Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Default GCA atlas FreeSurfer 6?
by Douglas N. Greve 27 Mar '20

27 Mar '20

Hi Andrei, in the future, please post to the FS list. On 3/23/2020 5:21 PM, Andrei Mouraviev wrote: > > External Email - Use Caution > > Hello, > > I’m trying to find the default atlas that was used to segment T1W > images(freesurfer v6.0.1). > > Is this the still the right file? > > $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca > Yes > > Is there a variable that points to the default atlas? > You mean an environment variable? No, just create it yourself > > Regards, > > Andrei >

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Convert cespct.nii to subject's own anatomy space (for ROI analysis)
by Star Xi 26 Mar '20

26 Mar '20

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Re: [Freesurfer] Hippocampal Volume Extraction
by Devika K 26 Mar '20

26 Mar '20

External Email - Use Caution Hi, I want to extract hippocampal volume from longitudinal samples. I am less aware of it. I ran recon-all-all with longitudinal pipeline for all those samples. How I need to process further (Commands that I need to follow). Would you please help me out? Thanks and Regards Devika K

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Misalignment of boundaries and T1 (Freesurfer/SamSrf)
by Mason Wells 26 Mar '20

26 Mar '20

External Email - Use Caution Hello Freesurfer developers, I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all command which finished without errors. However, the white/grey matter boundaries are significantly misaligned with the subjects T1 (images attached). Below are the steps I have taken to reach this point in the analysis: 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain. 2. Ran Feat · Distortion correction of the EPI · Motion correction · No smoothing · Highpass filter · No registration to whole brain · Register to T1_biascorr_brain · Register to standard space 1. Ran recon-all on T1_biascorr 2. Convert T1/T1_brain/orig(001) from mgz to nii 3. Check registration (using the SurfaceProjection command from the SamSrf package) which leads to the attached images named S1 and S1. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux 5.3.0-40-generic x86_64 Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux As you can see, the registration is significantly misaligned. Can anyone offer any advice on this/suggest a way to rectify it? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Freeview CLI feature request
by VINCENT KOPPELMANS 25 Mar '20

25 Mar '20

External Email - Use Caution Dear FreeSurfer team, I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39 Would it be possible to add the following features as command line flags to FreeView? 1) Set opacity for a surface It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself. 2) Set smoothing iterations for isosurfaces This can only be done in the GUI, not yet via the CLI. Thank you for your consideration. - Vincent

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Re: [Freesurfer] mri_deface download link not found
by Hoopes, Andrew 25 Mar '20

25 Mar '20

Hi Hailey, Can you provide some more info about your issue, like what version you downloaded and a copy/paste of the command line you ran with the error message. Thanks Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "D'Silva, Hailey" <hailey.mulder(a)yale.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 24, 2020 at 7:24 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_deface download link not found External Email - Use Caution Hello Freesurfer Experts! I'm trying to anonymize a number of T1s by using mri_deface, but am getting a "Not Found" error when I try to download the tools for it. Thanks for your help, Hailey

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Re: [Freesurfer] VM_setup
by fsbuild 25 Mar '20

25 Mar '20

External Email - Use Caution Hello Pierpaolo, Just sent it to your email.  You can email me back directly if you need something. - R.On Mar 25, 2020, at 14:34, Pierpaolo Croce <pierpaolo12croce(a)gmail.com> wrote:        External Email - Use Caution        Dear List, I have followed the virtual machine setup for virtual box freesurfer installation... Starting ubuntu, ask me developers account informations. Which is the password?-- Ing. Pierpaolo Croce, PhD.Institute for Advanced Biomedical Technologies - ITABandDepartment of Neuroscience and ImagingUniversity of Chieti "G. D'Annunzio"Via dei Vestini, 3366013 Chieti, Italy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM_setup
by Pierpaolo Croce 25 Mar '20

25 Mar '20

External Email - Use Caution Dear List, I have followed the virtual machine setup for virtual box freesurfer installation.. Starting ubuntu, ask me developers account informations. Which is the password? -- Ing. Pierpaolo Croce, PhD. Institute for Advanced Biomedical Technologies - ITAB and Department of Neuroscience and Imaging University of Chieti "G. D'Annunzio" Via dei Vestini, 33 66013 Chieti, Italy

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PhD student opportunity: Caen, France
by briend 25 Mar '20

25 Mar '20

External Email - Use Caution PhD position at the University of Caen (in the Cyceron platform for the MRI part and in the INSERM 1075-COMETE, Caen, France) "Can orthostatic intolerance be predicted by an anatomical indicator?" All the information for the application are here: https://recrutement.cnes.fr/en/annonce/898759-94-can-orthostatic-intoleranc… To apply, we invite you to contact the PhD/research supervisor at COMETE herve.normand(a)unicaen.fr and fill, with him/her, the co-financing part of the online application form by April 15, 2020.

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Re: [Freesurfer] ERROR - build stamps do not match
by Hoopes, Andrew 25 Mar '20

25 Mar '20

Hi Laura, For any study, it is essential that you process all of your subjects on the same operating system. Even though the same FS version is used, there will be underlying system-level differences that may lead to small inconsistencies across your linux and mac results. Also, are your recons dying after printing “build stamps do not match”? That message should just be a warning and not force a recon-all exit unless REQUIRE_FS_MATCH is enabled (it’s not by default). Best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Danielian, Laura (NIH/NINDS) [E]" <danielil(a)ninds.nih.gov> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 24, 2020 at 10:05 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] ERROR - build stamps do not match External Email - Use Caution Hi, I have been processing datasets on my Linux on v6.0 but have recently been made to work from home where I only have access to a Mac. I’m getting the following error message when continuing the editing on datasets that were already started on my Linux: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c A few questions: Is it feasible to override this error message for subjects that I have already started processing since they are both using v6.0? I have about half of my data set already fully processed using a Linux – if I start processing the second half from scratch using my Mac, can I eventually combine the 2 parts of the dataset for comparison? If I use a mix of Freesurfer builds on different data sets, can I still process data sets from the same subject using the longitudinal stream? Thanks, Laura Danielian

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