works well. However, some of my ROIs (specifically my insular ROIs) are being either shifted or lost in the transition from annotation to segmentation. Note that each hemisphere's new annotation files look perfect on tksurfer (which is where they were originally drawn). It's only when I try and make them fill the full cortical ribbon with the mri_aparc2aseg command that I get this issue. I piloted everything out on averaged subject and it all worked perfectly. However, when I attempted things on individual subject data I received the problem described above. I've attached a picture illustrating the discrepancy between the an averaged subject and a single subject. I have also attached my script code. The overall goal is to create a gmroi_volume which will allow me to determine an aux number of each manual ROI so as to export each one to AFNI space. I'd *really* appreciate help on how to fix this. Thanks, Paul -- Paul Beach DO/PhD candidate - Year V Michigan State University

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bblabels??
by Anupa AV 06 Apr '13

06 Apr '13

Hello experts, I'm in a process to make coronal cuts using tksurfer Please help me with the following questions: 1. How to map the label(merged) to fsaverage? 2. How to use bblabels? 3. How to map back to the individuals? What is the coomand line function used for the above questions? Any help will be appreciated.!!

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Error map
by Valtina Pouegue 06 Apr '13

06 Apr '13

Hi, I am looking for a tool of FreeSurfer. In fact, the tool is supposed to take in input 2 surfaces ( hemispheres) of subjects, registrate the surfaces and display the difference between the 2surfaces ( like 'euclidian distance'). What I want is exactly that output (http://www.sciencedirect.com/science/article/pii/S1053811909010064) availablein this article (http://www.sciencedirect.com/science/article/pii/S1053811909010064).Do you know the tool in question ?Thanks,VP

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R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 05 Apr '13

05 Apr '13

Hi Anastasia, yes, for some subject the low-b volume is in the end.Some subjects have again incomplete tracts.I'm attacking an example of configuration file that I'm using.I hope that you can check it please. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-apr-2013 18.45 A: <stdp82(a)virgilio.it> Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] incomplete tracts Hi Stefano - In your case we determined that the ones that had the low-b volume in the end didn't run correctly, right? In that case, I didn't need to see anything, you were going to try running 5.2. a.y On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > could I send you the data of a subject that I don't run correctly? > > I still have some subjects with tracts incomplete and I do not know if it depends from > my analysis or whether the images are not good. > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-apr-2013 17.37 > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] incomplete tracts > > > Hi Gerit - If it's not an issue with the gradient table but instead a > tractography initialization issue, I strongly recommend running 5.2 with > bbregister for the registration (which is the default in 5.2 anyway). > > You can also upload an example data set with issues (include: dmri, > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > Hope this helps, > a.y > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > Dear Anastasia, > > > > thanks for the help. There is also a line option in freeview. However we still have > > brains with missing tracks, I rerun them with increasing the ncpts and registering > to > > bbr (since that is default in Tracula 5.2.). We are reasonable confident that our > bvel > > and bvac are correct, since we have roughly 20 cases out of 90 processed brains > where > > there are no missing tracts. Further sometimes only one tract is missing, sometimes > it > > is more severe. We could not find any correlation with recon-all problems or DTI raw > > data issues (all but one were without moving artefacts). Since we are running > bedpostx > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an > issue > > that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0? > > I guess we need to change the dcmrirc files only a bit. > > > > Kind regards > > Gerit Pfuhl > > > > > > On 3 April 2013 16:59, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus > > callosum follow the curvature of the corpus callosum, and in a sagittal > > view to see if the lines in the cingulum follow the curvature of the > > cingulum. Does this make sense? > > > > a.y > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > Dear Anastasia, > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our > > gradient table is wrong but I am not really sure how to analyse > > these informations. You wrote to Stefano the lines have to point in > > the right direction and that the eigenvectors are not pointing along > > his corpus callosum. Can you give me a more detailed description > > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > > dtifit_FA. > > > > Thanks and kind regards > > Benjamin > > > > _______________________________________________ > > 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. > > > > > > > > > > -- > > http://gerit-orientation.blogspot.com > > http://team-arzgebirg.blogspot.com > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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R: Re: incomplete tracts
by stdp82＠virgilio.it 05 Apr '13

05 Apr '13

Hi Anastasia, could I send you the data of a subject that I don't run correctly? I still have some subjects with tracts incomplete and I do not know if it depends from my analysis or whether the images are not good. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-apr-2013 17.37 A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] incomplete tracts Hi Gerit - If it's not an issue with the gradient table but instead a tractography initialization issue, I strongly recommend running 5.2 with bbregister for the registration (which is the default in 5.2 anyway). You can also upload an example data set with issues (include: dmri, dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Hope this helps, a.y On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > Dear Anastasia, > > thanks for the help. There is also a line option in freeview. However we still have > brains with missing tracks, I rerun them with increasing the ncpts and registering to > bbr (since that is default in Tracula 5.2.). We are reasonable confident that our bvel > and bvac are correct, since we have roughly 20 cases out of 90 processed brains where > there are no missing tracts. Further sometimes only one tract is missing, sometimes it > is more severe. We could not find any correlation with recon-all problems or DTI raw > data issues (all but one were without moving artefacts). Since we are running bedpostx > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an issue > that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0? > I guess we need to change the dcmrirc files only a bit. > > Kind regards > Gerit Pfuhl > > > On 3 April 2013 16:59, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus > callosum follow the curvature of the corpus callosum, and in a sagittal > view to see if the lines in the cingulum follow the curvature of the > cingulum. Does this make sense? > > a.y > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > Dear Anastasia, > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our > gradient table is wrong but I am not really sure how to analyse > these informations. You wrote to Stefano the lines have to point in > the right direction and that the eigenvectors are not pointing along > his corpus callosum. Can you give me a more detailed description > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > dtifit_FA. > > Thanks and kind regards > Benjamin > > _______________________________________________ > 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. > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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