Freesurfer

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30084 discussions

Run FreeSurfer recon-all on isoDWI
by Yixin Ma 27 Mar '20

27 Mar '20

External Email - Use Caution I was trying to use the average of DWI images (isoDWI) to run recon-all, and it didn't work. I understand that FreeSurfer can only take a T1-weighted image for now. But how hard would it be to modify the code by myself to make it work? If it works, how accurate do you think it would be to run FreeSurfer on isoDWI? All the best and thank you for your help, Yixin Message: 8 Date: Fri, 13 Mar 2020 18:44:18 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer Cortical Parcellation using isoDWI image only? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <14b89d9d-130f-08f0-d593-71f2cdef3107(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" you are trying to run a DWI image through recon-all? Sorry, it can only take T1w right now On 3/12/2020 3:28 PM, Yixin Ma wrote: > > ????????External Email - Use Caution > > Hi Freesurfer experts, > > I'm writing to ask if it's possible to run FreeSurfer Cortical > Parcellation by just using the isoDWI image. If it's possible, it will > reduce the scan time and avoid misregistration between T1 and DWI. > > I started from just input the masked isoDWI (mask generated from > MRtrix3) for -reconall command, and attached is a screenshot of the > image of NU.mgz, which shows a clear delineation of WM/GM matter. So I > think it's promising, although the recon-all stopped because of the > wrong contrast. > My ideas on tackling this problem are: > 1) generate a corresponding "fake" T1-weighted image by > either?adjusting the value directly or using a brain Atlas and > deformable registration to create one. > 2) Tweak some parameters in FreeSurfer. > > Any suggestions or comments on my ideas are appreciated. > > Thank you very much and all the best, > > Yixin Ma >

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mri_deface download link not found
by D'Silva, Hailey 27 Mar '20

27 Mar '20

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] 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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