Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Convert aseg.mgz to .nii and into MNI space with FSL dimensions
by Douglas N Greve 15 Feb '13

15 Feb '13

mri_label2vol will take segmentations as an input look at the --help doug On 02/15/2013 04:25 PM, Roderick McColl wrote: > Sorry for the bother, but there isn't a label for L or R WM. > Should I use mri_vol2vol on the aseg.mgz file and the mni152.register.dat > file instead i.e. just register aseg.mgz into MNI152 space? > Not sure how to make this use a nearest neighbor interpolation though. > Thanks > -roddy > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Friday, February 15, 2013 3:04 PM > To: Roderick McColl > Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL dimensions > > In that case, use mri_label2vol with the following reg $FREESURFER_HOME/average/mni152.register.dat > doug > > On 02/14/2013 11:02 AM, Roderick McColl wrote: >> Thanks very much. >> I should have made myself clearer. >> I would like to use $FREESURFER_HOME/subjects/fsaverage/mr/aseg.mgz >> for some analysis in MNI512 (FSL) space. >> So should I use mni152reg on the orig.mgz file in that folder to generate the transform? >> -roddy >> >> ________________________________________ >> From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, February 13, 2013 4:48 PM >> To: Roderick McColl >> Cc: 'Clark Fisher'; freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL >> dimensions >> >> you can use mni152reg to compute the registration to the MNI152 space. >> Make sure to spec the 1mm target. You can then use mri_label2vol to >> map aseg.mgz to the MNI152 space. >> >> doug >> >> On 02/13/2013 03:40 PM, Roderick McColl wrote: >>> Hello all, >>> I have a need to generate LH and RH WM masks for analysis. >>> I can convert aseg.mgz to aseg.nii but the dims are 256x256x256 and I >>> need to use the FSL MNI format which is 182x218x182. >>> Is there a recipe for cropping / translating etc to match the >>> aseg.mgz atlas with the FSL atlases? >>> Thanks >>> -roddy >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >> -- >> 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/ >> >> >> >> 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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- 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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Recon-all with my own template
by Sophie Maingault 15 Feb '13

15 Feb '13

Hello Freesurfer experts ! I created a new template with make_average_subject called 80tvs and I would like to re-run some of my subjects with this new template. I can't find the command line in FAQ. Is it for example : recon-all -all -s t0001 -target 80tvs ?? So I need the repertory of this new template in the subject_dir ? Thank you for the answer ! Sophie

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Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all
by Douglas Greve 15 Feb '13

15 Feb '13

Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: > Hi Doug, thanks for replying, here is the file attached. In case the > attachment doesn't go through please let me know if I should send it > to a different address. > Tudor > > On 18 December 2012 17:34, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Can you send the recon-all.log file (located in the > subject/scripts folder). > doug > > > On 12/18/2012 11:41 AM, Tudor Popescu wrote: > > Hello, > > > > First of all, apologies for asking for help three times today! > THings > > will hopefully become clearer once I get used to FS a bit; I > really do > > appreciate the amazing support provided by the team behind > FreeSurfer! > > > > I ran the following command on one of my structurals: > > > > /recon-all -subject M01 -i M01.nii.gz -all/ > > > > After a few minutes, recon-all ended with the following message: > > > > /Assertion failed at line 827 in file templates/CachedArray.cc/ > > /nu_estimate_np_and_em: crashed while running volume_stats > > (termination status=256)/ > > /nu_correct: crashed while running nu_estimate_np_and_em > (termination > > status=256)/ > > /ERROR: nu_correct/ > > /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > 01:57:59 > > UTC 2009 i686 GNU/Linux/ > > > > I apologise for reporting an error that's already been reported > in the > > past, but unfortunately the solutions suggested in those past > threads > > did not work in my case. To address a few of them: > > > > * my PATH (listed below) does not seem to include two MNI > installations > > > //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ > > * the version of FreeSurfer that I installed is the latest disk > > image available on the website > > (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did > > not see any dev version that would presumably include any > missing > > libraries presumably implied by the above error > > * I tried updating the Xubuntu inside my VirtualBox, however it > > reports an insufficient space problem that from I can see > does not > > have a trivial fix > > > > Advance thanks for any help! > > Tudor > > > > > > _______________________________________________ > > 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 > Fax: 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > >

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Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change
by Clark Fisher 14 Feb '13

14 Feb '13

Hi Doug and the list, I think I still have a problem understanding what cesvar.nii contains. As a sanity check, I tried to create 95% confidence intervals around my CES. I found that in some voxels (or ROIs in my case) that had a p-value of less than 0.05, my 95% confidence interval for my CES included zero. Here's one example: >> clear >> cesNii = MRIread('ces.nii'); >> cesVol = cesNii.vol; >> cesVarNii = MRIread('cesvar.nii'); >> cesVarVol = cesVarNii.vol; >> sigNii = MRIread('sig.nii'); >> sigVol = sigNii.vol; >> pValue = 10^-abs(sigVol(4,1,1)) pValue = 0.0199 >> ces = cesVol(4,1,1) ces = -0.0028 >> cesVar = cesVarVol(4,1,1) cesVar = 6.4511e-06 >> ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96 ces95pctCI = -0.0078 0.0022 Are the p-values calculated in a way that assumes non-Gaussian error of the ces, or am I otherwise doing something wrong? Thanks, Clark Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 13 Feb 2013 15:11:27 -0800<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> 1). Yes 2) Right, pull the scale outside of the sqrt() doug On 02/13/2013 03:36 PM, Clark Fisher wrote: > Hi Doug, > > Thanks for the help, that seemed to worked great. I have a few > follow up questions about how to process the resulting statistics. > > I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and > would like to get the % signal change for certain contrasts with error > bars. Looking through the listserv, I see that the values in > cespct.nii require correction by a scale factor in this version of > fsfast. The most recent conversation I could find on this comes from > 2010, when you told Thomas Janssens: >> Hi Thomas, you may have found a bug in my scale factor calculation. Can >> you compute the new scale factor as described below? BTW, these issues >> are fixed in version 5. >> >> cd bold/analysis >> x = load('X'); >> tirf = x.flac0.ev(3).tirf; >> Xirf = x.flac0.ev(3).Xirf; >> scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)])); >> TR = x.flac0.TR; >> dt = tirf(2)-tirf(1); >> scalefNew = sum(Xirf)*TR/dt; > I can't find a follow up to this message. 2 questions. > 1) The results with scalefNew look reasonable to me; do you still think that > this is the proper way to adjust cespct.nii in v4.5? > 2) If I want to put error bars on my % signal change, how do I scale the > values in cesvarpct.nii? I would guess that if I wanted to put a 95% CI on > my % signal change, it would be: > (cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96) and NOT > (cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96) > Does this sound right, or am I misinterpreting what cesvarpct.nii contains? > Thanks again, > Clark > >> Hi Clark, >> >> On 02/06/2013 05:55 PM, Clark Fisher wrote: >> > Hi everyone, >> > >> > In a previous discussion on this list >> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html) >> > Pablo Polosecki was asking the best way to perform hypothesis testing >> > using functional data within an ROI. The final opinion was that it >> > was best to average all of the time courses in the ROI, and re-run the >> > analysis from scratch, so that all of the appropriate whitening, etc. >> > occurred. >> > >> > I was considering doing this, creating a small volume (say, 10 voxels >> > total) that had each voxel holding the average time course from one of >> > 10 ROIs. I would then set up and run a usual fsfast analysis using >> > these tiny volumes. I am using freesurfer 4.5. I have a few questions. >> > >> > 1) Is this reasonable? >> In general, it is reasonable. Though I'm curious what you are ultimately >> trying to do. Do you want p-values for each subject in each ROI? Or will >> you be combining the ROI beta values across subject in a group analysis? >> If so, then the whitening will probably make little, if any, difference, >> especially if this is a blocked design. In expectation, the whitening >> does not affect the beta values. >> > >> > 2) One area where I expect to run into problems is with the whitening. >> > If I set -acfbins to the total number of my dummy voxels, and >> > -acffwhm to 0, will this use the autocorrelation function of the >> > average timecourse within each individual ROI? Is that an appropriate >> > approach? How sensitive will this be to the number of actual voxels >> > averaged to get each ROI (for instance, would this bias me to finding >> > more significant results in ROIs containing fewer voxels?). >> That might work, but no promises! It is an appropriate approach. It >> might be sensitive to the number of voxels if the number is small (say, >> less than 100). >> > >> > 3) Are there other steps that depend upon the spatial arrangement of >> > voxels that I am forgetting, and will these steps choke on these small >> > volumes (or worse, fail in silent but pernicious ways). >> Nothing I can think of off the top of my head. >> doug >> > >> > Thanks for all of the help, >> > Clark >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> >Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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 >> gr...(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 >> <http://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<mailto:Freesurfer@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 gr...(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<http://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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] talairach transformation troubleshooting problem
by Rongxiang Tang 14 Feb '13

14 Feb '13

Hi Bruce, I checked the skullstrip stage using this command: tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs.... and both of the brainmask and T1 images look fine.... the wm.mgz is problematic, with some area missing..... I was wondering if I need to manually adding control points to solve the problem. Thanks, Catherine ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Rongxiang Tang <rongxiangtang(a)yahoo.com> Sent: Thursday, February 14, 2013 2:03 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine that looks like something went wrong in the surface recon, not in the talairaching. Maybe a skullstrip problem? You need to investigate. Also, please cc the list so that others can answer! thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: > Hi Bruce, > > I attached two images...one is the target view and the other is the moveable > view. > > Thanks, > Catherine > > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Rongxiang Tang <rongxiangtang(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, February 14, 2013 1:33 PM > Subject: Re: [Freesurfer] talairach transformation troubleshooting problem > > Hi Catherine > > can you send us an image of what you are looking at? > > thanks > Bruce > On Thu, 14 Feb 2013, > Rongxiang Tang wrote: > > > Dear All, > > > > When I was checking the talairach transformation output, I noticed that > some of the white matter was not included inside > > the green line. Instead of drawing the green line to include all of the > white matter of the whole brain, it somehow only > > includes the bottom half of the white matter of the brain. > > > > Is there a way to fix that? > > > > Thanks, > > Catherine > > > > > > > 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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Fw: talairach transformation troubleshooting problem
by Rongxiang Tang 14 Feb '13

14 Feb '13

----- Forwarded Message ----- From: Rongxiang Tang <rongxiangtang(a)yahoo.com> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Thursday, February 14, 2013 2:00 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Bruce, I attached two images...one is the target view and the other is the moveable view. Thanks, Catherine ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Rongxiang Tang <rongxiangtang(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, February 14, 2013 1:33 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine can you send us an image of what you are looking at? thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: > Dear All, > > When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside > the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only > includes the bottom half of the white matter of the brain. > > Is there a way to fix that? > > Thanks, > Catherine > > 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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talairach transformation troubleshooting problem
by Rongxiang Tang 14 Feb '13

14 Feb '13

Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matter of the brain. Is there a way to fix that? Thanks, Catherine

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running freesurfer on multi core machine
by Jon Wieser 14 Feb '13

14 Feb '13

Hi, I am runnning fressurfer on a Mac with 2 3.06 Ghz 6-core intel Xeon processors. is it possible to run recon-all and trac-all on multiple cores. Jon

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CORRECTING DEFECT
by Varghese Chikku 14 Feb '13

14 Feb '13

Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processing failed for the same data set ,and patiently waited 36 hrs at Correcting Defect 10 before logging off .Do you know why this is happening.Does it have some thing to do with the data itself. In Thanks Chikku

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longitudinal processing of one timepoint
by Luigi Angelo Maglanoc 14 Feb '13

14 Feb '13

Dear FreeSurfer experts, I know that it is possible to submit data with only one timepoint into the longitudinal stream with FreeSurfer 5.2. My question is, what is the exact command? is it: 1) recon-all -base <templateid> -tp <tp1id> -all or 2) recon-all -base <templateid> -tp <tp1id> -tp <tp1id> -allI have accidently run them with the second command, and I am also wondering whether this will have a negative impact? Thank you for your time and consideration! Sincerely Luigi

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