Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

Monte Carlo correction
by Johnson, Eileanoir 20 Jun '14

20 Jun '14

Hi there, I am trying to run a monte carlo correction on my average subject, using the full mri-mcsim run with 10000 iterations (and about 200 participants). This is taking a long time, and the cluster I have access to has a limit of 72 hours which isn't long enough to finish processing. Is there a way to cut down on this processing time, i.e. cutting down on the iterations etc? Many thanks, Eileanoir

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mri_label2label results
by Yang, Daniel 20 Jun '14

20 Jun '14

Dear all, I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel

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Problem with freeview
by Bernardoni, Fabio 20 Jun '14

20 Jun '14

Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~>tcsh ~>source $FREESURFER_HOME/SetUpFreeSurfer.csh ~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~>cd $SUBJECTS_DIR ~>freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information. 1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64 Could anybody please telle me what's my problem? Thanks Fabio

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Can some send me rh.average.curvature.filled.buckner40.tif file
by Venkateswaran Rajagopalan 20 Jun '14

20 Jun '14

Dear All, when I run recon-all I encounter errro saying that rh.average.curvature.filled.buckner40.tif file is missing. I found this file missing in my average folder so if someone can send it as an attachment or guide me to where I can find it it will be great help. Many thanks in advance Venkat

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Control Points ignored
by Victor Kovac 19 Jun '14

19 Jun '14

Hello, I have run recon-all on two timepoints of a subject (MPS1011-4 and MPS1011-5). I added control points to MPS1011-4 after the initial recon-all processing because large areas of white matter were excluded. Unfortunately, ~50% of the control points I added were apparently ignored, as they did not cause the missed wm areas to be segmented (see attached images). I have run into this problem in a few other subjects as well, where large wm areas are missed even after adding control points and running recon-all -autorecon2-cp -autorecon3 The other timepoint exited with errors, leaving the brain unsegmented. Any advice on how to accurately analyze these timepoints would be greatly appreciated. Their recon-all logs are also attached. Thank you! Victor

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Decimate surface during recon-all
by Kai Schlamp 19 Jun '14

19 Jun '14

Hello again. I am still trying to project a label on a decimated surface. I tried to decimate the appropriate surface after recon-all and then to create a new label for this decimated surface, but this doesn't seem to work (see here <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36473.html>, unfortunately no answer yet). Is there a way to customize the recon-all pipeline, so that every surface that is generated is decimated? I guess, that this would solve the problem. Best regards, Kai

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Segfault error
by Jace Bradford King 19 Jun '14

19 Jun '14

Hello, I am running into a segfault error when trying to use tkmedit or tksufer. I am currently running OSX 10.7.5 and have the most current version of XQuartz installed. Below are the contents of the .xdebug files: .xdebug_tkmedit: tkmedit started: Wed Jun 18 10:58:41 2014 /Applications/freesurfer/tktools/tkmedit.bin bert brainmask.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/jaceking Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: .xdebug_tksurfer: Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut I also get a "Segmentation fault" note when trying to launch qdec. Do you have suggestions on how to fix this? Thanks in advance for your assistance. Best, Jace King

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CSF volume
by pfotiad＠nmr.mgh.harvard.edu 19 Jun '14

19 Jun '14

Hi FS community, I was wondering whether there is a way to calculate accurately the CSF volume with FreeSurfer (I have both T1 and T2 images). Should I just add the ventricular structures and the CSF volume reported in aseg.stats or is there another way to account for the sulcal CSF based on the T2 and add it to the other volumes? Thanks in advance, Panos

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Re: [Freesurfer] Seg fault (fwd)
by Cooke, Gillian 19 Jun '14

19 Jun '14

Hi Nick, Thank you so much for your response. Turns out that the XQuartz had updated to 2.7.6, I've reinstalled 2.7.5 and it is working! Finally I can finish this study! Best wishes, Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Beckman Institute University of Illinois, Urbana Email: gillian.e.cooke(a)gmail.com<mailto:gillian.e.cooke@gmail.com> gcooke(a)illinois.edu<mailto:gcooke@illinois.edu>

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Re: [Freesurfer] Linear Mixed Models in FS?
by jorge luis 19 Jun '14

19 Jun '14

Yes there is numerical instability when p-values becomes extremely low and your solution is OK. You are just being conservative. Your actual p-value might have been 1e-25 but you couldn't observe it exactly (got zero instead) because of numerical limitations of the Matlab's fcdf function. I'll fix this issue on github:https://github.com/NeuroStats this weekend. Best -Jorge >________________________________ > De: Lars M. Rimol <larilin(a)gmail.com> >Para: jorge luis <jbernal0019(a)yahoo.es> >CC: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >Enviado: Jueves 19 de junio de 2014 5:01 >Asunto: Re: [Freesurfer] Linear Mixed Models in FS? > > > >Hi Jorge, > >Thank you! Yes this makes sense, because this confirms that the second covariate in fact tests for an effect across all groups, just as I expected. >Now, there's another problem with these analyses: Please consider the attached figure lh_model1_01000_interaction_nopatch_lateral.tif, which shows a p-map (cortical > >area, smoothed with 30 mm fwhm) with two gray regions in the temporal lobe and the insula/IFG in the middle of highly significant regions. There is no darker blue transition > >into the non-significant regions. These gray regions appear to be artifacts based on eye balling of the maps. I checked the output of the significance testing in those regions and it > >appears that the output of this formula (in lme_mass_f.m) is extremely low: pval(i) = 1-fcdf(Fstat,szC,m); > >I assume there may be numerical instability when pval becomes extremely low? Could that explain this? > >I changed the code so that if > >1-fcdf(Fstat,szC,m) is zero or less than 1e-15, then pval(i) = max(1-fcdf(Fstat,szC,m),1e-15); > >(or, if it's negative pval(i) = min(1-fcdf(Fstat,szC,m),-1e-15) ) > >If it's not, then the old code applies: pval(i) = 1-fcdf(Fstat,szC,m); > >This seems to have fixed the problem as the figure model1_area_lh_01000_winteraction_wpatch_lateral.tif shows. Again, based on >eye-balling the maps. > >I have seen this problem in several data sets, both cortical and subcortical data. In all cases using a lower limit for 1-fcdf(Fstat,szC,m) - >either 1e-15 or 1e-20 - seems to fix the problem. > >Do you concur that the problem is numerical instability and is this a good way to fix it? > > >Thank you! > >yours, >LMR > > > > > >On Wed, Jun 18, 2014 at 3:49 PM, jorge luis <jbernal0019(a)yahoo.es> wrote: > > >> >>Hi LMR >> >> >>If the interaction term is not statistically significant then there is no evidence of the existence of two different groups in your sample (as far as the longitudinal trajectory is concerned they are all controls, the groups might be different at baseline though). This is why main effects are only tested after the interactions have been previously tested. In your model a common “base time slope” is assumed for both groups (the second coefficient) but you are also explicitly modeling the possibility of the case-group slope being exceeding the control/common base slope by an extra quantity. That quantity is the interaction term. >> >> >>Hope this makes sense >> >> >>Best >>-Jorge >> >> >> >> >> >>>________________________________ >>> De: Lars M. Rimol <larilin(a)gmail.com> >>>Para: FS maling list <freesurfer(a)nmr.mgh.harvard.edu> >>>Enviado: Miércoles 18 de junio de 2014 8:57 >>>Asunto: Re: [Freesurfer] Linear Mixed Models in FS? >>> >>> >>> >>>Hi Jorge, >>> >>>Thank you for your reply! >>> >>>Again considering the same model from before >>> >>> intercept(random effect) + centered age + group + group x centered age + sex >>> >>> >>>I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. >>> >>>On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. >>> >>> >>> >>>Just for the sake of argument, please consider the following model >>> >>> intercept(random effect) + (1-group) x centered age + group + group x centered age + sex >>> >>> >>> >>>and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only includes numbers from the control-group. Applying the contrast [0 1 0 0 0] to this model, would this not be more appropriate for consider the effect of [centered age] on the control-group alone? >>> >>>Given your previous answers I suspect I'm missing something here, but I would greatly appreciate if you could please take the time to explain to me how I've gone wrong. >>> >>>Thanks! >>>LMR >>> >>> >>>------------------------------------------------------------------- >>>Hi LMR >>> >>>1) Yes, you should >>>use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 >>>and Case 2) the model would be: >>> >>>intercept(random >>>effect) + centered age?(might be a random effect too)?+ ?Case1 + Case1 x centered age + Case2 + >>>Case2 x centered age + sex >>> >>>2)In model: >>> >>>intercept(random >>>effect) + centered age + group + group x centered age + sex >>> >>>the fourth coefficient is >>>the interaction term that represents the difference in slope between >>>the patient and control groups. This is easy to see from your >>>Question 1 equations. It's also easy to see from those equations >>>that [0 1 0 0 0] tests the effect of time in the control group since >>>the group-specific slope is only equal to the coefficient of the time covariate (the >>>second covariate) when the group covariate is zero (i.e for the >>>controls). >>> >>> >>>Hope this makes >>>sense. >>> >>>Best >>>-Jorge >>>-- >>> >>>yours, >>> >>>Lars M. Rimol, PhD >>>St. Olavs Hospital >>>Trondheim, >>>Norway >>>_______________________________________________ >>>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. >>> >>> >>> > > >-- > >yours, > >Lars M. Rimol, PhD >St. Olavs Hospital >Trondheim, >Norway > >

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Freesurfer June 2014