Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Editing Question -- Isthmus Cingulate
by Luke W. Bonham 12 Dec '13

12 Dec '13

> Hi, > > I'm having trouble figuring out how to correct this error around the > isthmus cingulate (screenshot attached). It's come up several times in the > cohort I'm editing and there's been little success in correcting the pial > boundary. It doesn't seem to be addressable with cp, wm edits, or the > expert options I know of. Any tips are greatly appreciated! > > Thanks >

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Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
by Bruce Fischl 12 Dec '13

12 Dec '13

yes, I think so. Why are you restarting? Or do mean start another one? On Tue, 26 Nov 2013, pablo najt wrote: > Thank you Bruce for your reply.Yes the computed has over 32 GB. > Let me check if I understood. > So far I have been running recon -all in a snow leopard for running as part > of the longitudinal stream. > If I want to re-start with this analysis in the FS 5.3 version for Centos > you are suggesting I can use the a new recon -all command (-openmp 8 flag to > recon-all)? > Thanks. > Pablo > > Date: Tue, 26 Nov 2013 16:41:31 -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 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 Cent > os > > 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 wit > h > > 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 ti > me > > > and it took around 20 hours. Would I be able to run 6 subjects in parall > el > > ? > > > 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 a > ny > > > > > reason to not use this version in your CentOS 6, if you have some ot > he > > 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.ed > u> > > > > > 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 informati > on > > 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 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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after editing pial boundary in tkmedit
by Rujing Zha 12 Dec '13

12 Dec '13

Hi Doug and Bruce, I have run "recon-all -autorecon-pial -s my_subject" after editing the pial by tkmedit. I donot know wether "-autorecon-pial" option running the process stages 24-31. So I want to know wether I need run "-autorecon3" option as I run "-autorecon-pial" not "-autorecon2-pial" previously. Can I ensure 24-31 steps being done by running the "recon-all -autorecon3 -s my_subject". GM thickness group analysis should be done correctly. Thanks. All the best. 2013-12-12 Rujing Zha

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Tracula error ? set: Variable name must begin with a letter
by Matthieu Vanhoutte 12 Dec '13

12 Dec '13

Hello experts, I am running the first pre-processing step in Tracula on FS 5.1 and come across the error: *set: Variable name must begin with a letter* I have attached my dmrirc file. Did I make a mistake in this file? Best regards, Matthieu

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Freesurfer versions
by Erik Lindberg 12 Dec '13

12 Dec '13

Dear Freesurfer experts, I am attaching a document showing the segmentation of a brain in version 5.1 and 5.3 with and without a 3-T flag. Image is from a 3-T camera. What I am wondering about is that it seems that the cortex is too thin in the later version of Freesurfer (both when using 3T flag and when not using this flag). Is there some other flag that could be used to deal with this? Thanks Olof Erik

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paired analysis of cortical thickness - Freesurfer group analysis vs. SPM8 analysis
by Govindarajan, Koushik Athreya 11 Dec '13

11 Dec '13

Dear Freesurfers, I have a question regarding how Freesurfer's paired glmfit and monte-carlo analysis compares with SPM8 GLM design analysis on cortical thickness. If I were to export thickness maps as nifti files and do a paired comparison on SPM8, would that be a fair comparison with Freesurfer or is Freesurfer's analysis more appropriate for surface maps such as cortical thickness? Thanks Koushik

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freesurfer *.deb-packaging
by Peter Wendorff 11 Dec '13

11 Dec '13

Hi, for running freesurfer in a cloud environment I want to build *.deb-Packages for freesurfer as installation of packages via puppet is much easier than copying plain file structures. As my machines are different in their use and I would like to have it modular, I think about dividing the freesurfer suite into several parts: 1) the freesurfer core, containing recon-all and everything inside 2) freesurfer-subjects, containing the demo-subjects as I think they are only necessary for debugging, tests and demonstration (for a cloud machine I could omit these) 3) fs-fast, containing the fsfast additions, as this part is only necessary where Matlab is availlable. 4) fs-tools, as the cloud machines don't have any gui, no real person will log in to them; the gui will be externalized somehow, so these have to be separate as well. The only dependency I'm sure exists is, that fs-fast depends on fs-core. Are the tools independent? I guess so, but please correct me if I'm wrong. What I'm not completely sure about is how this separation is reflected in the package availlable for download from the project website. Therefore I'd like to get remarks or corrections where my assumptions are wrong: / (files in the root directory) legal stuff, setups, so necessary for all parts /average data directory for the calculation, necessary for core /bin fs-core (the binaries) /data fs-core /diffusion fs-core /docs not necessary technically, documentation only /fsafd fs-core? /fsfast fs-fast /lib has to be differentiated: /lib/bem fs-core /lib/cuda fs-core /lib/images tools /lib/KWWidgets tools? /lib/petsc fs-core /lib/qt tools? /lib/resource tools? /lib/tcl tools? /lib/tcltkixblt tools? /lib/vtk tools? /lib/vtk tools? /matlab fs-fast /mni fs-core /subjects fs-subjects (of course) /tktools tools /trctrain ? I would apprechiate your help, even if incomplete. regards Peter Wendorff C-Lab, Paderborn

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New features in TRACULA
by Ruth Carper 10 Dec '13

10 Dec '13

Hi Anastasia, We discussed your paper at our lab meeting yesterday so this was perfect timing on the release of motion measures in your updated TRACULA. But I wasn't clear where the numbers are coming from in your new update. Is this from EDDY? eddy_correct? Some other registration step? Thanks, Ruth

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Do these bvec and bval files match?
by Emad Ahmadi 10 Dec '13

10 Dec '13

Hello, I'm using TRACULA to analyze images obtained by a non-Siemens scanner, and I'm using dcm2niigui app to generate bvec and bval files from DICOMs. My question is whether or not the attached bvec and bval files match, because the 0 bval is the first entry while the <0,0,0> bvec is somewhere in the middle. If they don't, how should I generate the correct bval/bvec files from dicoms? Lots of thanks, Emad

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part of GM missing
by Rujing Zha 10 Dec '13

10 Dec '13

Dear all, In tkmedit brainmask.mgz -surfs, there are a bit of GM part missing. I want to know how to paint the voxels to lable it as GM. And then run recon-all in a specific style to reconstruct the surfs. Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com

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Freesurfer December 2013