Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

Study-average brain and Talaraich
by Adam David Felton 23 Jan '12

23 Jan '12

Hello. Instead of using Freesurfer's averaged brain in qdec, I ran the following command to create an average of our participants: recon-all -s [subject] -qcache target avgsub While running, it reported the following for every subject: Error: could not open file "/Users/Tiana/ucr_freesurfer_data/subjects_10/avgucr/mri/transforms/talairach.xfm". System message: No such file or directory mri_surf2surf: could not load transform file '/Users/Tiana/ucr_freesurfer_data/subjects_10/avgucr/mri/transforms/talairach.xfm' and Reading smoothing mask label lh.cortex.label No such file or directory NN smoothing output with n = 68 Saving target data Saving to lh.thickness.fwhm10.avgucr.mgh rm: No match. (It couldn't find the Talairach file, which becomes another problem...) After finishing the command for all of the participants, I ran a simple analysis in qdec and no brain displayed for the results. However, it did say that there were significant clusters. When I clicked on "find significant clusters" (of course) the Talairach coordinates were missing. Does anyone know what I might've done incorrectly? Specifically, 1) how can I get the study-average brain to display in qdec and 2) how can I get the Talairach coordinates to display? Thank you for your help, Adam PS: Candy at the CNS conference for anyone who helps me.

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mri_glmfit-sim --grf? --cache?
by yukoyy 23 Jan '12

23 Jan '12

Dear all, I'm conducting volume based group analysis and corrections for multiple comparisons. My environment :Mac OS 10.6.8, Freesurfer 5.0.0 I followed the instruction I found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel When I first successfully ran: mri_glmfit --y ces.005.nii --wls cesvar.005.nii --osgm --glmdir F2glm.wls --nii.gz tkmedit fsaverage orig.mgz -aparc+aseg -overlay F2glm.wls/osgm/sig.nii.gz -fminmax 3 7 Then, I wanted to do corrections for multiple comparison. mri_glmfit-sim --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 However, FreeSurfer does not seem to recognize --grf, and I don't understand what does grf do. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ERROR: Flag --grf unrecognized. --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I chose to use --grf because it was suggested in the tutorial, and in FreeSurfer mailing list archive. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html I am guessing that I cannot use --cache for volume analysis because I don't have /Applications/freesurfer/average/mult-comp-cor/fsaverage/volume/cortex/fwhm12/pos/th30/mc-z.csd I also tried monte-carlo simulation, and it worked okay. So, here is my question. What does --grf do? and Is there any documentation? Thank you! Yuko Yotsumoto yukoyy(a)a7.keio.jp

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Ubuntu 11.10 64 bit
by octavian lie 23 Jan '12

23 Jan '12

Dear All, I am in the process of getting a powerful linux laptop to run Freesurfer. Can I run Freesurfer on a 11.10 version of Ubuntu 64 bit ? Are there any incompatibilities between the latest Freesurfer version and Ubuntu? Is there any configuration issues and solution particular to my situation that you can comment on? Thank you, Octavian.<mhtml:{57E897FE-D0ED-4693-ACA6-A3EF0E2D03DA}mid://00000000/!x-usc:mailto:Octavian.octavian.lie@gmail.com>

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qdec and scatterplots
by Cat Chong 22 Jan '12

22 Jan '12

Hello Experts, I apologize for the basic question. I am currently examining the cortical thickness differences between two groups, contolling for age. On the scatterplot, I thought there was a way to view slopes and intercepts (between groups)? I can't however, figure out a way to get these trendlines to show up. best regards, and Happy Chinese New Year Catherine

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problems with license
by pietro de rossi 22 Jan '12

22 Jan '12

Dear Experts, I'm sorry to bother you with a very silly question but...I'm trying to setup free surfer on my Mac and I'm having problems due to the fact that it keeps giving me errors saying that I don't have a valid license.... I've received the email with the three line license after the download...I've created a .txt file and I moved it to .license in the free surfer directory. What else should I do to make it work?

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Signal inhomogeneity
by Mahinda Yogarajah 22 Jan '12

22 Jan '12

Thanks for the advice on cerebellum and pia Bruce. I had one other question for freesurfer experts, I have a few subjects that I want to salvage and use where there appears to be significant signal inhomogeniety in the last few frontal slices (see T1.mgz in attached figure 1). Despite the use of control points (placed with careful adjustments of windowing parameters), I still can't encompass all of the the gyri right at the front (see brainmask.mgz coronal slice in figure 2). I would really appreciate some advice on how to proceed from here. Thanks. Mahinda

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memory allocation error with mris_register
by Arno Klein 22 Jan '12

22 Jan '12

i get the following memory allocation error for only one out of 20 oasis subjects that i processed with freesurfer 5.1 on an ubuntu 11.10 machine with 24gb memory: mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere templates_freesurfer/lh.KKI_2.tif subjects/OAS1_0061_MR1/surf/lh.sphere_to_KKItemplate.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from subjects/OAS1_0061_MR1/surf/lh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory system information: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.0.0-14-generic x86_64 cheers, @rno

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Pial surface and cerebellum
by Mahinda Yogarajah 21 Jan '12

21 Jan '12

Dear Freesurfer Experts, This might be a very basic question, and sorry for posting again, but I would be grateful for any advice. I have read the advice on the wiki regarding what to do when pial surfaces extend into the cerebellum. I had a few questions to clairfy things: 1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and added control points can I simply do cp brainmask.mgz brain.finalsurfs.manedit.mgz edit the cerebellum voxels out on the brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Will this then apply non-cerebellar and cerebellar edits (as well as control points) and give appropriate subcortical segmentations ? OR Do I have to make non-cerbellar edits to brainmask.mgz cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz make cerebellar edits to brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Thanks. Mahinda

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QATools
by Irwin, William 20 Jan '12

20 Jan '12

Hi - The link to download the QATools script (http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken, and I couldn't find it by looking through the ftp download directories. Regards, Wil

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Re: [Freesurfer] Freesurfer flips brains?
by Léoné, F.T.M. (Frank) 20 Jan '12

20 Jan '12

Hi everyone, Just a quick word of warning (plus two follow-up questions): there are more instances where your brain can get flipped. For example, I just regenerated my surface, using the correct orientation, certain about that. If I then do bbregister afterwards using the structural I convert back from the struct freesurfer used to contruct the surface (001.mgz, so mri_convert 001.mgz freesurferstruct.nii) like this bbregister --mov freesurferstruct.nii --init-spm --reg someRegFile.dat --t1 Note: this should be perfect to start with. But, in contrast, it's flipped again. Why? Because of the init-spm. If I use init-header (or use tksurfer to generate the reg file) everything is fine, which makes kinda sense (I use a converted freesurfer file) not quite (it is a nifti file which has the right orientation in SPM viewer). So why is this happening? Because of an incorrect/incomplete dicom conversion by the SPM-tools, which causes it to lose crucial orientation information? Moreover: is there an easy sanity check to see whether the orientation is right now? I thought about superimposing the original structural, to see how it ends up on the surface (should nicely follow the sulci/gyrii), but apparently there is a strong gradient in there and it is quite dotted, so it ends up not showing me all gyrii, just a subset, and a bit scattered. Is there a better way? Thanks again, hope also this is useful for others, best, Frank ----- "Dan Wakeman" <dgwakeman(a)gmail.com> schreef: > Van: "Dan Wakeman" <dgwakeman(a)gmail.com> > Aan: "F.T.M. Léoné (Frank)" <f.leone(a)donders.ru.nl> > Verzonden: Donderdag 19 januari 2012 18:14:07 > Onderwerp: Re: [Freesurfer] Freesurfer flips brains? > > Hi Frank, > > If your problem is solved then it's fine. I didn't understand what > you > said, and I am not sure I still understand your hemisphere problems. > Especially, because you cannot check the left right alignment (or > even > view any volume) in tksurfer. > > In general I would say it makes more sense to align your functional > data to your structural (as your higher resolution more accurate scan > is then the "gold standard" that others get matched to: though I > don't > know if there is any scientific validity to that claim). It also fits > better with the general FreeSurfer approach (correct me if I'm wrong > list). I would also recommend converting your dicoms to nii using > mri_convert, because mri_convert has much broader support for the > nifti format than the SPM tools for converting dicoms i.e. more > coordinate frame information is included in a nifti generated by > mri_convert than by the default SPM tools. > > D > > On Thu, Jan 19, 2012 at 11:59 AM, Léoné, F.T.M. (Frank) > <f.leone(a)fcdonders.ru.nl> wrote: > > Hi Dan, > > > > Sure. It was in my earlier e-mail of today: I use tksurfer, see > below. For this last test, I used the SPM display function though, > that now shows them to both have the same orientation, so appears to > be okay. Or am I still missing something? > > > > best, > > > > Frank > > > > Hi Douglas, > > > > Ah, makes sense, sorry for that. > > > > I do most of the work in SPM, so: > > > > - I have a highres structural scan, nii file format > > - I convert it to a surface using recon-all > > - Coregister the highres structural to the functional scan, so it > is > > in the voxel size and orientation as the functional scans (SPM) > > - I try to bbregister the coregistered and resliced T1 with the > > surface using something like: > > bbregister --s S7_FS --mov > ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii > --init-spm --reg > ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat > --t1 > > and view it with > > vglrun tkregister2 --mov > /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii > --reg > /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat > --surf > > > > Here you see that I already use a flipped structural scan. If I do > it like this, bbregister converges to a nice and correct solution > (everything aligns). If I don't, tkregister2 showms unregistered struc > and func, while it is obvious it would be roughly aligned if you would > flip either of them. > > > > In addition/in general: What would be the recommended way to do the > coregistration etc. if you do all you analyses in SPM? Would it for > example be better to coregistrate and reslice all functionals with the > structural, so they are automatically aligned with the surface? Now I > have a structural which is coregistered with the funcional and I > realign that one, but that makes for one extra step where it can go > wrong. Don't think this is related to the flip, but I also have a few > alignment problems for other subjects. > > > > Thanks a lot in advance, > > > > best, > > > > Frank > > ----- "Dan Wakeman" <dgwakeman(a)gmail.com> schreef: > > > >> Van: "Dan Wakeman" <dgwakeman(a)gmail.com> > >> Aan: "F.T.M. Léoné (Frank)" <f.leone(a)donders.ru.nl> > >> Cc: freesurfer(a)nmr.mgh.harvard.edu > >> Verzonden: Donderdag 19 januari 2012 17:09:28 > >> Onderwerp: Re: [Freesurfer] Freesurfer flips brains? > >> > >> Hi Frank, > >> > >> I think we still need to know. What software are you using to view > the > >> volumes? > >> > >> D > >> > >> On Thu, Jan 19, 2012 at 10:59 AM, Léoné, F.T.M. (Frank) > >> <f.leone(a)fcdonders.ru.nl> wrote: > >> > Hi Doug, > >> > > >> > Ah, I found the cause myself, which might be useful for others. > It > >> happens already in the first step, before the ones I listed: in > >> mri_convert. I do: > >> > > >> > mri_convert struct.nii 001.mgz > >> > > >> > And it flips. This I can see because I converted the mgz back > >> (mri_convert 001.mgz orig.nii) and then it's indeed reversed (and > >> shifted, rotated, all rigid body transformations one can think > of). > >> Why does this happen? Is it normal for nii-files? I see that I can > >> specify the orientation in mri_convert by doing mri_convert > >> -in_orientation and then a three letter specification. I chose PSR > and > >> now the changes are far less severe (only a small shift still) and > >> most importantly: no flip anymore. Do I now need to reconvert my > all > >> my surfaces? I don't hope, but I'm at least glad I have this one > >> fixed. > >> > > >> > best, > >> > > >> > Frank > >> > > >> > ----- "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> schreef: > >> > > >> >> Van: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > >> >> Aan: "Frank Leoné" <f.leone(a)donders.ru.nl> > >> >> Cc: freesurfer(a)nmr.mgh.harvard.edu > >> >> Verzonden: Woensdag 18 januari 2012 18:34:31 > >> >> Onderwerp: Re: [Freesurfer] Freesurfer flips brains? > >> >> > >> >> Hi Frank, we'll need a lot more detail. Are you doing all of > this > >> in > >> >> FreeSurfer? What are your command lines? How are you evaluating > >> >> whether > >> >> volumes are flipped? > >> >> doug > >> >> > >> >> Léoné wrote: > >> >> > Dear all, > >> >> > > >> >> > I must be missing something really obvious, but it seems my > >> brains > >> >> are flipped. What I do: > >> >> > > >> >> > - I have a highres structural scan, nii file format > >> >> > - I convert it to a surface using recon-all > >> >> > - Coregister the highres structural to the functional scan, so > it > >> is > >> >> in the voxel size and orientation as the functional scans > >> >> > - I try to bbregister the coregistered and resliced T1 with > the > >> >> surface > >> >> > > >> >> > But then: hey, it doesn't fit, my low-res T1 is flipped > compared > >> to > >> >> my y surface, hence to my original T1. So is it indeed true that > my > >> T1 > >> >> might have been flipped? If so, does it make a wrong assumption > on > >> >> neurological vs radiological convention, or what is going on? > >> >> > > >> >> > Thanks in advance, > >> >> > > >> >> > best, > >> >> > > >> >> > Frank > >> >> > _______________________________________________ > >> >> > 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. > >> > > >> > _______________________________________________ > >> > 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

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Freesurfer January 2012