Freesurfer

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30132 discussions

R: Re: Statistical concerns
by stdp82＠virgilio.it 19 Aug '13

19 Aug '13

Dear Doug, thank you very much for your reply!Point c, is now ok. Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-ago-2013 20.34 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Statistical concerns On 8/1/13 7:56 AM, stdp82(a)virgilio.it wrote: Hi list, I have some questions please. 1- I have carried out Monte Carlo Simulation to assess the difference among three groups (23, 24 and 32 subjects). Main results were confirmed also by FDR, but I prefer to shown the Monte Carlo becouse it better describes my thesis. Recently I have submitted my paper but a referee asked me "Why use cluster based Monte Carlo methods for correction of multiple comparisons instead of the more conventional vertex-wise FDR correction? I suspect the former is much less conservative than the latter. It would be interesting to know the results for FDR corrected thresholds (p<0.05), and whether the present results would remain statistically 'active'. Now, I'm looking literature and I'm noting that several recent articles published on top journals used Monte Carlo Simulation (Ehrlich et al., 2013 Schizophr Bull.; Sasamoto et al., 2013 Schizophr Bull). What do you think about it? How do you advise to reply to the referee? I'd like to show Monte Carlo results. This is a very surprising request by the reviewer. FDR is hardly "conventional", and the brain imaging community has been using clusterwise correction for 20 years. I'm not even sure what "voxelwise" FDR is. Is that different than the one introduced by Genovese in 2002? As for how to respond to the reviewer, I'm not sure. You can certainly make a case that doing the clusterwise correction is the "industry standard". You can also site a paper out of the Friston group from a few years back critisizing the Genovese-style FDR. Have you applied the Genovese-style FDR that we offer in FS? If that works out, then there is no need to fight with the reviewer. 2- I should do also correlation analysis. I'm using QDEC as recommanded in guideliness (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freev…) In one group, after fsgd creation, I'm performing correlation analysis between thickness and neuropsychiatric test scores (it has been put in covariete windows-it should be dipendent factor). I'm also putting some nuisance factors (they should be dipendent factor in the regression analysis) to exclude the their effect on data. a- Is this procedure corrected? b- Is corrected to talk regression analysis in the text of my manuscript? c- Is corrected whether I explain this correlation analysis as reported in the description performed above? I'm confused. If you are using qdec, then you put your factors (which are independent) in the qdec table, not in the FSGD file. Otherwise the procedure looks correct and you can talk about "regression analysis" in your ms. I don't understand (c). doug Thank you very much, Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Trouble with mris_label2annot
by Stephen Politzer-Ahles 19 Aug '13

19 Aug '13

Hello, I have a set of custom labels and I want to plot them all at once on one brain, so I'm trying to use mris_label2annot for that. However, I'm getting several problems. Here is an example of what I get: http://i.imgur.com/Sw1Z9UT.png The labels I'm using were originally defined on a decimated source space (that was created using the MNE toolbox), so it's normal that most of them show up as lots of dots rather than contiguous areas. However, I don't know why some of them actually are showing up as contiguous areas; when I plot the labels one by one, all of them show up as series of dots rather than contiguous areas, so it seems that creating the annotation is messing something up. I also have a few other problems that you can't see in the image. Firstly ( and most seriously), the locations of the labels that show up when I plot this annotation do not at all match where the labels actually are--that is, if I hover my mouse over one of the labels in this, it doesn't match where the label actually should be if I plot that label by itself. Secondly, there seems to be some indexing issue with my color lookup table--I have 58 labels per hemisphere, so I created a color table that starts at label 0 and goes up to 57 (as per the example at http://ftp.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles and the automatically-generated annotations such as lh.aparc2009s.annot). In my color lookup table, label 0 is called 'amygdala' and label 1 is called 'anteriorcommisure'. But when I actually run mris_label2annot, the output seems to suggest that the program is 1-indexed instead of 0-indexed (because it skips the 0th label, andlooks for the 57th label, see output snippet below): Reading ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab Number of ctab entries 58 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ ... cmdline mris_label2annot --ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab --subject fsaverage --annot MRATparc --hemi lh --l lh.amygdala.label --l lh.anteriorcommissure.label --l lh.anteriornucleus.label --l lh.ba1.label --l lh.ba10.label --l lh.ba11.label --l lh.ba13.label --l lh.ba17.label --l lh.ba18.label --l lh.ba19.label --l lh.ba2.label --l lh.ba20.label --l lh.ba21.label --l lh.ba22.label --l lh.ba23.label --l lh.ba24.label --l lh.ba25.label --l lh.ba27.label --l lh.ba28.label --l lh.ba29.label --l lh.ba3.label --l lh.ba30.label --l lh.ba31.label --l lh.ba32.label --l lh.ba33.label --l lh.ba34.label --l lh.ba35.label --l lh.ba36.label --l lh.ba37.label --l lh.ba38.label --l lh.ba39.label --l lh.ba4.label --l lh.ba40.label --l lh.ba41.label --l lh.ba42.label --l lh.ba43.label --l lh.ba44.label --l lh.ba45.label --l lh.ba46.label --l lh.ba47.label --l lh.ba5.label --l lh.ba6.label --l lh.ba7.label --l lh.ba8.label --l lh.ba9.label --l lh.caudatebody.label --l lh.caudatehead.label --l lh.caudatetail.label --l lh.corpuscallosum.label --l lh.culmen.label --l lh.declive.label --l lh.hippocampus.label --l lh.hypothalamus.label --l lh.mammillarybody.label --l lh.medialdorsalnucleus.label --l lh.optictract.label --l lh.pulvinar.label --l lh.putamen.label ... subject fsaverage hemi lh SUBJECTS_DIR /media/LAPTOP_HD/WW3_newanalysis/subjects ColorTable /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab AnnotName MRATparc nlables 58 LabelThresh 0 0.000000 Loading /media/LAPTOP_HD/WW3_newanalysis/subjects/fsaverage/surf/lh.orig 1 3988503 anteriorcommissure 2 11811863 anteriornucleus 3 3957823 ba10 ... 56 1326221 pulvinar 57 14423183 putamen 58 -1 NOT_FOUND Does anyone have suggestions about any or all of these issues? Thank you, Steve Politzer-Ahles Stephen Politzer-Ahles New York University, Abu Dhabi Psychology Department http://www.nyu.edu/projects/politzer-ahles/

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error for autorecon3
by Troebinger, Luzia 19 Aug '13

19 Aug '13

Hi all, I am trying to run recon-all on a structural for one of my subjects, but freesurfer exited with errors during the last few stages (the ones covered by autorecon-3). It appears that it is just missing some label - the problem occurs at the following stage: painting output onto subject ME. processing subject lh.EC_average... MRISread (filename) could not open file I've used freesurfer before, same subject directory, but didn't get this error - it appears from the path after the MRISread command that it is just the subject directory, but not the directory for this particular subject. It appears freesurfer is looking for this file, which it can't find: /home/virtualuser/freesurfer/s_sub/lh.EC_average/surf/lh.sphere.reg where /home/virtualuser/freesurfer/s_sub is my subject directory. Can anyone advise as to how to fix this? Any help would be much appreciated. Best Luzia

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Re: [Freesurfer] freeview problem
by Salil Soman 19 Aug '13

19 Aug '13

Thank you Zeke. I am trying to run freeview remotely and display locally on a machine (using Xming). The computer from which I am connecting can successfully run freeview from a different ubuntu 13 machine (one which does not have a cuda graphics card / cuda drivers). When I run glxgears (required me to install mesa-utils), for the NV-GLX missing on display localhost:10.0. A window did popup via xming, but it was black. While it was up the remote machien kept listing x frames in y seconds = z fps The machine did have cuda 5.0 working with the nvidia 319 linux driver, so freesurfer could be gpu accerlated. Any suggestions on how to fix this would be great. A similar problem I would like to run by you is regarding the local display on the other ubunut machine I mentioned above. I can connect to this other machien remotely and run freeview, however if I actually use the local monitor attached to the machine, the frreeview window comes up, but in place of imaging data or black, it shows a kind of tie-dye color pattern. The rest of the screen is normal ubuntu, but the freeview window has problems. This other machine has an nivida card that predates cuda (and so no cuda drivers are installed). Any suggestions on how to fix this problem would also be a great help. Best wishes, Sal On Fri, Aug 16, 2013 at 8:13 AM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > Hello Sal, > > Are your trying to run freeview remotely and display locally machine? If > you type 'glxgears' at the command line does a window popup displaying > spinning gears? > > -Zeke > > > > On 08/16/2013 05:55 AM, Salil Soman wrote: > >> Hi, >> >> When I try to run freeview on my ubuntu 13 machine, running the nvidia >> 5.0 cuda drivers, I get the following errors: >> >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> X Error: GLXBadContext 150 >> Extension: 143 (Uknown extension) >> Minor opcode: 5 (Unknown request) >> Resource id: 0x8000c0 >> X Error: GLXBadContext 150 >> Extension: 143 (Uknown extension) >> Minor opcode: 5 (Unknown request) >> Resource id: 0x8000c0 >> X Error: GLXBadContext 150 >> Extension: 143 (Uknown extension) >> Minor opcode: 5 (Unknown request) >> Resource id: 0x8000c0 >> >> Any suggestions on how i can fix this problem? >> >> Thanks! >> >> Sal >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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Talairach error - Talairach file seems to not be written correctly.
by West, John D. 19 Aug '13

19 Aug '13

Hello. We are trying to run freesurfer on a Super Computing system here at IU. Unfortunately, we keep running into the following error: #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 18 14:17:32 EDT 2013 /N/dc/projects/shenlab/subjects/10025_5/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ltMNIreadEx:transforms/talairach.xfm does not start as 'MNI Transform File' ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux nid00170 2.6.32.59-0.7.1_1.0401.6845-cray_gem_c #1 SMP Thu Nov 15 00:24:59 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10025_5 exited with ERRORS at Sun Aug 18 14:17:37 EDT 2013 For more details, see the log file /N/dc/projects/shenlab/subjects/10025_5/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The talairach file shows this: 1.059250 0.121638 -0.012966 -0.232872 -0.118758 0.992805 0.165794 -34.672363 0.032261 -0.111376 1.084429 -0.219055; Note, the file does not have the typical header. We've run this same subject on other systems with no issue. Is there any reason the header would not be written? Any help would be greatly appreciated. Thanks. -John West Systems Administrator IU Center for Neuroimaging

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Re: [Freesurfer] Longitudinal Two stage model limitations
by Martin Reuter 18 Aug '13

18 Aug '13

Yes sounds good. Maybe say "depending on the number and spacing of time points" . As distance in time is also important. And maybe you want to cite our longitudinal paper 2012 neuroimage within subject template ... Good luck with your paper. Best Martin Sent via the Samsung Galaxy S™ III, an AT&T 4G LTE smartphone -------- Original message -------- From: Alex Hanganu <al.hanganu(a)yahoo.ca> Date: To: FS Mailing List <Freesurfer(a)nmr.mgh.harvard.edu> Cc: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Longitudinal Two stage model limitations Dear Martin, we used the longitudinal two stage model for our analysis and we are writing the manuscript. In the discussions we want to add the limitations of this procedure, as described in the wiki. We want to say that this model "does not account for different certainty of within subject slopes depending on the number of time points, but we used the same number of time points for all subjects, so this disadvantage was diminished considerably". Can you please tell if this sentence is correct, and if I understood correctly this limitation ? Thanks, Alex.

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Re: [Freesurfer] Antw: Re: [tracula] error running trac-all -prep
by Borsodi Florian 18 Aug '13

18 Aug '13

Hi Anastasia, Thanks for your help. I renamed the directories and reran trac-all. It worked for the moment. However, then I got another error: "bvecs and bvals don't have the same number of entries." I don't know why, because they actually have the same number of entries. I attached the logfile so that you may see what is going on. The error occours at line 1463. Thank you in advance for your help. Sincerely, Florian >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> Hi Florian - I see what's going on. Can you please rename the directory /data/physics/florian/nii into something that doesn't include "nii", and rerun? Because "nii" is a file extension, this confuses some of the scripts. Thanks, a.y On Thu, 15 Aug 2013, Borsodi Florian wrote: > Hi Anastasia > > I ran the command you sent me and it runs without any errors. > I also attached the command line for you. > > Furthermore i ran data with 12 diffusion directions and i keep getting the > same kind of problems. > > sincerely > Florian > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr >>> > > Hi Florian - Can you please run this command directly on the command line > and see if there are any errors? > > flip4fsl > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > Thanks, > a.y > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia > > > > Thank you for your answer. > > > > Yes, those files exist. > > I also extracted the bvec an bval files with anotther software then > dcm2nii > > and i keep getting the same kind of error. > > Also, about the 6 diffusion direction, those data i sent you, are just > > testdata for running tracula. > > > > sincerely > > Florian > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr >>> > > > > Hi Florian - Do these files exist? > >/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs > > > > >/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and this > > has nothing to do with the error you're getting) I have to warn you that > > you may not be able to get good results running probabilistic tractography > > on this data. It looks like you're acquiring the same 6 diffusion > > directions, repeated 8 times. Six directions is the absolute minimum for > > reconstructing the tensor model, but will probably not be sufficient for > > the crossing fiber model that bedpostx reconstructs (and is used by > > tracula). Your scan time is better spent acquiring 48 different > > directions, rather than the same 6 directions 8 times. > > > > a.y > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > Hello, > > > > > > I have been trying to run tracula on my data and i keep getting the same > > > kind of error repeatedly. > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > diffusion protocol. However, tracula cannot read the bvec and bval data > > out > > > of the dicom header. Therefore, I implemented bvec and bval files into > the > > > config file. > > > After doing so, I got the error which says that tracula cannot find the > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > I have tried many options, but still cannot find a solution. > > > I am hoping to get some troubleshooting help. > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > files. > > > To uphold patient confidentiality, I have encode the name patient's data > > as > > > "AAAAAA". > > > > > > I believe the problems are the bvec and bval files or their structures. > > The > > > log-file lete me assume this, especially the lines 202 - 205, 264 - 268 > > and > > > 1480 - 1484. > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > With kind regards, > > > > > > Florian Borsodi > > > Department of Neurology > > > Medical University of Graz > > > > > > > > > > > > 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 > >

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Robust brain extraction using Freesurfer
by Sourena Soheili-Nezhad 18 Aug '13

18 Aug '13

Hello Freesurfer community I am trying to perform a voxelwise longitudinal analysis (outside FS). I have been searching for brain extraction algorithms and it seems that Freesurfer provides the most accurate solution. If the primary objective is highest accuracy, should I use recon-all products proximal to surface generation (e.g. brain.mgz), or it would be wiser to further proceed to surface generation? Could someone advise me how to stop the recon-all at an optimal step? Cheers, Sourena Soheili-Nezhad -- Sourena Soheili-Nezhad, M.D. Research Associate Laboratory of Computational Neuroscience Institute for Cognitive Science Studies and Tehran University of Medical Sciences Tehran, Iran

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mris_thickness threshold
by Giusy Chinnici 18 Aug '13

18 Aug '13

Hi all, I'd like to understand the difference in using the default value for maximum threshold (5 mm) instead of a custom value in mris_thickness function. Is the map of cortical thickness the same in both cases and the difference resides in the saturation (all values above 5mm are cut to 5 mm) or do we have a completely different map (all values above 5 mm have their own value but saturated value is displayed from 5 mm and above)? please find in attachment an example of what I'm saying... I aspected to find same values for thickness within the threshold value, why this is not the case? Thanks cheers -- Giusy Chinnici

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Longitudinal Two stage model limitations
by Alex Hanganu 18 Aug '13

18 Aug '13

Dear Martin, we used the longitudinal two stage model for our analysis and we are writing the manuscript. In the discussions we want to add the limitations of this procedure, asdescribed in the wiki. We want to say that this model "does not account for different certainty of within subject slopes depending on the number of time points,but we usedthe same number of time points for all subjects, so this disadvantage was diminished considerably". Can you please tell if this sentence is correct, and if I understood correctly this limitation ? Thanks, Alex.

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