Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)
by MCLAREN, Donald 26 Sep '13

26 Sep '13

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist. The stipend program will provide at least 6 stipends for partial or full registration fees [if 24 attendees apply, you have a 25% chance of getting a stipend]. The exact breakdown of stipends provided will depend on the number of applicants and the cost of attending the conference for those applicants. The application for stipend requires: (1) A poster abstract (2) A 1-2 page Brainhack project proposal (pdf format) (3) NIH Biosketch/CV (pdf format) To apply, please send the above details to Donald McLaren ( mclaren.donald(a)gmail.com) This change is being made due to technical difficulties of the website. I will email everyone on Saturday morning to confirm that their application is being considered. If you do not receive and email on Saturday morning, please resend your application. The Brainhack 2013 Organizing Committee will decide which applications will receive stipends based on their abstract and proposed brainhack projects. The deadline to apply for one of the stipends is 11:59PM EST on September 27th. All decisions will be made by October 3rd and must be accepted within 24 hours of being awarded. Good luck. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Re: [Freesurfer] Surface to nifti prime vertices
by Douglas N Greve 26 Sep '13

26 Sep '13

I would actually put the data straight onto fsaverage, smooth there, and do the FSL analysis there. You will need to put it on fsaverage eventually for group analysis, and you're better off doing that before doing the FEAT analysis. Remember to turn off temporal pre-whitening when running FEAT. For nifti1, there is no solution to the prime number of vertices problem. The problem is fixed in nifti2, so, assuming that FSL is reading nifti2, you could write a mgh to nifti2 converter. But I would do it on fsaverage anyway doug On 09/26/2013 01:53 PM, Connor Lane wrote: > Hmm, that's unfortunate. > > The reason I'm interested in this surface to nifti conversion is that I'm trying to incorporate surface based pre-stats smoothing into my FSL fMRI analysis stream. My strategy has been: preprocess with FSL --> map to surface space and smooth --> convert mgh surface to nifti surface and continue with FSL analysis. > > Do you think the surface smoothing benefits of this kind of stream justify the trouble associated with either a) modifying the data as you suggest every time this factoring issue shows up, or b) writing an mgh <-> nifti utility that avoids the issue? > > Some other possible answers I've thought of are: > -After surface smoothing, map the functional data to fsaverage and then convert back to nifti (since we know there's no factoring problem with fsaverage). The drawback here is we never get to see statistics in subject-specific space. > -Switch from FSL to FsFast, where surface smoothing is built in. > > Or maybe I should forget about surface based smoothing altogether, and actually volumetric smoothing works just fine? > > I would really appreciate hearing your overall recommendation on this. > > Connor > > > > -- 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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Demean Covariates Qdec
by Erik Lindberg 26 Sep '13

26 Sep '13

Dear Doug and Freesurfers, I noticed that the DOSS option no longer exists in qdec and that Doug said there was a bug related to it. If i want to assess the differences in cortical thickness between groups while covariating for age and gender, since i don't expect any interactions, can i just demean the covariates and make my analysis in qdec with dods? Thanks!

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Re: [Freesurfer] [FreeSurfer] multiple sets of control points
by Bruce Fischl 26 Sep '13

26 Sep '13

Hi Francesco please cc the list so that others can answer! This isn't the way recon-all works, but I think you can achieve what you want by copying the control.dat to control.1.dat or some such before you add additional control points so you can always go back to a previous version cheers Bruce On Thu, 26 Sep 2013, Francesco Siciliano wrote: > Hi Bruce, > > When I edit a brain a second and third time, it is helpful to create new control point files while maintaining the old ones. Because edits are not an exact science, I've noticed that sometimes new problems arise after a first edit. In my experience, creating a new control.dat file and overwriting the old one will undo the edits of the original set of control points (hence why it is useful to have multiple sets such that the original set remains in place and the second set can adjust new errors that have arisen). I understand what you mean - I try to place all of the control points I need in one sweep - however I cannot anticipate with certainty the combined effect of my edits, thus some situations call for multiple sets of control points on subsequent edits. Is it not possible to have multiple sets of control points recognized during a recon-all? > > Thanks, > Francesco > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, September 26, 2013 12:06 PM > To: Francesco Siciliano > Cc: freesurfer(a)nmr.mgh.harvard.edu; Louis Nicholas Vinke > Subject: Re: [Freesurfer] [FreeSurfer] multiple sets of control points > > Hi Francesco > > recon-all assumes that all the control points are in the single file > <subject>/tmp/control.dat. Why are you separating them? Can you combine > them? > > cheers > Bruce > On Thu, 26 Sep 2013, Francesco Siciliano wrote: > >> Hello, >> I am currently having an issue getting my recon's to recognize multiple sets >> of control points. When I create a control point set, I make sure I select >> "control points", place them on the brainmask, and save them in the "tmp" >> folder as control.dat, control2.dat, control3.dat, etc. >> >> I have been using the command recon-all -autorecon2 -autorecon3 -s Subject1 >> >> There does not seem to be a problem when I just have one set of control >> points. However, when I have multiple sets, I can see where control points >> have not been taken into account and have not altered the intensity of the >> voxels at all. I currently have them re-running with the command recon-all >> -autorecon2-cp -autorecon3 -s Subject1 to see if that makes a difference. >> >> However, as I said before, one set of control points was previousy effective >> simply using the command recon-all -autorecon2 -autorecon3 -s Subject1 >> >> Any ideas? >> >> Thanks, >> Francesco >> >> >> >> Francesco Siciliano, B.A. Research Assistant >> Department of Child and Adolescent Psychiatry >> The New York State Psychiatric Institute >> Columbia University >> 1051 Riverside Drive, Unit 74 >> New York, NY 10032 >> (212) 543-6155 >> >> > > > 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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Editing multiple volumes simultaneously in Freeview
by Jonathan Holt 26 Sep '13

26 Sep '13

I'd like to know whether or not this is possible. I am unable, at this point to figure it out. In the volumes tab I've selected both of my volumes but it seems like voxel editing only takes effect on whichever volume is in the top position. I'd like to know if I could edit both at the same time similar to tkmedits brush option allowing one to edit both main and auxiliary volumes simultaneously. Jon

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Re: [Freesurfer] Watershed and Normalization Problem.
by Erica Tatham 26 Sep '13

26 Sep '13

Hello NMR users, Here is a link to my files containing the below Watershed Error. <http://gate.nmr.mgh.harvard.edu/filedrop2/?p=in9je36> Thank you for taking the time to look at the files. Erica Tatham Hi Erica if you upload this subject dir we will take a look cheers Bruce On Thu, 12 Sep 2013, Erica Tatham wrote: Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz and the transform.xfm, and both seem to be reasonable. I was hoping for some guidance/expert advice for how to precede from here. I have not tried to add control points as I am fairly novice to freesurfer and not quite sure how to complete this task. Thank you for any advise you are able to give, Cheers, Erica Error: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all.

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Mixed effects: is data ordering always required?
by Aldo Cordova 26 Sep '13

26 Sep '13

FreeSurfer's LME wiki site states: "For computational efficiency reasons, these tools require the data ordered according to time for each individual (that is, your design matrix needs to have all the repeated assessments for the first subject, then all for the second and so on)." The dataset I need to process includes pairs (and trios) of brothers, and although they're definitely clustered statistical units, there is no pre-defined sorting of individuals within a family (at least in this study). Please note that mine is not a longitudinal study, and the need for a cluster-correction arises from brotherhood... Is FreeSurfer's LME still the appropriate choice? How should this dataset be processed in FreeSurfer for cortical thickness analysis? Would you recommend another option? Regards, Ricardo

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[FreeSurfer] multiple sets of control points
by Francesco Siciliano 26 Sep '13

26 Sep '13

Hello, I am currently having an issue getting my recon's to recognize multiple sets of control points. When I create a control point set, I make sure I select "control points", place them on the brainmask, and save them in the "tmp" folder as control.dat, control2.dat, control3.dat, etc. I have been using the command recon-all -autorecon2 -autorecon3 -s Subject1 There does not seem to be a problem when I just have one set of control points. However, when I have multiple sets, I can see where control points have not been taken into account and have not altered the intensity of the voxels at all. I currently have them re-running with the command recon-all -autorecon2-cp -autorecon3 -s Subject1 to see if that makes a difference. However, as I said before, one set of control points was previousy effective simply using the command recon-all -autorecon2 -autorecon3 -s Subject1 Any ideas? Thanks, Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
by Douglas N Greve 26 Sep '13

26 Sep '13

Hi Daniel, please remember to post to the list instead of me directly ... to answer your question, this is probably just a matter of scaling. Try removing the mean and dividing by the standard deviation of the linear, quad, and cubic. More recent versions of FS should do this automatically. doug On 09/25/2013 06:01 AM, Daniel Klein wrote: > Hi Doug, > > thanks a lot. > I want to use qdec for this pupose. > > When i add Age (cubic) as continous factor and age as nuisance factor > in the model it works fine. > > In the model age (square) as continous factor and age as nuisance i > get the following error: > > Creating output directory > /Users/dolphinede/Desktop/Probanden/qdec/Untitled > Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh > INFO: gd2mtx_method is dods > Saving design matrix to > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat > Normalized matrix condition is 22042.4 > Design matrix ------------------ > 1.000 169.000 13.000; > 1.000 225.000 15.000; > 1.000 225.000 15.000; > 1.000 256.000 16.000; > 1.000 225.000 15.000; > 1.000 400.000 20.000; > 1.000 196.000 14.000; > 1.000 256.000 16.000; > 1.000 144.000 12.000; > 1.000 169.000 13.000; > 1.000 361.000 19.000; > 1.000 289.000 17.000; > 1.000 289.000 17.000; > 1.000 196.000 14.000; > 1.000 361.000 19.000; > 1.000 196.000 14.000; > 1.000 169.000 13.000; > 1.000 324.000 18.000; > 1.000 225.000 15.000; > 1.000 225.000 15.000; > 1.000 324.000 18.000; > 1.000 529.000 23.000; > 1.000 400.000 20.000; > 1.000 484.000 22.000; > 1.000 529.000 23.000; > 1.000 324.000 18.000; > 1.000 484.000 22.000; > 1.000 324.000 18.000; > 1.000 256.000 16.000; > 1.000 361.000 19.000; > 1.000 256.000 16.000; > 1.000 289.000 17.000; > 1.000 289.000 17.000; > 1.000 256.000 16.000; > 1.000 256.000 16.000; > 1.000 441.000 21.000; > 1.000 289.000 17.000; > 1.000 289.000 17.000; > 1.000 225.000 15.000; > 1.000 256.000 16.000; > 1.000 225.000 15.000; > 1.000 225.000 15.000; > 1.000 400.000 20.000; > 1.000 289.000 17.000; > 1.000 324.000 18.000; > 1.000 256.000 16.000; > 1.000 484.000 22.000; > 1.000 361.000 19.000; > 1.000 256.000 16.000; > 1.000 529.000 23.000; > 1.000 400.000 20.000; > 1.000 484.000 22.000; > 1.000 441.000 21.000; > 1.000 324.000 18.000; > 1.000 361.000 19.000; > 1.000 484.000 22.000; > 1.000 361.000 19.000; > 1.000 441.000 21.000; > 1.000 324.000 18.000; > 1.000 144.000 12.000; > 1.000 361.000 19.000; > 1.000 441.000 21.000; > 1.000 441.000 21.000; > 1.000 441.000 21.000; > 1.000 529.000 23.000; > 1.000 324.000 18.000; > 1.000 361.000 19.000; > 1.000 289.000 17.000; > 1.000 529.000 23.000; > 1.000 484.000 22.000; > 1.000 441.000 21.000; > 1.000 196.000 14.000; > 1.000 169.000 13.000; > 1.000 196.000 14.000; > 1.000 361.000 19.000; > 1.000 196.000 14.000; > 1.000 169.000 13.000; > 1.000 400.000 20.000; > 1.000 361.000 19.000; > -------------------------------- > ERROR: matrix is ill-conditioned or badly scaled, condno = 22042.4 > -------------------------------- > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > If you seek help with this problem, make sure to send: > 1. Your command line: > mri_glmfit --y > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh --fsgd > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/qdec.fsgd dods > --glmdir /Users/dolphinede/Desktop/Probanden/qdec/Untitled --surf > fsaverage lh --label > /Users/dolphinede/Desktop/Probanden/fsaverage/label/lh.aparc.label --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat > --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-pial_lgi-Alter2-Cor.mat > > 2. The FSGD file (if using one) > 3. And the design matrix above > Error in Analyze: command failed: mri_glmfit --y > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh --fsgd > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/qdec.fsgd dods > --glmdir /Users/dolphinede/Desktop/Probanden/qdec/Untitled --surf > fsaverage lh --label > /Users/dolphinede/Desktop/Probanden/fsaverage/label/lh.aparc.label --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat > --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-pial_lgi-Alter2-Cor.mat > > Best wishes > > Daniel > > > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Di, 24 Sept 2013 9:35 pm > Betreff: Re: [Freesurfer] Effects of age on different parameters > (thickness, lGI...) > > Hi Daniel, you can do this the way that you have specified, but, as you > point out, one of the covariates will have to be a nuisance variable, > meaning that it will not get tested. If you need to test all 3, then > you'll have to use mri_glmfit with and FSGD file > doug > > > On 09/24/2013 05:39 AM, Daniel Klein wrote: > > Dear FreeSurfer experts, > > > > I want to test linear, square and cubic effects of age on different > > parameters (thickness, lGI....) with qdec. > > > > I add age (square) and age (cubic) as column in my qdec table. > > > > Am i right to see only the square effects: > > Add Age square as continous factor and age (maybe age cubic too?) as > > nuisance factor in the model. > > > > Best wishes and thanks a lot. > > > > Daniel > > > > > > _______________________________________________ > > 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 > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > 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. > -- 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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Surface to nifti prime vertices
by Connor Lane 26 Sep '13

26 Sep '13

Hi all, I am trying to convert a surface file to nifti using mri_surf2surf. The problem is that my surface has a prime number of vertices, so I can't use —reshape. Is there a way around this issue? Thank you in advance, Connor Lane

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Freesurfer September 2013