Freesurfer

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30070 discussions

Re: FS 6 matlab runtime and libcurses in docker
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution  End users of the Matlab runtime need to download it directly from the Mathworks web site and agree to whatever the current licensing terms are during the download/install process. - R.

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Re: FS 6 matlab runtime and libcurses in docker
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution Hello Jeanette, Freesurfer 6 was released back in 2017 for CentOS6,https://secure-web.cisco.com/1qAg_caL2ITqoSd4EdvasaCD0R467g8zXSJtKo… We don’t expect the freesurfer 6 distribution (FS6) to entirely work on Rocky8 linux, e..g., you will probably get run time library errors, because the Linux system libraries have been updated to newer (incompatible) versions some 8 years later for more recent versions of Linux such as Rocky8.  The fs_install_mcr script is part of more recent FS7 and FS8 distributions, but is not part of (or supported in) FS6. If you must use FS6, then your best bet is to make a CentOS6 or CentOS7 docker container and run FS6 in that instead, e.g., download and unarchive the tar images from the above link into your CentOS6/CentOS7 docker container.  Or put whatever version of FS6 you have already been running into that (new) container. Then you could subsequently download and install a version of Matlab that supports the version of CentOS6/CentOS7 running in the container.  I’m not sure there is a Matlab run time environment matching those older OS's, but there should be a full version of Matlab. Unless there is work already done with Freesurfer 6 that you need to continue to work on or support with that same version for continuity, then on Rocky 8 linux, e.g., for new work, we recommend you download and run the FS8 rocky8 linux installer from,https://secure-web.cisco.com/1rRWbe99ZqpjzP3febIH36G6i9KHdZ0XgXI5CkUhv… - R. On Jun 25, 2025, at 12:55, Kenley, Jeanette <jkkenley(a)wustl.edu> wrote:        External Email - Use Caution        Hello installation experts. I am creating a docker which runs OS Rocky 8.I am placing FS6 in said docker. I would like to run recon-all with the -hippocampal-subfields-T1(T2) flag, which requires the libcurses libraries. I cannot download and execute this file in the docker successfully because it throws a VM library error when executed.  (I apologize the exact error is no longer available to me)https://secure-web.cisco.com/1FrIuq3tL5KO5-jI1Oe1gFi4SMTOD-zRut9HpuxOnMx… Thus I was attempting to load this file into the docker:https://secure-web.cisco.com/1H8IPq9NQ0AlAR3Mk_yBocmB1PiA1VAT4Abzh_A… Which I planned to subsequently untar and add the libcurses to the MCRv80 output folder, but unlike on 18 June 2025, the file is no longer available. Is there a reason this file was removed?Or do you have a recommendation on how to make the above script run, which then I can add the libcurse libraries to? Thank you for your time.Jeanette The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.  The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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High-resolution Data in FreeSurfer
by Mahta Abbaspour 27 Jun '25

27 Jun '25

External Email - Use Caution Hi, I had a question regarding how FreeSurfer handles high-resolution MRI scans. I understand that it typically accepts isotropic 1 mm scans (and up to 1.5 mm). I wanted to confirm whether using the -hires flag alone is sufficient for processing this type of data, and if there are any additional considerations I should be aware of when reviewing the outputs. I’m using v8.0.0. and working with a dataset acquired at 0.5 × 0.5 × 1 mm resolution. I used the -hires flag with recon-all, and FreeSurfer preserved the resolution and resampled it to isotropic 0.5 mm voxels. Also, does using high-resolution data affect the alignment or reliability of atlas-based parcellations (like Desikan-Killiany), given that those templates were originally developed on standard-resolution scans? Thank you for your help. Best

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Extracting Z score from surface single subject level
by Federica Tomaiuolo 27 Jun '25

27 Jun '25

External Email - Use Caution Hi, I'm experiencing a problem while trying to extract Z score from single subject's z.nii.gz map coming from FSFAST. More in detail, I created different .label files in freeview from the group-level statistics maps (in fsaverage space), each one containing a thresholded z-stat cluster. Then, I wanted to use this label files to extract from each z.nii.gz (still in fsaverage space) single subject's map, the Zscore values corresponding to the ROI associated to the cluster coming from the label. I've always made this process with volume files using FSL, by combing fslmaths and fslstats, but I didn't find a corresponding command in FreeSurfer for surface files. I tried using mri_segstats but I'm not sure is able to work with surface maps. Could someone help me, please? Thank You, Federica Tomaiuolo

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R: Certificate of Partecipation - Virtual FreeSurfer Course
by Giuseppe CIULLO 27 Jun '25

27 Jun '25

External Email - Use Caution Dear Sirs, Could you kindly provide me with the certificate of participation, with my name and surname on, for the last Virtual FreeSurfer course attended two weeks ago? Thank you very much for your support. Best regards, Giuseppe ________________________________ Da: Giuseppe CIULLO Inviato: venerdì 27 giugno 2025 11:51 A: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Oggetto: Certificate of Partecipation - Virtual FreeSurfer Course Dear Sirs, Could you kindly provide me with the certificate of participation, with my name and surname on, for the last Virtual FreeSurfer course attended two weeks ago? Thank you very much for your support. Best regards, Giuseppe

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Trouble shooting
by andrew cardona 26 Jun '25

26 Jun '25

External Email - Use Caution Good morning, I am trying to troubleshoot one participant, yet It keeps failing and starting this error “ mri_convert : can’t determine type of output volume” we have tried changing the file manually to mgz and it works yet when running recon all it crashes. Any guidance would be appreciated! Thank you in advance! Best, Andrew cardona

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Re: Freesurfer Digest, Vol 256, Issue 51
by Sambamoorthy, Sowmya 26 Jun '25

26 Jun '25

External Email - Use Caution I would like to unsubscribe from these email threads. Thank you > > On Jun 26, 2025, at 11:14 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Trouble shooting (andrew cardona) > 2. Re: Trouble shooting (Huang, Yujing) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 26 Jun 2025 11:17:01 -0400 > From: andrew cardona <ascardona0908(a)gmail.com> > Subject: [Freesurfer] Trouble shooting > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CALzLCbYtA3WhkLWeUbFgetvz80yyyCwYXLA5Sm4CO4aCwx2=Ow(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="00000000000056e03706387b0eec" > > External Email - Use Caution > > Good morning, > I am trying to troubleshoot one participant, yet It keeps failing and > starting this error “ mri_convert : can’t determine type of output volume” > we have tried changing the file manually to mgz and it works yet when > running recon all it crashes. Any guidance would be appreciated! Thank you > in advance! > Best, > Andrew cardona > -------------- next part -------------- > A message part incompatible with plain text digests has been removed ... > Name: not available > Type: text/html > Size: 698 bytes > Desc: not available > > ------------------------------ > > Message: 2 > Date: Thu, 26 Jun 2025 16:13:30 +0000 > From: "Huang, Yujing" <YHUANG43(a)mgh.harvard.edu> > Subject: [Freesurfer] Re: Trouble shooting > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SN6PR04MB4894C07B82DA86EE935361F49D7AA(a)SN6PR04MB4894.nam > prd04.prod.outlook.com> > Content-Type: multipart/alternative; boundary="_000_SN6PR04MB4894C0 > 7B82DA86EE935361F49D7AASN6PR04MB4894namp_" > > If you run mri_info on the image, what does it report? > > Can you send recon-all.log? > > Yujing > > From: andrew cardona <ascardona0908(a)gmail.com> > Sent: Thursday, June 26, 2025 11:17 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Trouble shooting > > > External Email - Use Caution > Good morning, > I am trying to troubleshoot one participant, yet It keeps failing and starting this error “ mri_convert : can’t determine type of output volume” we have tried changing the file manually to mgz and it works yet when running recon all it crashes. Any guidance would be appreciated! Thank you in advance! > Best, > Andrew cardona > -------------- next part -------------- > A message part incompatible with plain text digests has been removed ... > Name: not available > Type: text/html > Size: 3414 bytes > Desc: not available > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu > To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1mnES9oZX2EyF9fQ8CCf_CmPINrvqbFAPrwtT2Xj6T0bMH… > > > ------------------------------ > > End of Freesurfer Digest, Vol 256, Issue 51 > ******************************************* > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1GpExnL4BtRfz6VzjP1gfhFQva7rNRAgcIRq_Hpypatriv… <https://secure-web.cisco.com/1GpExnL4BtRfz6VzjP1gfhFQva7rNRAgcIRq_Hpypatriv…> . > Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Issue with TRACULA - Empty dwi.bvecs file after LAS orientation
by Gabriella Monopoli 26 Jun '25

26 Jun '25

External Email - Use Caution Hi everyone, I hope this email finds you well. I'm trying to run TRACULA on a subject using FreeSurfer 8 (working on Ubuntu 22). However, when launching the first step of TRACULA (-prep), I encountered some issues with the creation of the dwi.bvecs file: after the LAS orientation, the dwi.bvecs file is empty. As a result, the symbolic links created afterward are incorrect, and the subsequent dtifit step produces empty files. To make it work, I had to manually edit the files, copying the original bvecs into the empty one before the ditifit step started. However, this can't be a valuable solution, especially since I need to run TRACULA on multiple subjects. I've attached the log file, the script, and the configuration file I used to this email. I would greatly appreciate any help you can provide in finding a solution. Best regards, Gabriella Monopoli

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FS 6 matlab runtime and libcurses in docker
by Kenley, Jeanette 25 Jun '25

25 Jun '25

External Email - Use Caution Hello installation experts. I am creating a docker which runs OS Rocky 8. I am placing FS6 in said docker. I would like to run recon-all with the -hippocampal-subfields-T1(T2) flag, which requires the libcurses libraries. I cannot download and execute this file in the docker successfully because it throws a VM library error when executed. (I apologize the exact error is no longer available to me) https://secure-web.cisco.com/138efIQZshTarPWNEmLuTTSKddKw63h6p6_Pc8nb8LPiXa… Thus I was attempting to load this file into the docker: https://secure-web.cisco.com/1nH-LDNNVbQyp-GCy7wT_on7m7UGZSJzAfth7KFfbUQPeV… Which I planned to subsequently untar and add the libcurses to the MCRv80 output folder, but unlike on 18 June 2025, the file is no longer available. Is there a reason this file was removed? Or do you have a recommendation on how to make the above script run, which then I can add the libcurse libraries to? Thank you for your time. Jeanette The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: Nonhomogenous PVC with mri_gtmpvc
by Finn, Quentin 20 Jun '25

20 Jun '25

External Email - Use Caution That's exactly what I mean — the word I should have used was "nonisotropic". Is there an easy way to tell what axes row/col/slice corresponds to? Is it correct that row/col are coronal and sagittal and slice is axial ? Thanks again! Message: 1 Date: Thu, 19 Jun 2025 12:35:13 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: [Freesurfer] Re: Nonhomogenous PVC with mri_gtmpvc To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <a04213db-3e4c-48e6-b116-992332d96a13(a)mgh.harvard.edu> Content-Type: multipart/alternative; boundary="------------900rUdJVaa2J4kXp3DWC9VFg" I'm not sure what you mean. Are you saying the fwhm varies across axes? If so, you can pass different fwhms for each axis to mrI_gtmpvc with the --psf-col, --psf-row, --psf-slice options. If you are saying that PSF is space variant, then we don't have good options. Houston Methodist. Leading Medicine. Houston Methodist Hospital has been named the Best Hospital in Texas for 13 years in a row by U.S. News & World Report and recognized on the Honor Roll eight times. For more than 100 years, we have provided patients with the highest quality care, the most advanced technology and the best patient experience. That’s the difference between practicing medicine and leading it. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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