Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

mris_calc recon-all problem
by Johnson, Eileanoir 27 Nov '13

27 Nov '13

Hi there, I am currently trying to run freesurfer version 5.3.0 on a cluster and am encountering an error when running recon-all. The error is: Writing to ./tmp.mri_nu_correct.mni.2867/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2867/nu2.mnc ./tmp.mri_nu_correct.mni.2867/nu2.mnc mul Linux blue34 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 22057 exited with ERRORS at Wed Nov 27 12:31:54 GMT 2013 Does anyone know what might be causing recon-all to exit at this point? I have attached the full log file. Thanks, Eli Eli Johnson Research Assistant, Track-On UCL Institute of Neurology, Box 104 Queen Square, London, WC1N 3BG Tel:+44(0)207 242 0038

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can I run Monte Carlo simulation without calling mri_glmfit
by Wang, Xin 27 Nov '13

27 Nov '13

Hello, I repeated same mri_glmfit at multiple depth of cortical thickness and merged the maximal values of the sig.mghs for all depths to a merged_sig.mgh (as in Wang X, et al. Neuroimage. 49(4):3075-85; 2010). I need to run Monte Carlo simulation<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/030604.html> on the merged_sig.mgh. I have the .fsgd and .mtx files for this glm design but I don't have a smoothed input image as fs.8.mgh for this merged sig.mgh. Can I modify the mri_glmfit-sim to run the correction without calling fs.8.mgh? Thank you. Xin

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Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
by Bruce Fischl 26 Nov '13

26 Nov '13

Hi Pablo it also depends on how much ram it has. You should be able to run 1 significantly faster using the -openmp 8 flag to recon-all, or 8 (if you have enough ram, probably at least 32G) cheers Bruce On Tue, 26 Nov 2013, pablo najt wrote: > Dear Bruce,Last week I emailed with the question of how many recon -all > separate subjects I could run in parallel with the FS version 5.3 for Centos > 6. You answered that this depends on how many cores my machine has. > I just found out that our workstation has two processors with 4 cores each > (8 cores in total). > Would you be able to tell me how many subjects could I run in parallel with > our workstation? > Thank you for your support, > Pablo > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: pablonajt(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > Hi Pablo > > it depends on how many cores you have > > Bruce > On Thu, 21 Nov 2013, pablo najt wrote: > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I a > m > > wondering up to how many recon -all for separate subjects I can run in > > parallel. With the version of Snow Leopard 32b I was running two at a time > > and it took around 20 hours. Would I be able to run 6 subjects in parallel > ? > > If so would this process still efficient or there is an optimum number? > > Thank you, > > Pablo > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > From: zkaufman(a)nmr.mgh.harvard.edu > > > To: garikoitz(a)gmail.com > > > CC: pablonajt(a)hotmail.com; freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > CentOS 6 > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > CentOS6 build. > > > > > > -Zeke > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any > > > > reason to not use this version in your CentOS 6, if you have some othe > r > > > > requirements maybe Nick or Zeke could help you better, I am just an us > er > > :) > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt(a)hotmail.com > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > Dear Gari, > > > > Thank you for the advice. One additional question. > > > > Considering that I will start from scratch the processing in the > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > Thanks, > > > > Pablo > > > > > > > > ---------------------------------------------------------------------- > -- > > > > From: garikoitz(a)gmail.com <mailto:garikoitz@gmail.com> > > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > > To: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > and CentOS 6 > > > > > > > > > > > > Hi Pablo, > > > > you shouldn't mix different OS-s or software version in the same > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > operating system version on anatomical volume and cortical thickness > > > > measurements. /PloS one/, /7/(6), e38234. > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > it works too). > > > > regards! > > > > Gari > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt(a)hotmail.com > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > Dear FS experts, > > > > I am forwarding my question (please see below), in case it got > > > > lost among the intense flow of messages. > > > > Thank you for your consideration. > > > > Pablo > > > > > > > > ---------------------------------------------------------------------- > -- > > > > From: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > Date: Mon, 18 Nov 2013 16:38:41 +0000 > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > and CentOS 6 > > > > > > > > > > > > Dear FS experts, > > > > I have a question about compatibility for running recon-all > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > wondering if I could process additional subjects in parallel > > > > with this other machine that are also intended to be included in > > > > the longitudinal stream. > > > > Also, I am not sure about whether I should be installing in the > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > because of compatibility issues. > > > > Thank you very much for your attention, > > > > Pablo > > > > > > > > > > > > _______________________________________________ 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. > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > _______________________________________________ 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. > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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. > >

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talairach_mixed_with_skull.gca file missing in average directory of local version stable5_3_0
by Koene Van Dijk 26 Nov '13

26 Nov '13

Hi there, We've been using this local version of Freesurfer: /cluster/freesurfer/centos6_x86_64/stable5 And this file was relevant: /cluster/freesurfer/centos6_x86_64/stable5/average/talairach_mixed_with_skull.gca We want to switch to the newest version of Freesurfer at the beginning of a new study but we can't find that "talairach_mixed_with_skull.gca" file in the /cluster/freesurfer/centos6_x86_64/stable5_3_0 directory. Is it possible to also include the "talairach_mixed_with_skull.gca" file in: /cluster/freesurfer/centos6_x86_64/stable5_3_0/average/? Thanks, Koene -- Koene R.A. Van Dijk, PhD Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology - Massachusetts General Hospital 149 Thirteenth Street (Suite 2301) Charlestown, MA 02129

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Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit
by Clark Fisher 26 Nov '13

26 Nov '13

Thanks again, I have 3 subjects, and want to tests for effects using data collected across all 3 subjects. The multiple sessions for each subject have already been concatenated into a single BOLD folder (3 folders total: 1 for each subject). I have actually already performed the fixed effects analysis by concatenating all 3 subjects into a single bold folder and re-running the first level analysis. While that works, I now want to try to normalize the data for each subject to minimize the variability introduced by the contrast agent we use, and that would be easier to do by normalizing the outputs of the first level analysis. If I wanted to normalize per-subject and then combine them into a first level analysis, what would be the best way to do this? My naive assumption would have been that using glmfit for this should be very similar to the repeated measures ANOVA example that is on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) Rather than time points for each subject, I will have the beta from each condition for each subject. In both cases (multiple time points from a single subject and multiple conditions from a single subject/set of runs), the within-subject measurements are not independent. How is my situation different? Cheers, Clark On Nov 26, 2013, at 1:41 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > Are the different input to glmfit different runs within a session or across sessions? Either way, for within subject analysis, can you put all of the runs into a single "bold" folder? Then it automatically does the FFX analysis across runs, which can include an F-test. The problem is that glmfit expects all the inputs to be independent, which conditions within a run will not be. > doug > > > On 11/25/2013 01:35 PM, Clark Fisher wrote: >> Thanks Doug, >> >> I had forgotten that my roadblock was actually in isxconcat_sess, not mri_glmfit. This worked out great. >> >> Following this up, how would you recommend calculating the fixed-effects significance of a complex (within subject) contrast with mri_glmfit? For simple contrasts, I have been calculating the contrast at the single subject level, then performing an osgm fixed-effects analysis on the output ces and cesvar volumes for each subject. However, I have some 2D F-contrasts that don't output ces volumes (naturally). >> >> One possibility would be to concatenate the ces and cesvar from the omnibus contrasts of each subject, set up an appropriate fsgd (as in http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) and then define the contrasts at the level of mri_glmfit with .mtx files. Would that be the way to go? >> >> Thanks, >> Clark > > -- > 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/ > > > > 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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tkmeditParcColorsCMA
by André Ribeiro 26 Nov '13

26 Nov '13

Dear Freesurfer, Is it possible to obtain a label image with tkmeditParcColorsCMA regions, similar to aseg+aparc.mgz or aparc.a2009s+aseg.mgz ? If so how should I proceed ? Thank you in advance. Regards, Andre Santos Ribeiro

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Bad white surfaces
by Yue Cui 25 Nov '13

25 Nov '13

Hi Freesurfers: I have processed images acquired from GE Sag 3D Bravo sequence, however, the white surfaces are always messy and extend into gray matter (please see the attached example). The CNR is not bad: white = 96.0+-10.2, gray = 66.4+-18.0, csf = 38.1+-19.3 gray/white CNR = 2.053, gray/csf CNR = 1.149 lh CNR = 1.601 white = 95.8+-10.6, gray = 65.9+-18.4, csf = 36.4+-19.0 gray/white CNR = 1.985, gray/csf CNR = 1.246 rh CNR = 1.616 total CNR = 1.608 Bad white surface seems a sever problem for us, as it happens for every subject. Is it a reason of low GM/WM contrast? Does anyone have an idea about how to fix this kind of error? Thanks so much. Regards, Yue

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Re: [Freesurfer] glm_fit --prune
by Douglas N Greve 25 Nov '13

25 Nov '13

In that case, I think you will want to change the design at each voxel based on which subjects are present. I have not tried to do this with pvr, but there is no reason it should not work. To do this, create a binary volume from your data that has the 0s in it, something like mri_binarize --i y.mgh --abs --min .0000000000001 --o framemask.mgh The run mri_glmfit with --frame-mask framemask.mgh doug On 11/08/2013 01:11 PM, celine(a)nmr.mgh.harvard.edu wrote: > Thanks Doug, > Actually it is still the --pvr analysis, so I am regressing vertex by > vertex two different modalities in one group of subjects, but for one of > them, we apply a threshold to remove regions that have bad quality data. > Let me know if I am not clear! > Celine > >> you will want to use the -no-prune flag.If thisis a group analysis, you >> should be very, very careful that you know what you are doing. In >> general, setting values to 0 prior to group analysis will create biased >> results. What you really need to do is have adifferent model for each >> voxel that includes/excludes certain subjects at certain voxels. If this >> is what you want, let me know and I'll give you instructions on how to >> do it. >> >> doug >> >> >> On 11/08/2013 12:46 PM, celine(a)nmr.mgh.harvard.edu wrote: >>> Hi, >>> When using glm_fit with an input volume that has many voxels with a 0 >>> value (due to a previous thresholding for quality reasons), and the >>> voxel >>> removes might be distributed randomly across our population, is there a >>> way not to take into account those voxels in the glm_fit model? I saw >>> the >>> --pune flag, but I am not sure if it is the one to use. >>> Thanks >>> Celine >>> _______________________________________________ >>> 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 >> >> >> > -- 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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Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups
by Rujing Zha 25 Nov '13

25 Nov '13

Dear professor Bruce, Thanks for your attention. After recon-all, I get the cortex thickness of all subjects. Then I check the segmentations by tkmedit your_subject_name brainmask.mgz -surfs -aseg. However, my fundamental knowledge is so little that I donot know whether the quality of segmented data I can use in further analysis. That is to say, I donot know whether 3d structure of subjects is appropriate in further cortex thickness analysis. Thanks, All the best. 2013-11-25 Rujing Zha 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2013-11-25 22:23 主题：Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Rujing, sorry, I don't understand. Can you clarify what you are trying to do? Bruce On Mon, 25 Nov 2013, Rujing Zha wrote: > Dear freesurfer experts, > I met a question about how to decide objectively whether I can use the > segmented data of one subkects to analyze cortex thickness between 2 groups. > Thanks. > All the best. > > 2013-11-25 > > ____________________________________________________________________________ > Rujing Zha > > _______________________________________________ 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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curvature and its normalisation
by Koopmans, P.J. (Peter) 25 Nov '13

25 Nov '13

Dear all, Could anyone tell me how to interpret the curvature files that you can create with mris_curvature/mri_make_surfaces? The description on the website tells that the values represent something like: Value in curvature file(*.H) = 1/R, with R being the radius of a sphere tangent to the white matter surface with units in mm. It gets slightly more complicated however due to a normalisation step: In recon-all, the normalisation flag is turned on by default. To what are the values normalised? Normalising R to the local cortical thickness or something similar? Or is normalised referring to statistical procedures like a z-transform or equivalent perhaps? I am interested in the local geometry of the cortex and need to be able to interpret a value in millimetres but at the moment I don't know whether the default normalised values already are in 1/mm and without scaling or that I should re-run it without the normalise flag. Cheers Peter

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Freesurfer November 2013