Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

tarball installer for version 8.1
by Drucker, Daniel 28 Jul '25

28 Jul '25

Is there a tarball installer available for v8.1.0? I don't see one on https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads (and, by the way, perhaps the download page for 8 shouldn't have a 7 in it?) Thanks! -- Daniel M. Drucker, Ph.D. Director of IT, MGB Imaging at Belmont McLean Hospital, a Harvard Medical School Affiliate

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Re: [UpdateNeeded] Syntax error
by fsbuild 24 Jul '25

24 Jul '25

External Email - Use Caution Try running the bash shell as the default dash shell might not work with all scripts. Type “bash” before setting up the environment and running any commands, $ bash$ export FREESURFER_HOME=/usr/local/freesurfer/8.1.0$ source $FREESURFER__HOME/SetUpFreeSurfer.sh - R.

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[UpdateNeeded] Syntax error
by Óscar Peña-Nogales 24 Jul '25

24 Jul '25

External Email - Use Caution Dear, I'm attempting to execute the recon-all command on the recently released FS 8.1.0 version, however I get an error that I was not getting in prior versions (6.0 and 7.4.1). Command: *recon-all -subjid FREESURFER -sd "/OUTPUT" -i "/INPUT/DATA input_t1/003MSVISMPRAGE_02.nii.gz" -all * Output Log: Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph fs-check-version --s FREESURFER --o /tmp/tmp.HYwr24 Thu Jul 24 09:29:43 AM UTC 2025 setenv SUBJECTS_DIR /OUTPUT /usr/local/freesurfer/8.1.0/bin/fs-check-version --s FREESURFER --o /tmp/tmp.HYwr24 -rwxr-xr-x 1 root root 18565 Jul 19 00:36 /usr/local/freesurfer/8.1.0/bin/fs-check-version freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed $Id$ Linux 83857eca32d0 6.8.0-1021-gcp #23~22.04.1-Ubuntu SMP Thu Jan 16 02:17:57 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux pid 126 Current FS Version freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Subject does not have a bstampfile, copying /usr/local/freesurfer/8.1.0/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /OUTPUT Actual FREESURFER_HOME /usr/local/freesurfer/8.1.0 Linux 83857eca32d0 6.8.0-1021-gcp #23~22.04.1-Ubuntu SMP Thu Jan 16 02:17:57 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux /OUTPUT/FREESURFER mri_convert /INPUT/DATA/input_t1/003MSVISMPRAGE_02.nii.gz /OUTPUT/FREESURFER/mri/orig/001.mgz mri_convert /INPUT/DATA/input_t1/003MSVISMPRAGE_02.nii.gz /OUTPUT/FREESURFER/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=1) reading from /INPUT/DATA/input_t1/003MSVISMPRAGE_02.nii.gz... TR=1970.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0348693, -0.999392, 0) j_ras = (-0.0330512, -0.00115315, 0.999453) k_ras = (0.998845, 0.0348502, 0.0330713) writing to /OUTPUT/FREESURFER/mri/orig/001.mgz... #-------------------------------------------- *#@# MotionCor Thu Jul 24 09:29:52 AM UTC 2025Found 1 runs/OUTPUT/FREESURFER/mri/orig/001.mgzChecking for (invalid) multi-frame inputs.../usr/local/freesurfer/8.1.0/bin/UpdateNeeded: line 14: syntax error near unexpected token `('/usr/local/freesurfer/8.1.0/bin/UpdateNeeded: line 14: `set Sources = ($argv);'if: Expression Syntax.* More info: 1) FreeSurfer version: *freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed* 2) Platform: Distributor ID: Ubuntu Description: *Ubuntu 22.04.5 LTS* Release: 22.04 Codename: jammy 3) uname -a: *Linux eec78b7407cc 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linu* Note, I have the 6.0 and the 7.4.1 on the same environment and executed their recon-all on the same data and they do work. Best

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Re: Freesurfer Digest, Vol 257, Issue 59
by vittal korann 23 Jul '25

23 Jul '25

External Email - Use Caution They just described this regarding the ICC in their methods section: "For the present study, intrinsic cortical curvature was calculated using Gaussian curvature calculations in the following regions of interest from both the left (LH) and right (RH) hemispheres: the caudal anterior cingulate cortex (henceforth “ACC”), the rostral middle frontal cortex (henceforth “DLPFC”), the superior parietal region (henceforth “parietal cortex”), and the superior temporal region (henceforth “temporal cortex”). The regions of ICC quantification were chosen from their delineation atlas, the Desikan-Killiany cortical atlas (Desikan et al., 2006), for their approximation to regions of observed glutamatergic dysregulation (Iwata et al., 2019; Shah et al., 2020b) and structural decline (Anderson et al., 2015; Bodnar et al., 2010; Fan et al., 2023; Wannan et al., 2019) in available literature." Thanks, Vittal On Wed, Jul 23, 2025 at 3:50 PM <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. Inquiry Regarding Intrinsic Cortical Curvature (ICC) Calculation in > FreeSurfer > (vittal korann) > 2. Re: Inquiry Regarding Intrinsic Cortical Curvature (ICC) Calculation > in FreeSurfer > (Fischl, Bruce R.,PHD) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 23 Jul 2025 15:44:14 -0400 > From: vittal korann <vittalkorann(a)gmail.com> > Subject: [Freesurfer] Inquiry Regarding Intrinsic Cortical Curvature > (ICC) Calculation in FreeSurfer > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CACyMoT3Vps-CC9G= > mFeHvNJJCh9LfhSVbVNskAwfi8H-6np7ow(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="000000000000b91b68063a9def84" > > External Email - Use Caution > > Dear FreeSurfer Team, > > I’m currently working on a project involving cortical morphology and am > particularly interested in calculating Intrinsic Cortical Curvature (ICC) > using FreeSurfer. > > I came across a recent publication ( > > https://secure-web.cisco.com/1oL8IZPRfQ5o5UDqVHfF8rU4SLPTHeXEdS4OHOftgKkxaX…) > that utilized ICC in their > statistical analysis. I’d like to clarify a couple of points regarding how > ICC is derived within the FreeSurfer framework: > > 1. Is Gaussian curvature as computed by FreeSurfer considered equivalent to > ICC? > > 2. If not, are there additional steps or specific tools required to compute > ICC beyond the standard curvature outputs (e.g., via mris_curvature or > mris_curvature_stats)? > > Any guidance or documentation you could share would be greatly appreciated. > I’m aiming to ensure methodological consistency with published work and > would be grateful for your insights. > > Thank you for your time and support. > > With regards, > Vittal >

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Inquiry Regarding Intrinsic Cortical Curvature (ICC) Calculation in FreeSurfer
by vittal korann 23 Jul '25

23 Jul '25

External Email - Use Caution Dear FreeSurfer Team, I’m currently working on a project involving cortical morphology and am particularly interested in calculating Intrinsic Cortical Curvature (ICC) using FreeSurfer. I came across a recent publication ( https://secure-web.cisco.com/1oL8IZPRfQ5o5UDqVHfF8rU4SLPTHeXEdS4OHOftgKkxaX…) that utilized ICC in their statistical analysis. I’d like to clarify a couple of points regarding how ICC is derived within the FreeSurfer framework: 1. Is Gaussian curvature as computed by FreeSurfer considered equivalent to ICC? 2. If not, are there additional steps or specific tools required to compute ICC beyond the standard curvature outputs (e.g., via mris_curvature or mris_curvature_stats)? Any guidance or documentation you could share would be greatly appreciated. I’m aiming to ensure methodological consistency with published work and would be grateful for your insights. Thank you for your time and support. With regards, Vittal

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`recon-all -base` fails with glibc/license error, but cross-sectional `recon-all` works
by Foyzul Rahman 23 Jul '25

23 Jul '25

External Email - Use Caution Hi FreeSurfer community, I'm running into an issue with the longitudinal FreeSurfer pipeline. Background: I'm working with T1-weighted MRI scans from an aerobic exercise intervention study in older adults (age 60+). I have two timepoints per subject: pre- and post-intervention. Cross-sectional `recon-all` has successfully completed for both timepoints. I'm now trying to run the longitudinal pipeline using `recon-all -base`, but I'm getting a glibc/license-related error. Command: ```bash recon-all -base sub002base \ -tp /rds/projects/s/segaertk-chbh-00077/Structural/FreeSurfer/sub002_tp1 \ -tp /rds/projects/s/segaertk-chbh-00077/Structural/FreeSurfer/sub002_tp2 \ -all ``` Error: ``` GNU libc version: 2.28 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://secure-web.cisco.com/1S-XRYZwdfIh6LBaYDmryClXzVhMGn3s7IZR6N9Pa3Ony7_… ``` Notes: I have a valid, updated license file (downloaded from the official site). I set the license path before running the command: ```bash export FS_LICENSE=${HOME}/license.txt ``` Weirdly, the cross-sectional `recon-all` works fine using the same environment and license file. I'm using FreeSurfer version: FreeSurfer/6.0.1-centos6_x86_64 My system is running glibc 2.28. What I've Tried: * Verified that `$FS_LICENSE` is exported and correct. * Checked for any outdated `license.txt` in `$FREESURFER_HOME` and replaced it. * Confirmed that `recon-all -version` and `which recon-all` return the expected FreeSurfer install. * Deleted partial `sub002base` folder and retried clean. Has anyone encountered this behaviour - where the cross-sectional `recon-all` works, but `recon-all -base` fails due to the license/glibc issue? Any help would be greatly appreciated! Warmest regards, Foyzul. Dr Foyzul Rahman Centre for Human Brain Health (CHBH) University of Birmingham United Kingdom

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FreeSurfer 8.1.0 released (includes important bug fix!)
by Douglas N. Greve 22 Jul '25

22 Jul '25

We are pleased to release freesurfer 8.1.0. This contains an important bug fix so we recommend that you this instead of 8.0.0. It will give the same output as 8.0.0 while avoiding the "symlink" bug described below. The biggest new feature is the new infant freesurfer pipeline. Congrats to Lilla Zoelli, Ashvath Balgovind, and Jackson Nolan for getting this completed!. More details below and at https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes * New features: infant_recon, dcm2niix upgrade, a few speed ups, gtmseg uses samseg by default, better support for ANTS N3, mideface works better with multiple frame, vlrmerge-mni, mri_gtmpvc can create PMOD compatible csv files, added -skip-nu-intensity-cor to recon-all, * Bug fixes: o Fixes recon-all where it would create a symlink from orig.mgz to nu.mgz when run a second time. This could happen if you edited your data and then rerun recon-all. o All the things from the patch (csvprint, xhemi, mri_segstats, -nonuintensitycor). o Fixed --lesion-mask-pattern in samseg script.

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TRACULA statistics - len_center issue
by Gabriella Monopoli 21 Jul '25

21 Jul '25

External Email - Use Caution Dear experts, I analyzed a few subjects from my dataset using TRACULA (FreeSurfer version 8). While examining the pathstats.overall.txt file for the left anterior longitudinal fasciculus, I noticed an anomaly: the Len_Center value is greater than Len_max. This occurs for all the subjects analyzed and also appears in other tracts. I was wondering whether this issue might be related to my data, a bug in the anlysis, or perhaps it's not actually an error at all. I'm sure you'll be able to help me understand how to resolve this and properly analyze my data. I've attached, as example, the pathstats.overall.txt file of one of my subjects. Best regards, Gabriella

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2D vs 3D gradient distortion correction (mri_gradunwarp)
by Annchen Knodt 20 Jul '25

20 Jul '25

External Email - Use Caution I have a longitudinal dataset collected on a Siemens Skyra, where online distortion correction on the T1s was turned OFF for the first wave several years ago, and with an upgrade to XA30 since then, it is now turned ON for the second wave of data collection and performing a 2D (in-plane) correction. Obviously, we want the acquisitions to match as closely as possible between the two timepoints, so I am trying to figure out how to use gradunwarp to perform post-hoc correction on the first scans. A problem I am running into (see my thread on HCP’s gradunwarp github page<https://secure-web.cisco.com/1UEsGaoLMJInc49tXx1leDHidHoj0m6ydT6viNz9VH1gN5…>) is that the software performs a 3D correction, which is not the same as the 2D correction being applied to my wave 2 data. I don’t yet know of a way to either: 1. apply just a 2D correction to my wave 1 uncorrected data to match what the scanner is doing at wave 2 (I’ve communicated with a Siemens rep who says there is no documentation he can share on the 2D correction to help me figure out how to do this) or 2. UNDO the 2D correction on my wave 2 data, so that I can then use gradunwarp to apply the 3D correction to both waves. I don’t have a very good understanding of the differences between the 2D and 3D corrections, and I do not currently have a dataset with both uncorrected and 2D-corrected copies of the same scan to allow me to experiment with and test various strategies (hoping to get this soon, but not sure when I’ll be able to). As such, I am hoping that someone with more experience or knowledge on this might be able to shed some light on the nature of the issue and severity of the problem and/or offer guidance on how I might be able to correct it. Thanks! Annchen

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Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
by fsbuild 18 Jul '25

18 Jul '25

External Email - Use Caution This posting indicates that changing the path to ./stats from ../stats got rid of a segmentation fault.  I would at least check that all paths in the arguments ro mris_anatomical_stats are correct though. https://secure-web.cisco.com/17sKLSeDVET5-5S3ZEgRGL6lX55gFUMqV2UWISNObj-rC9… But I don’t see the error in the recon -all log you sent which is apparently from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux 7.5. - R. On Jul 10, 2025, at 16:24, Samantha Hendry <shendry2(a)ed.ac.uk> wrote:mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white

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