Freesurfer

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30132 discussions

Flip brain
by Tadeu Kubo 18 Jul '12

18 Jul '12

Hi Dear FS experts, Doug sent these links, but I can't download them. Do you have the new links? Download these filesftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregf… Thank you. Regards, Tadeu

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Hc segmentation: crosssectional stream with v4.5, longitudinal with v5.1
by Wenger, Elisabeth 17 Jul '12

17 Jul '12

Dear FreeSurfer experts, we have processed a dataset crossectionally within version 4.5, and then ran the longitudinal stream with v5.1. we are interested in the hippocampus segmentations and now i'm wondering whether i should go back and run the whole analysis from scratch with the newest version. I understand that it might or even will give me slightly different results, but would it also be the assumption that the new results would be somewhat more correct, that is anatomically more accurate, because maybe for example the processing has been optimized for hippocampal segmentation or anything like that in the newer version? Or would they just be different, as they would also be different when running it on a different computer, Mac or PC, OSX version, etc? Thank you very much for your help in advance!! Best wishes, Elisabeth

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I had a Computer Failure, how can I resume recon-all for base (longitudinal processing)
by Natacha Beck, Ms 17 Jul '12

17 Jul '12

Hello, I know that we can resume a recon-all command, if it's a cross-sectionnally process. In this case the command is: recon-all -make all -s subject But I had a power failure during a longitudinal study, when I try to execute : recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2' That's why I would like to resume this command, that's why I tried : recon-all -make all -sd . -s 'Test_base_22' But I received this error : ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \' So I tried this command: recon-all -make all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2' But I received the same error: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Subject 'Test_base_22': make all recon-all -s /Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22 -talairach -tal-check ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \' make: *** [/Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22/mri/transforms/talairach.auto.xfm] Error 1 Somebody can help me and tell me which command I need to execute. Natacha

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Memory allocation problem trac-all -prior
by Rui Lavrador 17 Jul '12

17 Jul '12

---------- Forwarded message ---------- From: Rui Lavrador <ruilavrador(a)gmail.com> Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Rui - How many voxels are in your diffusion volume? How many of them > are inside the mask? > > a.y > > > On Thu, 12 Jul 2012, Rui Lavrador wrote: > > Hi all, >> I'm running tracula and when doing the step: >> trac-all -prior -c single_subject >> >> After some time it gives this error: >> >> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice >> >> Cannot allocate memory >> >> I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is >> DTI with 64 directions. >> >> This happens many times? I need more memory? >> >> Best regards, >> >> -- >> Rui Lavrador >> >> >> >> > > 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. > > -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador(a)fmed.uc.pt e-mail2: ruilavrador(a)gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador(a)fmed.uc.pt e-mail2: ruilavrador(a)gmail.com

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Question on longitudinal statistics
by Kairys, Anson 17 Jul '12

17 Jul '12

Hi, In the longitudinal tutorial it states that: "In order to analyze your longitudinal data, you have different options. You could, e.g., open the stats text files in each tpN.long.templateID/stats/ dir, containing statistics such as volume of subcortical structures or thickness averages for cortical regions. These statistics can be fed (after conversion) into statistical packages to run whatever analysis you are interested in, such as linear mixed effects models (often used in longitudinal analysis). I am wondering what conversion this refers to? I would like to run the stats in SPSS without having to use qdec for now. Any help would be great Best Anson K. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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hippocampus subfilelds mask
by lorenzo pasquini 17 Jul '12

17 Jul '12

Dear Freesurfer experts, I successfully run a hippocampal subfield segmentation on anatomical data of one subject (resolution 1 mm^3). Now I am building hippocampal subfields masks. I used the FreeView interface to load the mgz volume files of hippocampal subfields. I saved each subfield separately, binarized and transformed it in my dimension space through marsbar (spm8). I tried as well the mri_binarize command with the codes for hippocampal subfields, but the extracted masks were strangely empty (no voxels found). Is this a right way and the simplest way to build hippocampal subfields ROIs? Is there any apparent error in these procedure? Binarized mask might overlap, is there any suggested threshold? Thank you very much, greets, Lorenzo Pasquini

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Re: [Freesurfer] white-gray contrast algorithm
by Fred Lado 17 Jul '12

17 Jul '12

I found a thread (with same subject line) in the archive that referred to Freesurfer tools to measure white-gray contrast, but I could not find anything further on where the information resides. Is there a way to measure white-gray contrast in the manner described in several papers (difference in signal intensity 1/2 mm above and below white-gray junction)? I am interested in using these measurements to identify cortical dysplasias in patients with epilespy. Thanks, -- Fred Lado, MD PhD Chief of Service, Neurology - Moses and North Divisions Director, EEG Laboratory Montefiore Medical Center Associate Professor of Clinical Neurology 718-920-8499 (office) 718-920-9830 (appointments) 718-324-3730 (fax) ladofred(a)gmail.com

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Re: [Freesurfer] Measuring total cortical volume
by Douglas N Greve 17 Jul '12

17 Jul '12

This is computed by computing the volume inside the pial surface and subtracting the volume inside the white surface (and accounting for small amounts in the "unknown" region). doug On 07/17/2012 04:47 AM, Emelie Andersson wrote: > Thank You Douglas, > > May I ask if You know how the numbers were calculated? > > best regards > Emelie > > On Mon, Jul 16, 2012 at 6:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > In the aseg.stats file, there will be these values > > # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter > volume, 218425.204942, mm^3 > # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter > volume, 212261.052152, mm^3 > # Measure Cortex, CortexVol, Total cortical gray matter volume, > 430686.257094, mm^3 > > does this work for you? > doug > > > On 07/16/2012 03:17 AM, Emelie Andersson wrote: > > Hello, > > > > We have a some doubts about how to measure the total cortical > volume. > > Is it recommendable to use GM = pial surface - white matter? > > > > Hope to hear from You, > > > > Best regards > > Emelie > > > > > > _______________________________________________ > > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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> > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] How to register FLAIR to T1?
by Ed Gronenschild 17 Jul '12

17 Jul '12

Hi Doug, Thanks for your suggestion, but it didn't work out either. Ed On 16 Jul 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 18 > Date: Mon, 16 Jul 2012 11:32:06 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] How to register FLAIR to T1? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <500433F6.8010102(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Often with FLAIR there is not enough gray-white contrast to run the > registration. Try using the pial surface instead, with "-surf pial > --t1" > This tells it to use the pial surface as a boundary. The --t1 is > needed > because the intensity should go from bright to dark. Let me know if > that > does not fix the problem. > doug > > On 07/10/2012 11:58 AM, Bruce Fischl wrote: >> glad to hear it :). You may need to repost (and possibly upload your >> data) >> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >> >>> Hi Bruce, >>> >>> It is indeed from the same scan session. >>> I'll wait patiently, let Doug enjoy his vacation before >>> he gets bothered again by all our questions. >>> >>> Cheers, >>> Ed >>> >>> On 10 Jul 2012, at 16:57, Bruce Fischl wrote: >>> >>>> Hi Ed, >>>> >>>> sorry, you'll have to wait until Doug is back from vacation. Is >>>> this from >>>> the same session? I've always had it work on flair images using >>>> one of the >>>> types of initialization. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>> >>>>> Hi Bruce, >>>>> >>>>> Unfortunately, this has no effect. >>>>> >>>>> Ed >>>>> >>>>> On 10 Jul 2012, at 16:40, Bruce Fischl wrote: >>>>> >>>>>> Hi Ed >>>>>> >>>>>> you are using -t2, right? You can also try -init-header >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Tue, 10 Jul 2012, >>>>>> Ed Gronenschild wrote: >>>>>> >>>>>>> Hi Bruce, >>>>>>> >>>>>>> It is slightly better but still displacements >>>>>>> in all directions and rotations too exist. >>>>>>> >>>>>>> Ed >>>>>>> >>>>>>> On 10 Jul 2012, at 16:13, Bruce Fischl wrote: >>>>>>> >>>>>>>> try -init-spm >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I would like to register FLAIR to T1. >>>>>>>>> Specifications FLAIR: >>>>>>>>> axial acquisition, 24 slices, >>>>>>>>> pixel size = 0.45 * 0.45 mm^2 >>>>>>>>> slice thickness = 5.50 mm (no gap). >>>>>>>>> >>>>>>>>> The slices run from the top of the brain >>>>>>>>> to just below the eyes. This is contrary >>>>>>>>> to the T1 scan which covers the full head >>>>>>>>> down to the neck. >>>>>>>>> I have tried bbregiser as follows: >>>>>>>>> >>>>>>>>> bbregister --s 001 --mov 001_FLAIR.mgz \ >>>>>>>>> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >>>>>>>>> >>>>>>>>> and inspected the result with >>>>>>>>> >>>>>>>>> tkregister2 --mov 001_FLAIR.mgz \ >>>>>>>>> --reg 001_register.dat --surf >>>>>>>>> >>>>>>>>> The result looks bad, it is displaced and rotated >>>>>>>>> by about 20 degrees with respect to T1. >>>>>>>>> >>>>>>>>> It makes hardly any difference if instead of --t1 >>>>>>>>> --t2 as contrast setting was used. >>>>>>>>> >>>>>>>>> Is there a better way to do this registration? >>>>>>>>> For instance, should I crop T1 to about the >>>>>>>>> same space as covered by FLAIR? >>>>>>>>> >>>>>>>>> (FreeSurfer v4.5.0, MacOSX 10.5) >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> Ed >>>>>>>>> _______________________________________________ >>>>>>>>> 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. >>>>>>>> >>>>>>> >>>>> >>> >> _______________________________________________ >> 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

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Resend: error in compiling Freesurfer with GPU support
by Akio Yamamoto 17 Jul '12

17 Jul '12

Hi Freesurfer experts, Compiling FreeSurfer with GPU support failed with the error message which is added to the end of this email. The current build environment is as follows: GeForce GTX 690 CUDA Toolkit 4.2 CentOS 6.3 I wonder if there are any specific requirements for building CUDA-enabled FreeSurfer. Any information/help would be appreciated. Thanks, Akio ===== em_register_cuda.cu(347): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(350): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(353): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(357): error: calling a host function("TransformGenerator::TransformGenerator") from a __device__/__global__ function("TransformLogps") is not allowed 4 errors detected in the compilation of ...

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