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FS8.0 Patch - Next Step Clarification
by Carly McIntyre-Wood 01 Apr '25

01 Apr '25

2 1

Re: [Freesurfer] Issue with recon-all
by fsbuild 01 Apr '25

01 Apr '25

External Email - Use Caution  Assuming that you have set SUBJECTS_DIR to a path where you have read/write permission, then I wonder if you have an alias defined in your shell such that the rm command contains “-I” (the interactive switch) which would force rm to ask you for permission every time it wants to remove something.   Type “alias” into your shell prompt and see if something shows up for the remove command.  If so then I would remove that alias from your environment with unalias. $ alias... look for output containing rm -i ... $ unalias rm -R On Mar 31, 2025, at 20:48, Bedard, Patrick (NIH/NINDS) [C] <patrick.bedard(a)nih.gov> wrote:        External Email - Use Caution        Hello all I’m running the recon-all tool :    recon-all -all -sd .   -subjid  FS    -i   ${subj}_T1_al.niiIt works fine, but at some point, the program stops and asks at the terminal: writing to orig_nu.mgz...rm: descend into write-protected directory './tmp.mri_nu_correct.mni.41843'? yrm: remove write-protected directory './tmp.mri_nu_correct.mni.41843'? y and I have to answer “y”,but if I’m not checking it just sits and waits and take so much time… do you have any idea what might case that?I have all the permissions on the directories. BestPatrick  ===================Patrick Bédard, PhD, [C]ScientistNational Institutes of HealthNational Institute of Neurological Disorders and Stroke _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Issue with recon-all
by Bedard, Patrick (NIH/NINDS) [C] 31 Mar '25

31 Mar '25

External Email - Use Caution Hello all I’m running the recon-all tool : recon-all -all -sd . -subjid FS -i ${subj}_T1_al.nii It works fine, but at some point, the program stops and asks at the terminal: writing to orig_nu.mgz... rm: descend into write-protected directory './tmp.mri_nu_correct.mni.41843'? y rm: remove write-protected directory './tmp.mri_nu_correct.mni.41843'? y and I have to answer “y”, but if I’m not checking it just sits and waits and take so much time… do you have any idea what might case that? I have all the permissions on the directories. Best Patrick =================== Patrick Bédard, PhD, [C] Scientist National Institutes of Health National Institute of Neurological Disorders and Stroke

1 0

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

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