Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

ANTs denoising
by Alexopoulos, Dimitrios 15 Nov '23

15 Nov '23

External Email - Use Caution To which anatomical volume is ANTs denoising applied to for generating the orig surface? We do ANTS denoising to the input T1 before running recon-all and were wondering if we are denoising our data twice. Thx. Jim ________________________________ 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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recon_all_clinical and aseg.stat
by Biondo, Francesca 14 Nov '23

14 Nov '23

External Email - Use Caution Hello! I encountered 3 issues with recon_all_clinical: 1. Both version 7.4.0 and version 7.4.1 do not generate aseg.stat file. Is this normal? I would like to extract volume parcellations via asegstats2table given that I need the volume parcellations as typically presented in aseg.stat. Is there a way to extract aseg.stat from aseg.mgz or another solution to extract aseg.stat volumes? 2. Version 7.4.0 throws errors at the end of the script (even with the replacement file). "ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt" and "ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt." I checked, "colortable_BA.txt" exists but "colortable_BA_thresh.txt" doesn't. If I rename the latter file to "colortable_BA_thresh.txt", then it fixes the errors. Is this the correct way to address the problem? 3. Version 7.4.1 has a similar error as above, but it seems to be due to the incorrect path: ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt. Any help, particularly with problem 1, would be much appreciated! Thank you, Fran Francesca Biondo, PhD | Senior Research Fellow | Centre for Medical Image Computing | Computer Science | UCL | f.biondo(a)ucl.ac.uk<mailto:f.biondo@ucl.ac.uk>

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Running autorecon2-wm after wm edits
by Fernanda Hansen P. de Moraes 14 Nov '23

14 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran *recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3* nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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TRACULA error: lowb_brain_mask.bbr.nii.gz
by Lauren Stephens 13 Nov '23

13 Nov '23

External Email - Use Caution Hi FreeSurfers, I am attempting to run tracula on longitudinal DTI data however during trac-all -prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz from mri_concat. #------------------------------------- /Applications/freesurfer/7.3.2/bin/trac-preproc #------------------------------------- #@# Intra-subject registration (base template) Mon Nov 13 14:13:56 PST 2023 mri_concat --i /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/aparc+aseg_mask.nii.gz --min --o /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing min across all frames Writing to /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz mri_concat --i /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz --min --o /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz ninputs = 1 Checking inputs error: niiRead(): error opening file /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz ERROR: reading /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Wed Oct 4 21:25:26 PDT 2023; root:xnu-8796.141.3.701.17~4/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Nov 13 14:13:58 PST 2023 I am using FreeSurfer 7.3.2 on an iMac Pro running Ventura 13.6.1. Any suggestions for how to clear this error would be greatly appreciated! Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Recon all clinical with multiple input scans
by Lieshout, P.B. van (Pauline) 13 Nov '23

13 Nov '23

External Email - Use Caution Dear sir/madam, I have been trying out the new recon-all-clinical algorithm. In the FreeSurferWiki on recon-all-clinical, it is not specified if I can add multiple scans (T1, FLAIR and T2, for instance) of the same individual in the recon-all-clinical command, similar to the old recon-all command. Is this possible in your new algorithm? Thanks in advance, Best, Pauline van Lieshout ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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buffer overflow detected in mris_expand
by Amanda Rodrigue 13 Nov '23

13 Nov '23

External Email - Use Caution Hello, I am running some freesurfer processes (freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275) via fmriprep 23.1.3 (singularity container version) and I'm getting the error below when running the mris_expand command. Below is the output from frmiprep but it's clear it's a freesurfer-specific error (I've highlighted the freesurfer command, output, and error in red). There was another post with the buffer overflow detected error (different command though) and it did not have a posted solution. Node: _midthickness0 Working directory: /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0 Node inputs: args = <undefined> distance = 0.5 dt = <undefined> environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'} graymid = <undefined> in_file = /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/temp/_epo/derivatives/fmriprep23_1_3/sourcedata/freesurfer/sub-10412/surf/rh.white nsurfaces = <undefined> out_name = midthickness pial = <undefined> smooth_averages = <undefined> sphere = sphere spring = <undefined> subjects_dir = /opt/freesurfer/subjects thickness = True thickness_name = <undefined> write_iterations = <undefined> Traceback (most recent call last): File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _midthickness0. Cmdline: mris_expand -pial /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white 0.5 /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness Stdout: reading pial surface from /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial using distance as a % of thickness using thickness file /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness expanding surface /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white by 50.0% of thickness and writing it to /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness reading thickness... Stderr: *** buffer overflow detected ***: terminated Aborted (core dumped) Traceback: RuntimeError: subprocess exited with code 134. -- Amanda Rodrigue, PhD Boston Children's Hospital Harvard Medical School 1 Autumn St. Boston, MA 02215

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Requesting pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Yuxuan Liu 13 Nov '23

13 Nov '23

External Email - Use Caution I found there is a pass code required to unzip this file. Could someone send me this code? Thanks very much.

1 0

Request for Passcode to Open 7z. Archive
by José Dixon 11 Nov '23

11 Nov '23

External Email - Use Caution Dear FreeSurfer Support Team, I need the passcode to extract the archive for VirtualBox Ubuntu 18.04.06 compressed image with FreeSurfer 7.2.0 (FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thanks so much for fulfilling this request. -- Best, José Dixon Morgan State University | Ph.D. Student

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Importing atlas with mris_register: "hips not supported"
by Jasmine Cakmak 09 Nov '23

09 Nov '23

External Email - Use Caution Hello, Any help with this issue is greatly appreciated. I am trying to import the Neuromorphometrics atlas into Freesurfer as a part of my segmentation analysis. I have run recon-all on my template subject (IXI550) and the subject to register (PSCI15_003), and taken the atlas.nii and used mri_vol2surf and mris_seg2annot, all without errors. Now I am trying to register IXI550 and PSCI15_003 to each other so that I am then able to run mris_apply_reg. I am receiving the error "hips not supported," both on Ubuntu 22.04.2 LTS and my M1 mac. Is there a way to resolve this error (found below), or a different way for me to apply the atlas to the recon-all of my subjects? I am using freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. mris_register PSCI15_003/surf/lh.sphere IXI550/surf/lh.sphere reg_PSCI15003_IXI550.dat cwd /mnt/d/Jasmine2023/Neuromorph cmdline mris_register PSCI15_003/surf/lh.sphere IXI550/surf/lh.sphere reg_PSCI15003_IXI550.dat 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from PSCI15_003/surf/lh.sphere... reading template parameterization from IXI550/surf/lh.sphere... error: hips is not supported error: hips is not supported MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 -------------------- tol=5.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = 0.000, std = 3.574 Segmentation fault Thank you so much in advance for any help. Jasmine

1 1

Group analysis question
by Nicolette Barber 09 Nov '23

09 Nov '23

External Email - Use Caution Hello, I am working on a project using FreeSurfer, and I am trying to set up a whole brain group analysis. However, I am not sure how to set up the FSDG files, etc., as my dependent variable is not a cortical measurement. My dependent variable is a neuropsychological battery, culture, and brain measurement are my independent, and my covariate is ICV. I have been trying to figure this out for a while now. Is there a way to change the dependent variable for mriglm_fit? And if so, how would I set this up? I am using version 6. Thank you, Nicolette

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Freesurfer November 2023