Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
by fsbuild 07 May '20

07 May '20

External Email - Use Caution Hello Gonzalo, If you don’t mind using Ubuntu 18 as the OS in the virtual machine, then we already have a virtual machine you can run with virtualbox that is close to what you want.   It has the previous version 7 beta 1 release of freesurfer (and also freesurfer 6).  You could start with this VM and update to the 7.0.0 release. The Ubuntu VM is here,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 The 7.0.0 release archive is here,freesurfer-linux-centos7_x86_64-7.0.0.tar.gz Once you bring up the VM (instructions on the web site for doing it on MacOS and Windows), then you could:1) delete everything under /usr/local/freesurfer/7.0.0.0-1b12) rename that subdir from 7.0.0.0-1b1 to 7.0.03) untar the 7.0.0 release archive under the new 7.0.0 archive4) change the bashrc file to use 7.0.0 wherever it says 7.0.0-b1 You could also run the Ubuntu VM on linux - the instructions would be mostly the same as listed for the Mac or Windows. If you want to run some other OS besides Ubuntu and create your own VM from scratch, then you could use osboxes.org to get the base image to create a VM from. - R. On May 7, 2020, at 15:34, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi:  No... I don't have any specific issue... I have a previous freesurfer version installed that I want to continue using.. So I want to install version freesurfer 7.0 on a virtual machine...  Sincerely,Gonzalo Rojas Costa> Message: 4> Date: Thu, 7 May 2020 12:43:56 +0200 (CEST)> From: Tim Sch?fer <ts+ml(a)rcmd.org>> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>> Message-ID: <1445340988.123994.1588848236854(a)ox.hosteurope.de>> Content-Type: text/plain; charset="utf-8">>       External Email - Use Caution        >> There should be no difference to installation on a physical machine. Are you> running into any specific issues?>> Tim>>> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:>> >> >>         External Email - Use Caution        >> >> Hi:>> >>  How can install freesurfer 7.0.0 in a virtual machine ?>> >>   Sincerely,>> >> >> Gonzalo Rojas Costa>> _______________________________________________>> Freesurfer mailing list>> Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>--> Dr.. Tim Sch?fer> Postdoc Computational Neuroimaging> Department of Child and Adolescent Psychiatry, Psychosomatics and> Psychotherapy> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] FreeSurfer 7 stable
by Mina Rizkallah 07 May '20

07 May '20

External Email - Use Caution Hello again, I successfully installed FreeSurfer 7 on Centos 8 and it works smoothly. my concern is regarding the CUDA compatibility, in recon-all help I found the (-use-gpu) flag is present but when I tried to use it, I got error for unrecognized flag. Is there a way to take the part of code concerning CUDA from freesurfer 6 and include it in version 7 as it save a huge amount of time best regards Mina Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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FW: HCPMMP1 parcellation to aseg (.mgz)
by Glasser, Matthew 07 May '20

07 May '20

External Email - Use Caution From: Timothy Coalson <tsc5yc(a)mst.edu> Reply-To: Timothy Coalson <tsc5yc(a)mst.edu> Date: Thursday, May 7, 2020 at 2:30 PM To: "Glasser, Matthew" <glasserm(a)wustl.edu> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) The way to map data between freesurfer and fs_LR is in faq #9: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF… I seem to recall that the colors in the colored version of our MMP atlas ended up unique (at least within the hemisphere), so that should remove one hurdle from converting to freesurfer format. Tim On Thu, May 7, 2020 at 10:01 AM Glasser, Matthew <glasserm(a)wustl.edu<mailto:glasserm@wustl.edu>> wrote: That is our multi-modal parcellation. Tim has some instructions to get data from the fs_LR mesh to fsaverage in GIFTI format. Doug perhaps you can say how to convert from GIFTI to annot? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 7, 2020 at 9:59 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) * External Email - Caution * what's hcpmmp1? On 5/7/2020 4:46 AM, pooja prabhu wrote: External Email - Use Caution Hai list, Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation files) for fsaverage brain? For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz. Similarly I need for HCPMMP1. Can someone help me with this? Thank you _______________________________________________ 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 materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
by Gonzalo Rojas Costa 07 May '20

07 May '20

External Email - Use Caution Hi: No... I don't have any specific issue... I have a previous freesurfer version installed that I want to continue using. So I want to install version freesurfer 7.0 on a virtual machine... Sincerely, Gonzalo Rojas Costa > Message: 4 > Date: Thu, 7 May 2020 12:43:56 +0200 (CEST) > From: Tim Sch?fer <ts+ml(a)rcmd.org> > Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine... > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1445340988.123994.1588848236854(a)ox.hosteurope.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > There should be no difference to installation on a physical machine. Are you > running into any specific issues? > > Tim > >> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa < gonzalo.rojas.costa(a)gmail.com> wrote: >> >> >> External Email - Use Caution >> >> Hi: >> >> How can install freesurfer 7.0.0 in a virtual machine ? >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- > Dr. Tim Sch?fer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Compare individual to a group
by Xiaojiang Yang 07 May '20

07 May '20

External Email - Use Caution Dear FS experts, I have a group of healthy subjects. Given a new individual subject, I want to compare its cortical thickness to the healthy group so that I can find where the thickness is abnormal (thickening or thinning). I use fsaverage as the template subject to calculate mean and std of the healthy group. Since subjects in the healthy group have different ages, I do a "normalization" process to all the subjects in the group BEFORE calculating the mean and std. Thus the normalized healthy group can be regarded as all subjects having the same "standard" age. The normalization process is just multiplying some pre-obtained scale (varied by age, but not linearly ) to the file ?h.thickness.fwhm0.fsaverage.mgh of each subject that are already calculated by "recon-all --qcache" command. So the mean and std of the group are actually weighted in the sense of Freesurfer's recon-all results. My questions are: 1) If I do vertex-wise t-tests by simply comparing individual subject's thickness to the group using mris_calc but WITHOUT using mri_glmfit, can I still use mri_glmfit-sim to do multiple comparisons correction? If yes, how? 2) If the answer is no for the above question, how should I use mris_glmft to implement my above thoughts so that I can use use mri_glmfit-sim? Specifically, how can I use the weighted mean for the group? 3) Take a step back, if I consider the weight is linearly correlated with the age, how to design the fsdg and contrast file? Thank you very much! Xiao

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HCPMMP1 parcellation to aseg (.mgz)
by pooja prabhu 07 May '20

07 May '20

External Email - Use Caution Hai list, Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation files) for fsaverage brain? For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz. Similarly I need for HCPMMP1. Can someone help me with this? Thank you

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New PETSurfer Questions
by Ferraro, Pilar 07 May '20

07 May '20

External Email - Use Caution Dear Freesurfer experts, As previously mentioned, we are currently trying to test the effects of different PVC corrections on metabolism estimation in a group of patients. We would like to also include MZ and MG methods in the analyses, comparing them to SGTM and no PVC. However, while both MG and MZ provide voxel-wise results, we would like to use them in ROI analyses in order to be able to compare their outputs with the ones obtained with SGTM and no PVC. Are there any procedures that you would recommend to do this? Many thanks in advance for any help, Best, Pilar > Il giorno 7 mag 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu) > 2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve) > 3. Re: Recon-all exited WITH errors {Disarmed} (Mason Wells) > 4. Re: freesurfer 7.0.0 in a virtual machine... (Gonzalo Rojas Costa) > 5. Re: Recon-all exited WITH errors {Disarmed} (Douglas N. Greve) > 6. Re: flirt.fsl error (NEWMAT::SingularException) when running > bbregister in Freesurfer 7.0.0 (Hoopes, Andrew) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 May 2020 20:55:21 +0530 > From: pooja prabhu <prabhuppooja(a)gmail.com> > Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CANeOyKnobqGKPPSdX+Pr1CmvHRYE2d+ziRvEMfz9BQJ4-RsGbA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > HCPMMP1 parcellation is multi modal parcellation > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ > > We need the file something like we have for 'aparc' parcellation. > The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) > How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) > > -- > Thank You > Pooja Prabhu >

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Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
by pooja prabhu 07 May '20

07 May '20

External Email - Use Caution HCPMMP1 parcellation is multi modal parcellation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ We need the file something like we have for 'aparc' parcellation. The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) -- Thank You Pooja Prabhu

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conf2highres
by Dr. Ilona Lipp 07 May '20

07 May '20

External Email - Use Caution Hi, in the version 7 release notes it says this: "conf2hires. This is an alternative method to do hi-res recon byrunning part of the stream at 1mm, then placing the 1mm surfaces on the hi-res volume. This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.". I would be grateful if you could confirm whether this means that the conf2hires option is incorporated in the latest Freesurfer release or just that the compatibility is still ensured. If former, how can I actually run it, I tried using -conf2hires as a flag (instead of -hires), but this gave me an error message. Thanks a lot, Ilona

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recon-all-rms error < 2.00
by jiahui 07 May '20

07 May '20

External Email - Use Caution Hello FreeSurfer Developers, I run the recon-all -all command:this true error?how to resolve this problem? ERROR: 245/300: dt: 0.9000, rms radial error=134. 782, avgs=0 250/300: dt: 0.9000, rms radial error=134. 022, avgs=0 255/300: dt: 0.9000, rms radial error=133.265, avgs=0 260/300: dt: 0.9000, rMS radial error=132.513, avgs=0 265/300: dt: 0.9000, rms radial error=131. 766, avgs=0 270/300: dt: 0.9000, rmS radial error=131. 022 , avgs=0 275/300: dt: 0.9000, rMS radial error=130 .283, avgs=o 280/300: dt: 0.9000, rMS radial error=129.548, avgs0 285/300: dt: 0.9000, rmS radial error=128.817 , avgs=0 290/300: dt: 0.9000, rms radial error=128 .090, avgs=0 295/300: dt: 0.9000, rMS radial error=127 .367 , avgs=0 300/300: dt: 0.9000, rMs radial error=126.648, avgs=0 final distance error %24.71 pass 1: epoch 1 of 3 starting distance error %19.14 pass 1: epoch 2 of 3 starting distance error %19.08 starting distance error X19.04 final distance error %19.04 pass 1: epoch 1 of 3 starting distance error %19.50 pass 1: epoch 2 of 3 starting distance error %19.45 starting distance error %19. 41 final distance error %19.43 recon-all -s 100034 finished without error at 2020# 05A 05E 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

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Freesurfer May 2020