Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

custom ROI as a reference region for PET
by Lauri Tuominen 27 Mar '25

27 Mar '25

External Email - Use Caution Dear PETsurfers, I am trying to use PETsurfer and MRTM2 to analyze a SynVesT1 PET scan with centrum semiovale as a reference region. I have created a binary mask for centrum semiovale. I guess my issue is that I don't understand what mri_gtmpvc does if I don't want to do partial volume correction. So my question is if it's ok to extract the time series from the reference region using eg. mri_segstats and use it in the subsequent commands something like so: ``` mri_gtmpvc --i ${pet_dir}/mc_${pet_file} --reg ${pet_dir}/p2mri.reg.lta --seg gtmseg.mgz \ --default-seg-merge --auto-mask 1.01 --no-tfe --o ${pet_dir}/gtmpvc_hb.output \ --km-hb 11 12 13 50 51 52 --no-rescale --max-threads-minus-1 mri_segstats --i ${pet_dir}/mc_${pet_file} --reg ${pet_dir}/p2mri.reg.lta --seg $SUBJECTS_DIR/test_subject/mri/cs_eroded.nii.gz --id 1 --avgwf ${pet_dir}/ref.km.txt mri_glmfit --y ${pet_dir}/gtmpvc_hb.output/km.hb.tac.nii.gz --mrtm1 ${pet_dir}/ref.km.txt time.dat --o mrtm1 --no-est-fwhm --nii.gz ``` Thank you so much! Lauri Tuominen

2 1

Re: [Freesurfer] Freeview
by fsbuild 27 Mar '25

27 Mar '25

External Email - Use Caution  If freeview is expecting the X-server to provide fonts for text entry, then it could be the X-server on the Windows side does not have the fonts installed for text entry, etc. to work.    If you are using Xming for the X-Windows server, their web page has a section under “Xming-fonts” about how to download and install them.  It mentions the X-server side fonts were removed from the XMing installer because it makes the install footprint larger.http://secure-web.cisco.com/1zS8s2rRtdoUSrzMK09-pVLTbTdfLO3zYcUn-4Cn… In a Linux shell in WSL2 you try running the “xterm” command and when it comes up, see if you can type/enter text in the xterm window. An alternative would be to try a different X-server on the window host which I believe MobaXterm provides. My impression is MobaXterm is easier to setup compared to Xming.https://secure-web.cisco.com/11st5eZX41jBAC0zIGzcj2KhMZ_g2IWN6HKDzVV-… If however freeview is using the fonts on the linux side for text entry, then something may not be right with the font setup in the WSL2 Linux VM. - R. On Mar 24, 2025, at 18:07, Yoel HALIMI <yoel.halimi(a)inserm.fr> wrote:        External Email - Use Caution        I use WSL 2/Ubuntu-22.04 and i tried Ubuntu 20.04 De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Wang, Ruopeng <RWANG4(a)MGH.HARVARD.EDU> Envoyé : lundi 24 mars 2025 22:47 À : Freesurfer support list Objet : [*Suspicious Email*] Re: [Freesurfer] Freeview What unix system are you running under WSL? I don’t have a WSL setup at this point but I can install one to test it. Ruopeng On Mar 24, 2025, at 4:51 AM, Yoel HALIMI <yoel.halimi(a)inserm.fr> wrote:        External Email - Use Caution        Hello,  I have a problem with the tool: Voxel editing. Using Freeview When I open the window, it appears correctly but I can't modify it or enter values. I'm using WSL 2 and I've followed the tutorial. When I move my mouse over it, the cursor is transparent.    Here an image to describe my problem : <pastedImage.png> Thanks to reply, Best regards, Yoel _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1I10WldoqG7HsNV_JFEVUZIWZLRl-qvfYav87B… _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Inquiry Regarding SynthSeg Volumetric Measurements
by ringki.siewert＠gmx.de 26 Mar '25

26 Mar '25

1 0

Issues with FS 7.3 skull stripping but NOT mri_synthstrip
by Carly McIntyre-Wood 26 Mar '25

26 Mar '25

3 2

dt_recon, CC_Anterior (T1) and FA corregistration.
by Gonzalo Rojas Costa 26 Mar '25

26 Mar '25

External Email - Use Caution Hi: I used the following commands: dt_recon --i sub-OAS30003_ses-d1631_run-01_dwi.nii.gz --b sub-OAS30003_ses-d1631_run-01_dwi.bval sub-OAS30003_ses-d1631_run-01_dwi.bvec --s OAS30003_MR_d1631 --o dt_recon_result cd dt_recon_result mri_vol2vol --mov lowb.nii.gz --targ $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg.mgz --inv --interp nearest --o $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg2diff.mgz --reg register.dat --no-save-reg mri_segstats --seg $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg2diff.mgz --ctab /home/gonzalorojascosta/freesurfer/FreeSurferColorLUT.txt --i fa.nii.gz --sum fa.stats And, to view the results, I used: freeview -v $SUBJECTS_DIR/OAS30001_MR_d0757/mri/brain.mgz $SUBJECTS_DIR/OAS30001_MR_d0757/mri/orig.mgz $SUBJECTS_DIR/OAS30001_MR_d0757/mri/aseg.mgz:colormap=lut:opacity=0.2 fa.nii.gz:reg=register.dat:colormap=heat -colorscale -viewport coronal Why is there a corregistration error between the FA and the CC_Anterior (T1) section ? Sincerely Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Freeview
by Yoel HALIMI 25 Mar '25

25 Mar '25

External Email - Use Caution Hello, I have a problem with the tool: Voxel editing. Using Freeview When I open the window, it appears correctly but I can't modify it or enter values. I'm using WSL 2 and I've followed the tutorial. When I move my mouse over it, the cursor is transparent. Here an image to describe my problem : [cid:ac7bfccb-f87f-4f66-b768-408f41f2d50f] Thanks to reply, Best regards, Yoel

2 3

怎么取消
by yaoshanwen2022 25 Mar '25

25 Mar '25

1 0

freesurfer course
by Sikah, Kevin (BIDMC - Neurology) 25 Mar '25

25 Mar '25

External Email - Use Caution Hello, Sorry to message the wider list; I emailed the fscourse address previously but did not hear back. Is there a course planned for this spring, and if so, is the timing known? Thank you! Best, Kevin ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1QDxtk6PFb9zuBLlWWwdrTv1EM9Dw99G1f9rL-P9WVOCHa0… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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xhemi fsaverage_sym rh backward mapping
by Dr. Cornelius Kronlage 24 Mar '25

24 Mar '25

External Email - Use Caution Dear freesurfer team, in the wiki (https://secure-web.cisco.com/1WbYcGgb3srAnGYyZARo_Jad7UgANe_5pADqErCcDyQA2U…) the following is used to map surface data from an individual subject's right hemisphere to fsaverage_sym's left hemisphere: mris_apply_reg --src rh.map.mgh --trg rh.map.lh.fsaverage_sym.mgh --streg $SUBJECTS_DIR/subject/xhemi/surf/lh.fsaverage_sym.sphere.reg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg How would you recommend to perform the inverse mapping from fsaverage_sym's left hemisphere to an individual subject's right hemisphere? I would suspect the --streg arguments need to be swapped like so: mris_apply_reg --src rh.map.lh.fsaverage_sym.mgh --trg rh.map.mgh --streg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg $SUBJECTS_DIR/subject/xhemi/surf/lh.fsaverage_sym.sphere.reg Is that correct? Or would you need to first map to fsaverage_sym's right hemisphere? Thank you! Cornelius

2 1

Cortex thickness
by Feruza Turdialieva 22 Mar '25

22 Mar '25

External Email - Use Caution Can anyone explain how to use FreeSurfer (Freeview) to measure cortical thickness? I would really appreciate any help! please dm feraata4(a)gmail.com

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