Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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 for aboout 10 hours.1. I want to accelerate, is there any way, such as how to achieve multi-core parallelism? Or is there another way to speed things up? 2. What are the quick ways to check image quality after running results? I've had a lot of subjects and it's not realistic to look at them manually one by one. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

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Re: [Freesurfer] Compare individual to a group
by Xiaojiang Yang 07 May '20

07 May '20

External Email - Use Caution Hi Douglas, Sorry I didn't find an easy way to include previous email chain. Now I just copied all of them below, so that it's easy to follow. Thanks, Xiao <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from :%22Douglas+N.+Greve%22> Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date :20200507> Thu, 07 May 2020 14:56:08 -0700 sorry, please include the previous email chain so that I know what you are referring to On 5/7/2020 5:33 PM, Xiaojiang Yang wrote: External Email - Use Caution Douglas, Just as I mentioned in the initial email, subjects in the healthy group have different ages. Because average cortical thickness is believed to be declined as the age gets older, I want to "normalize" the group by multiplying each subject's thickness with an age-dependent scalar (pre-calculated constant). Suppose I take age 30 as the "standard" age, then subjects with ages greater than 30 will have scalars greater than 1 (depend on age); subjects with ages smaller than 30 will have scalars less than 1. In this way, all subjects in the group looks like to be at the same age (30). Of course, I also suspect that there is no need to do the above mentioned normalization if I use mri_glmfit. But my initial intention was using non-linear scalars, and mri_glmft can only use linear fit. Please give me your opinion. Thank you! Xiao <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from :%22Douglas+N.+Greve%22> Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date :20200507> Thu, 07 May 2020 14:06:27 -0700 I don't know what weight is. Can you elaborate? On 5/7/2020 4:54 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Douglas, Thank you very much! Could you please help me with more detailed information? 1)Should I use "Variables age" or "Variables age weight" in the fsgd file? If I can use either of them, which one is better? I don't know what weight is. Can you elaborate? 2)For the contrast file, the content "1 -1 0" you mentioned, it corresponds to the "Variables age" fsgd file, correct? Yes 3)If I use the "Variables age weight" fsgd file, what will be the content of the contrast file? Is it "1 -1 0 0"? Yes Thank you again! Xiao <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from :%22Douglas+N.+Greve%22> Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date :20200507> Thu, 07 May 2020 11:55:27 -0700 I think it will work properly if you use the raw data as input and create an FSGD file with two classes: (1) the individual subject and (2) healthy subjects. Also include age as a covariate. Use DOSS instead of DODS. Then set your contrast to be 1 -1 0 and run mri_glmfit. I think that should properly account for age. On 5/7/2020 2:44 PM, Xiaojiang Yang wrote: 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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Re: [Freesurfer] Compare individual to a group
by Xiaojiang Yang 07 May '20

07 May '20

External Email - Use Caution Douglas, Just as I mentioned in the initial email, subjects in the healthy group have different ages. Because average cortical thickness is believed to be declined as the age gets older, I want to "normalize" the group by multiplying each subject's thickness with an age-dependent scalar (pre-calculated constant). Suppose I take age 30 as the "standard" age, then subjects with ages greater than 30 will have scalars greater than 1 (depend on age); subjects with ages smaller than 30 will have scalars less than 1. In this way, all subjects in the group looks like to be at the same age (30). Of course, I also suspect that there is no need to do the above mentioned normalization if I use mri_glmfit. But my initial intention was using non-linear scalars, and mri_glmft can only use linear fit. Please give me your opinion. Thank you! Xiao

2 1

Re: [Freesurfer] Compare individual to a group
by Xiaojiang Yang 07 May '20

07 May '20

External Email - Use Caution Hi Douglas, Thank you very much! Could you please help me with more detailed information? 1) Should I use "Variables age" or "Variables age weight" in the fsgd file? If I can use either of them, which one is better? 2) For the contrast file, the content "1 -1 0" you mentioned, it corresponds to the "Variables age" fsgd file, correct? 3) If I use the "Variables age weight" fsgd file, what will be the content of the contrast file? Is it "1 -1 0 0"? Thank you again! Xiao

2 1

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

2 1

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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