Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

segmentHA_T2.sh ERROR:cannot find transform file
by Chunling Hu 16 Mar '26

16 Mar '26

External Email - Use Caution Freesurfer experts, I encountered an issue while using segmentHA_T2.sh. I am using Freesurfer 7.3, and the command I executed was: segmentHA_T1.sh SUB01 /home/huchunling/HP5T/SUB01_PID_20260313_132311_0037_43/sPID202603131323110037-0301-00001-000001-01.nii T2 1 Referring to the solution provided in a previous email, I ensured that the input file is a single frame rather than a multi‑frame image. Therefore, I need your help to identify where the problem lies. Best regards, Chunling Hu The error message I received is as follows: ------------------------------ USER huchunling HOST fox-c06 PROCESSID 2744600 PROCESSOR x86_64 OS Linux Linux fox-c06 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:03:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left 2026年 03月 16日星期一 13:34:54 CST ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//runtime/glnxa64:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//bin/glnxa64:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//sys/os/glnxa64:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/thinlinc/lib64:/opt/thinlinc/lib:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//sys/opengl/lib/glnxa64:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/thinlinc/lib64:/opt/thinlinc/lib Registering norm.mgz to additional volume makeIsotropic WARNING: not different enough, won't reslice! CostFunctions::centroid is NAN (empty image? n = 0 ) ERROR: cannot find transform file /home/huchunling/HP5T/OUTPUT/freesurfer_subjects/SUB01/mri/transforms/T1_to_T2.v22.lta gzip: /home/huchunling/HP5T/OUTPUT/freesurfer_subjects/SUB01/tmp/hippoSF_T1T2_v22_T2_left//T2resampledLikeT1.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or a character vector. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192) MATLAB:badSwitchExpression Command exited with non-zero status 249 @#@FSTIME 2026:03:16:13:34:54 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 22.89 S 3.89 U 7.50 P 49% M 1468976 F 0 R 705152 W 0 c 399 w 16444 I 0 O 288120 L 0.20 0.33 0.40 @#@FSLOADPOST 2026:03:16:13:35:17 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 0.65 0.43 0.44 Linux fox-c06 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:03:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at 2026年 03月 16日星期一 13:35:17 CST

2 1

Request to Remove Email Addresses from FreeSurfer Mailing List
by 강다정 12 Mar '26

12 Mar '26

External Email - Use Caution Hello, I am contacting you because I have been receiving FreeSurfer-related emails every day. It seems that the emails are being sent to the following addresses. Please take the necessary action so that these addresses are removed from the mailing list. danbidan2443(a)gmail.com / doramisister(a)naver.com The notifications arrive during the early morning hours, and the alerts are disturbing my sleep. I would appreciate it if you could check and resolve this issue. Thank you.

1 0

Request to Remove Email Addresses from FreeSurfer Mailing List
by 강다정 12 Mar '26

12 Mar '26

1 0

FREESURFER: undefined variable
by Wales, Ryan 12 Mar '26

12 Mar '26

External Email - Use Caution Hi, I’m trying to run FreeSurfer (v. 7.2.0) longitudinally, first creating the base template for my sample subject across both timepoints, using: recon-all -base sub_01-tp sub-01_ses-01_t1 -tp sub-01_ses-02_t1 -all Both cross-sectional timepoints were previously run separately. Just after ‘mri_pretess’ finishes, I encounter the error: “FREESURFER: Undefined variable”. I’m running FreeSurfer on my organization’s HPC, and I’ve ensured that SUBJECTS_DIR and FREESURFER_HOME are both set appropriately. I found another post with the same error, but they also had “nu_correct: Command not found”, unlike me. Both of us are using v. 7.2.0. https://secure-web.cisco.com/1KfETP9AssoehTvJ3VhjCNZJJg3rReFE0UsHzbxBF1de4x… Can’t figure this one out. Thanks all! Best, Ryan Wales ________________________________ Confidentiality Notice: This electronic mail transmission and any documents, files, or previous email messages attached to it may contain confidential information and are intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, or a person responsible for delivering such information to the intended recipient, you are hereby notified that any further review, disclosure, copying, dissemination, distribution, or use of any of the information contained in or attached to this email transmission is strictly prohibited. If you have received this message in error, please notify the sender immediately by email, discard any paper copies, and delete all electronic files of the message. Thank you for your cooperation.

2 5

use of a custom annot for mri_segstats
by Simone Cauzzo 12 Mar '26

12 Mar '26

External Email - Use Caution Hi all I am running Freesurfer 7.4 I am trying to extract QSM values at different cortical depths, and obtain statistics for the 400 Schaefer regions. my code is mri_vol2surf --mov [QSM coregistered to orig_nu.mgz ] \ --regheader $sub \ --hemi lh \ --surf white \ --o outputsurf.mgh \ --projfrac 0.2 mri_segstats --annot subjid lh 400Parcels_Yeo2011_17Networks \ --i outputsurf.mgh \ --sum outputstats.stats I get the following errors Reading annotation $SUBJECTS_DIR/$sub /label/lh.400Parcels_Yeo2011_17Networks.annot error: No such file or directory error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match ... trying local annot error: No such file or directory error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match The annot file is there, I checked, and that's verified by the fact that apparently it knows how many vertices are there. Moreover, it totally worked when I tried this command to extract anatomical stats from the same parcel mris_anatomical_stats -a $SUBJECTS_DIR/$sub /label/lh.400Parcels_Yeo2011_17Networks.annot -f $SUBJECTS_DIR/$sub/stats/$hemi.$parc.stats $sub $hemi Do you have any idea of what is going on? The volume [QSM coregistered to orig_nu.mgz ] was created by applying the QSM 2 T1 rigid transform with ants antsApplyTransform, with orig_nu.mgz as reference volume, which provided a new QSM volume that looks aligned to orig_nu.mgz and on the same grid. It is not a problem of this file since I tried producing an mgh file with orig_nu.mgz as --mov volume and the error persists. Thank you for your help Simone Cauzzo

2 2

mri_annotation2label on HCP-MMP1 atlas
by LE TUTOUR Tom 12 Mar '26

12 Mar '26

External Email - Use Caution Dear FreeSurfer community and developers, I have a question regarding the mri_annotation2label command. I am working using the fsaverage projection of the HCP-MMP1 parcellation ( [ https://secure-web.cisco.com/1WboGjsp1XDsnzClB7iD0-8so4xTNqnpjNoue_C06W_Mmq… | https://secure-web.cisco.com/1WboGjsp1XDsnzClB7iD0-8so4xTNqnpjNoue_C06W_Mmq… ] ). I was trying to extract each label of the annotation to individual files in order to combine some labels into a custom label. I am using FreeSurfer 8.1.0. For some reason, it works fine on the right hemisphere but the left hemisphere produces nothing. The command I ran was : mri_annotation2label --subject fsaverage --hemi lh --outdir ./labels-left --annotation HCP-MMP1 --surface white The output I got was : Reading surface /my/path/fsaverage/surf/lh.white Loading annotations from /my/path/fsaverage/label/lh.HCP-MMP1.annot Seg base 0 calling annotation2labelV2() ... error: Cannot allocate memory error: mri_annotation2label: LabelAlloc() could not allocate 0-sized vector I am assuming one of the labels is empty and this is causing the command to fail ? How could I fix this to get labels of interest for further analyses ? Best regards, Tom LE TUTOUR, PhD

2 1

extracting percent change values
by Victor Jenkins 11 Mar '26

11 Mar '26

External Email - Use Caution Hi everyone, I am using Fressurfer 7.4.1 for a longitudinal analysis with 4 timepoints. I followed this instruction below to see cortical thickness changes, and I found 3 significant clusters. https://secure-web.cisco.com/1zkw2d7WuvQHYpAKmrGwmY4HTHyJc1TV0m82jbLxopbfDf… -- Second Stage: Option QDEC This one from the website: long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label mri_glmfit --osgm \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --surf fsaverage lh I also ran mri_glmfit-sim. (mri_glmfit-sim --glmdir lh.testretest.thickness.fwhm15 --cache 4 neg --cwp 0.05 --2spaces) I want to extract the percent change values/numbers (pc1, *pc1 = rate / thick1*) from the 3 significant clusters we found so I could visualize those values for every participant. I was not able to find how to do this step. Is there a way to do this? Thank you for the help! Best regards, Victor

1 0

Difference between 7.3 and 7.4
by Aaron Tanenbaum 11 Mar '26

11 Mar '26

External Email - Use Caution Hello, I would like for our lab to move to freesurfer 7.4 from 7.3. Mainly because 7.4 can handle enhanced DICOMS. My lab will not move to 7.4 because of the potential difference between the recons. From my understanding there is no difference in the default recons. However we use the flag -3T. We finish using the segmentBS.sh command. With the -3T and segments.sh, will there be a difference in the results between 7.3 and 7.4? Thank you in advance.

3 3

Using HCPex on Freesurfer Data
by Carly McIntyre-Wood 10 Mar '26

10 Mar '26

2 1

Re: Missing vtk and qt dependencies in 8.1.0 compiled binaries
by fsbuild 10 Mar '26

10 Mar '26

External Email - Use Caution The Rocky8 8.1.0 release should run on Rocky9 and an installer can be found on the download page,https://secure-web.cisco.com/1Y-hgYUnsl39CGV1agic6tunpDoyDxITSoTLbdvGJ… There will be a Rocky9 installer in the forthcoming 8.2.0 release.  You could try the Rocky9 development build (which was previously announced on the Freesurfer mailing list), https://secure-web.cisco.com/1KnCLencGtvb2-jQPHIRiSpBXm1M0vkcx9… at this point,  I would wait for the 8.2.0 release to be announced on the mailing list in order to run a Rocky9 version of freesurfer because we do not recommend development builds for ongoing/long term work. I would check with your system administrator(s) about how they install of Linux .rpm packages and ask them to install and support freesurfer, e.g., the existing Rocky8 8.1.0 .rpm and the forthcoming Rocky9 8.2.0 .rpm.   Some sysadmins use a container to test (install) the .rpm, then take the list of dependencies and update their modules, Spack, etc.. configurations to provide the required system packages when freesurfer binaries run.   It’s not practical for us to support end users unarchiving a tar file and then try to diagnose what is missing on each remote system when the .rpm and .deb files should provide the dependency information. - R.

1 0

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