Freesurfer

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30099 discussions

Re: [Freesurfer] NHP surface reconstruction in FS5.3
by S.V.Shepherd [work] 13 May '14

13 May '14

I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough? Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint. stephen Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...(a)gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>

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bbregister surf2vol
by 刘东博 13 May '14

13 May '14

Dear Freesurfer I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?

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how to save an intensity contour?
by Burke, Sarah 13 May '14

13 May '14

Hello, I am using the intensity contour tool for defining a white/gray matter border of my ROI. I can adjust my ROI according to this contour and save it. However, the contour itself is not saved (to the same layer as the ROI) and will not be loaded when opening the ROI layer again later. Is there a possibility to save the contour (maybe to an extra layer)? Thank you very much! Sarah

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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
by Emil H.J. Nijhuis 13 May '14

13 May '14

Dear Bruce & Matt, thank you for your help. @Bruce: I would be happy to send you the data, just let me know by e-mail which files you would need. @Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below and how you would rerun the pipeline? Also what values would be recommended? I did not find any manual/help files regarding the flags, so it would be helpful to document it. NB. I found another thread in the maillist which probably relates to the issue: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03355… . However I could not verify this, due to expired dropbox files. Yours, Emil Probably Emil¹s current example would be best because it is failing in your recon-all setup. Matt. On 5/9/14, 9:31 AM, "Bruce Fischl" <fis...(a)nmr.mgh.harvard.edu> wrote: >Hi Matt > >if you can send me an example I'll try to find time to take a look >Bruce >On Fri, 9 >May 2014, Matt Glasser wrote: > >> Hi Bruce, >> >> For whatever reason, sometimes the T2w surface adjustment will be way >>off. >> Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up >>and >> down can get it out of the minimum and make it work, so there might be a >> bug. >> >> Peace, >> >> Matt. >> >> From: "Emil H.J. Nijhuis" <emil.nijh...(a)gmail.com> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Friday, May 9, 2014 at 4:53 AM >> To: <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] problem with pial surface reconstruction >>using T1 >> (MPRAGE) and T2 (SPACE) weighted images >> >> Dear Bruce, >> >> thank you for your help. >> >> attached I have put an fslview, tkmedit screen-shot of the T2 image and >>a tk >> surfer image of lh.woT2.pial. >> >> It appears that without consideration of the T2 this effect does not >>happen. >> >> What would be your recommendation if I would like to keep using the T2 >>weigh >> ted image? >> >> Yours, >> Emil >> >> Hi Emil >> >> how do the surfaces look before you apply the T2 deformation? And how do >> they look visualized over the T2 instead of the T1? >> >> cheers >> Bruce >> >> On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: >> >> Hi, >> >> I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm >> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T >>Trio >> scanner with a 32-channel head coil. Unfortunately for half of my >>subjects I >> receive an rather odd pial surface artefact, while the 'white' surfaces >>do >> not suffer from the same issue. >> >> The command line I have used was: >> >> recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz >>-T2pial >> -3T >> >> Are you familiar with this issue and do you have some advice for me? >> >> Thank you very much for your help. >> >> Yours sincerely, >> >> Emil >> >> -- >> ---------------------------------------------- >> Emil H.J. Nijhuis, PhD >> Researcher - Division of Diagnostic and Interventional Neuroradiology >> University Hospital Basel >> Petersgraben 4 >> CH 4031 Basel Switzerland >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> >>freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/li >>sti >> nfo/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 > > >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.

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lme and survival (time-to-event) analysis tools on github
by jorge luis 13 May '14

13 May '14

Hi everyone Just wanted to point out that all the technology required to implement the statistical methods used in our last paper: "Event time analysis of longitudinal neuroimage data. Neuroimage. doi: 10.1016/j.neuroimage.2014.04.015". is available on github: https://github.com/NeuroStats I will try to add more features when I have some time. There is already a new useful script included in lme to compute subject-specific random effects for mass-univariate analyses. The survival (time-to-event) statistical analysis toolbox works pretty similar to lme. You can load your neuroimage data from Freesurfer using the scripts in lme: fs_read_label.m, fs_read_surf.m, fs_read_Y.m and then perform a survival analysis alone or a lme-survival joint analysis. Hope those tools help you make new exciting findings! Cheers -Jorge

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LME Matlab toolbox
by Victor Montal Blancafort 13 May '14

13 May '14

Greetings, The aim of this mail is about some problems that I am facing using the standalone copy (that is becouse I am using v5.1) of the LNE Matlab Tool provided on the FreeSurfer Wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) Currently, I am carrying out a longitudinal mass-univariate study. However, I get blocked when I try to open the smoothed thickness '.mgh' file obtained using the 'mris_preproc' and 'mri_surf2surf' command or also when I try to open the fsaverage sphere. Analyzing the code, I have realized that problems are caused due to that some '.m' files such as 'load_mgh.m' or 'read_surf.m' can't be opened because they are not provided on the package. Should I download them from another source or maybe there is another problem I am not realizing? Thank you in advance for you attention and your help! Bests, Victor

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EM registration: brain centroid
by Mark Plantz 13 May '14

13 May '14

Hi Freesurfers, Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help! Best, MP

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Fwd: Overinclusion of brain volume during segmentation - Question
by Christina Chen 12 May '14

12 May '14

Hi! I've attached 2 pictures of some brain scans on Freesurfer -- is there any way we can fix the huge underinclusion of the gray matter, hopefully without changing the surfaces of the white matter? What should be done with these scans to fix them? Thanks! Christina On Thu, Mar 20, 2014 at 2:32 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > cortical stats reported by asegstats2table use the surfaces, not the > cortical segmentation in aseg.mgz > doug > > On 03/20/2014 05:29 PM, Christina Chen wrote: > > Thanks a lot!! I have a follow up question: > > > > We use the command > > > > asegstats2table > > > > to output the subcortical volumes (and other whole brain volumes) to > > table. If the aseg is incorrect, can we still believe those values? > > > > Thanks, > > Christina > > > > > > On Thu, Mar 20, 2014 at 1:27 PM, Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > > > Hi Christina > > > > if the aseg is incorrect but the surfaces are right, then you > > don't need to worry about it. This is the reason we typically use > > the surfaces instead of the aseg for things like brain > > volume/cortex modeling. > > > > cheers > > Bruce > > > > On Thu, 20 Mar 2014, Christina Chen wrote: > > > > Hi! > > If the cortical surface outlines are fine, but there is an > > overinclusion of > > brain volume during segmentation, how should I fix this? Can > > we calculate > > brain volume based on the cortical surface outlines -- if so, > how? > > > > Thanks! > > Christina > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: > 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 > > -- > 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 >

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Paradigm files
by Emily Boeke 12 May '14

12 May '14

Hi Freesurfers, I am doing some analyses for an experiment where paradigm files were automatically generated by Matlab during stimulus presentation. The script was designed to make paradigm files for an older version of freesurfer, so the files only have 2 columns. I am going to adjust these files so that they can be read by FS 5.3 (add in the extra columns needed). I noticed that there is a line for each TR as opposed to for the onset of each stimulus, for example, it looks something like this: 0 2 2 2 4 2 6 2 8 1 10 1 12 1 14 3 16 3 instead of 0 2 8 1 14 3 Is this a problem? Can I leave it as is and then just add a column of 2s and a column of 1s? Thanks! Emily

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2x3 DODS analysis question?
by Khadka, Sabin 12 May '14

12 May '14

Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DODS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low Class MaleGroup2Medium Class MaleGroup2High Class FemaleGroup1Low Class FemaleGroup1Medium Class FemaleGroup1High Class FemaleGroup2Low Class FemaleGroup2Medium Class FemaleGroup2High Variables Age normVol Input SUB001 MaleGroup1Low 18 0.4 . . . And also my contrast files as Group1Group2.mtx [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3 MainEffectState.mtx 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 HighvLow.mtx -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 HighvMed.mtx 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 GroupxState-interaction.mtx 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 I'd appreciate if anyone could please let me know that my design is correct. Thanks for help. -Sabin

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