Freesurfer

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30055 discussions

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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mri_vol2surf with "--vol2surf" argument generating error with non-FreeSurfer surfaces
by James Hengenius 19 Jun '25

19 Jun '25

External Email - Use Caution Hi FS list, I have some infant native space cortical surfaces generated by another software package. I would like to 'paint' them with some volumetric ROIs also in the native space. I noticed that mri_vol2surf has the "--vol2surf" option, which does not require typical FS output directory structure. I first converted the vtk surfaces from the other software to FS format. Here, the left hemi surface is called lh.pial and the corresponding volume is subject-168-T1w-iso.mgz (also used as regheader volume). I'm trying abs distance projection with 5mm distance, no projmap (0 as dummy var), and nearest neighbor interp. I get the errors below. My first guess is that using the native volume as the 'reg' argument is the issue, but any feedback is welcome! Searched a bit, but the "could not allocate xforms" error only comes up in one other thread on the listserv, and it's about mri_convert, not mri_vol2surf. Thanks, Jim H. mri_vol2surf --vol2surf \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/subject-168-T1w-iso.mgz \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/surf/lh.pial \ 0 \ 5 \ 0 \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/subject-168-T1w-iso.mgz \ novsm \ 0 \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/surf/lh.surf_ROIs error: Cannot allocate memory error: LTAalloc(1085915240): could not allocate xforms -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1fTLLOHBUxeHr_93Qy3ygesltkiuCLo-hiJm1MHYChZYxiu…>

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Fs-FAST preprocessing error
by Hibah Chughtai 19 Jun '25

19 Jun '25

External Email - Use Caution Hello Freesurfer Developers, I am currently running the fs-FAST preprocessing command, and this is a frequent error that I keep running into across various datasets of ours. DOF = 0 I have searched the listserv in order to find any possible solutions for my query, but to no avail. Another curious issue that comes up is when I re-run the preproc-sess command after the above error, it proceeds without issue and completes the process, which has further confused me as to what the possible issue could be. Attached is the terminal session output for you to take a look at. Thank you so much for all your help! Best, Hibah

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Nonhomogenous PVC with mri_gtmpvc
by Finn, Quentin 19 Jun '25

19 Jun '25

External Email - Use Caution Freesurfer experts, I have an older PET scanner that has a nonhomogenous FWHM, varying in the z-dimension (it's 5.1 x 5.1 x 5.6 ) How should I input this FWHM into mri_gtmpvc to get accurate PVC results ? Thanks so much! -qf 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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Vertex-wise cortical thickness analysis using longitudinal stream (across 3 groups and 2 timepoints)
by Jackson Lee 19 Jun '25

19 Jun '25

External Email - Use Caution Dear FreeSurfer community, I'm currently working on a study involving three groups, each with two timepoints, and I'm interested in analysing vertex-wise cortical thickness using FreeSurfer's longitudinal pipeline. I have already run recon-all, -base, and -long for all subjects. I would appreciate any clarification or recommendations on the following points: * Is it appropriate to perform vertex-wise group comparisons after longitudinal processing using mri_glmfit * Are there any recommended workflows or examples for group X timepoint interaction analysis at the vertex level? * Is it possible to conduct linear mixed-effects models (LME) at the vertex level within FreeSurfer (e.g., random intercepts for subject), or would this require extracting thickness data and performing the analysis externally (e.g., in R or Python)? * Can QDEC handle longitudinal vertex-wise analyses involving multiple groups and timepoints, or is it more suitable for simpler designs? I'd love to know if others have implemented similar longitudinal vertex-wise analyses and whether you used QDEC, custom scripts, or external tools! Warm regards, Jackson Lee

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FSGD file query
by Muskan Khetan 19 Jun '25

19 Jun '25

External Email - Use Caution Hi, I have a question related to setting up the FSGD file for my analysis. Specifically, I’m looking into the effects of hormone levels on the brain in a single group (i.e., not comparing different classes). My model includes both continuous and categorical covariates. From what I’ve gathered, most examples on the FreeSurfer website focus on group comparisons, which isn't the focus of my analysis. Therefore, I’ve set up an FSGD file with only one class (see the attached screenshot for reference). In this file: - Variables like soft_A, soft_B, soft_C, child_raceMixed, and child_raceWhite are *categorical covariates*. - Since these are covariates and not grouping factors, I haven’t created separate classes for them. I believe this approach is appropriate, but I wanted to confirm whether that understanding is correct. Additionally, regarding the contrast file: - My contrast vector is 0 1 0 0 0 0 0 0 0 0 0, where the number of elements matches the number of variables in my model (including the intercept). - As I’m specifically interested in the effect of E2_mean, I’ve set its position to 1 and all others (including covariates and intercept) to 0. Is this the correct way to set up the FSGD and contrast files for this type of single-group analysis? Thank you in advance for your guidance. Best, Muskan

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