Freesurfer March 2025

freesurfer@nmr.mgh.harvard.edu

49 participants
63 discussions

trac-all -bedpostx error
by Gabriella Monopoli 31 Mar '25

31 Mar '25

External Email - Use Caution Hello, I'm trying to run the second step of TRACULA processing (in bash), which is: trac-all -bedp -c /path/to/configuration/file I'm currently using the FreeSurfer version v7.1.4 and I get the following error: WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 -model 1 /home/gmonopoli//Prova_TRACULA/trc/sub-007_S_6341/dmri /usr/local/freesurfer/7.4.1//bin/bedpostx_mgh: 128: Syntax error: "(" unexpected Since I am not familiar with this, do you have any advice on how to overcome this problem? Thanks in advance, Gabriella

1 0

Incorrect segmentation and surface offset
by Tommaso Mariani 28 Mar '25

28 Mar '25

External Email - Use Caution Hi everyone, I am experiencing a tricky situation in freesurfer. Due to hypo- and hyper-intensity problems I obtained a bad reconstruction and I've been working on it since. My first question is then: do I need to refresh the aseg file after the wm.mgz intensities modifications? However I also noticed that when I loaded the surface to verify the corrections they were all with a significant offset and this message was printed on the console: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Together with that, I was also unable to obtain the final parcellization, possibly due to the absence of correlation between the volumes and surfaces. I already tried to manually adjust the offset and relaunch the reconstruction, as suggested in the Freesurfer documentation for tailarach errors, but it looks like it did nothing to it. If you need any file or info to examine the situation further, feel free to contact me, I would really appreciate your help. Thanks in advance, Tommaso Mariani

2 6

Recon-all using mni152 as template
by Davide Sabbadin 27 Mar '25

27 Mar '25

External Email - Use Caution Hi all, Is there the possibility to perform the segmentation through recon-all using a different template, e.g. mni152? Thanks, Sabbadin Davide

2 2

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

3 3

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

2 1

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

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Freesurfer March 2025