Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

longitudinal skullstrip issue
by KennethSPrice 27 Mar '23

27 Mar '23

External Email - Use Caution Hello all, I'm wondering if I can use brainmask or pial surface of timepoint1 as a reference for the skullstrip of timepoint2. TP2 is being problematic during skullstrip. I've tried -wsthresh and -gcut. Any option to use brainmask1 as a reference point for brainmask2? Sent with [Proton Mail](https://secure-web.cisco.com/1mDhhZToXGJnAuPW3XS4AmJXdzD8P3Gy61kty6fb… secure email.

2 1

Unable to quantify FWHM, everything significant
by Yuri Yeshinsky 27 Mar '23

27 Mar '23

External Email - Use Caution Dear FreeSurfer experts, I ran many analyses on a large sample and everything goes well. However, I encounter here a problem I've never encountered before about one of my analyses. I'm looking at the presence of a difference in slope between three groups while covarying for several variables and classes. My contrasts are: contrast1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 contrast2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 contrast3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 6 classes (gender 2, disease 3), so first 6 for intercepts, next 30 for the covariates 1 to 5, and the last columns to test the slope difference between the three groups on the variable I have used these contrasts to test the differences in slopes of several variables and I found significant clusters. However, for one variable specifically, mri_glmfit seems to be unable to quantify the FWHM from the data and when running mri_glmfit-sim, the resulting output, for every contrast (positive direction), gives a significant cluster where the whole cortex is included; see for contrast2 (it's the same result for every contrast anyways): yuri@rodonor:/lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13$ cat cache.th40.pos.sig.cluster.summary # Cluster Growing Summary (mri_surfcluster) # 7.3.2 # 7.3.2 # CreationTime 2023/03/16-13:19:18-GMT # cmdline mri_surfcluster --in lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/sig.mgh --mask lh.Cogn.moca.egfr.thickness.15.glmdir/mask.mgh --cwsig lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.cluster.mgh --sum lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.cluster.summary --ocn lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.masked.mgh --no-fixmni --csd-out lh.Cogn.moca.egfr.thickness.15.glmdir/csd/all.cache.th40.pos-Cogn-egfr-g13.csd --csd lab/yuri/FreeSurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm01/pos/th40/mc-z.csd --csdpdf lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.pdf.dat --vwsig lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.voxel.mgh --vwsigmax lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.voxel.max.dat --oannot lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.ocn.annot --bonferroni 2 --surf white # cwd /lab/yuri/egfrproject # sysname Linux # hostname rodonor.bri.upall.sv # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /lab/yuri/egfrproject # SearchSpace_mm2 74258.8 # SearchSpace_vtx 144277 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign pos # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 1e+10 at vertex 0 # Overall min 0 at vertex 8 # NClusters 1 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 10000000000.0000 0 74258.42 -36.8 -18.3 64.5 0.00020 0.00000 0.00040 144276 1442760045363200.00 precentral I feel that something is wrong in there, unless you think that it is possible that the slope difference manifests as a global effect for every contrast. It really seems to happen to happen specifically with this variable, as when replacing this variable by another, I can generate specific clusters that do not cover the whole cortex. Here is the terminal output from mri_glmfit when I run it on my "problematic" variable: yuri@rodonor:/lab/yuri/egfrproject$ mri_glmfit --y lh.Cogn.moca.egfr.thickness.15.mgh --fsgd analysis/egfr-Cogn-moca-egfr.fsgd dods --C analysis/Cogn-egfr-g12.mtx --C analysis/Cogn-egfr-g13.mtx --C analysis/Cogn-egfr-g23.mtx --surf fsaverage lh --cortex --glmdir lh.Cogn.moca.egfr.thickness.15.glmdir gdfRead(): reading analysis/egfr-Cogn-moca-egfr.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 60.1017 7.57085 1 Bmi 26.8664 4.97535 2 FRS 10.9088 9.29652 3 wm 1642.17 1761.49 4 educ 3.48198 0.959607 5 moca 27.2733 2.25488 Class Size and Means of each Continuous Variable 1 g1gender0 324 57.7939 25.8998 5.0538 1164.8920 3.4753 27.6883 2 g1gender1 309 58.2326 27.0854 14.3098 1722.7615 3.4822 26.9450 3 g2gender0 311 61.0777 26.8550 6.1809 1492.9781 3.4084 27.6785 4 g2gender1 345 62.4106 27.2979 16.8165 2059.6704 3.5391 26.8986 5 g3gender0 20 63.1610 27.9590 6.8020 1252.0200 3.4500 27.4000 6 g3gender1 23 67.2335 30.2713 26.5796 3377.0609 3.7391 25.8696 INFO: gd2mtx_method is dods Reading source surface /lab/yuri/FreeSurfer/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.3.2 cwd /lab/yuri/egfrproject cmdline mri_glmfit --y lh.Cogn.moca.egfr.thickness.15.mgh --fsgd analysis/egfr-Cogn-moca-egfr.fsgd dods --C analysis/Cogn-egfr-g12.mtx --C analysis/Cogn-egfr-g13.mtx --C analysis/Cogn-egfr-g23.mtx --surf fsaverage lh --cortex --glmdir lh.Cogn.moca.egfr.thickness.15.glmdir sysname Linux hostname rodonor.bri.upall.sv machine x86_64 user yuri FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.mgh logyflag 0 usedti 0 FSGD analysis/egfr-Cogn-moca-egfr.fsgd labelmask /lab/yuri/FreeSurfer/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.Cogn.moca.egfr.thickness.15.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.Cogn.moca.egfr.thickness.15.glmdir Loading y from /lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to lh.Cogn.moca.egfr.thickness.15.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 6285.08 Matrix condition is 8.72285e+09 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 144277 voxels in mask Saving mask to lh.Cogn.moca.egfr.thickness.15.glmdir/mask.mgh Reshaping mriglm->mask... search space = 71879.345725 DOF = 1290 Starting fit and test Fit completed in 28.4991 minutes Computing spatial AR1 on surface WARNING: ar1 = 0 <= 0. Setting fwhm to 0. Residual: ar1mn=0.000000, ar1std=0.000000, gstd=0.000000, fwhm=0.000000 Writing results Cogn-egfr-g12 maxvox sig=1e+10 F=0 at index 0 0 0 seed=1679933797 Computing efficiency Cogn-egfr-g13 maxvox sig=1e+10 F=0 at index 0 0 0 seed=1679933797 Computing efficiency Cogn-egfr-g23 maxvox sig=1e+10 F=0 at index 0 0 0 seed=1679933797 Computing efficiencymri_glmfit done Many thanks, Yuri

2 1

Structural covariance contrasts
by mariangela asimina 27 Mar '23

27 Mar '23

External Email - Use Caution Dear experts, I am looking into the covariance of the volume of subcortical structures with cortical vertex-wise volume, comparing between two groups, correcting for the effects of gender, age and eTIV. My approach was to extract the volume of a subcortical region from the aseg.stats file and add it as a covariate into the FSGD and Contrasts files. My FSGD therefore is in the form Class HCm Class HCf Class SZm Class SZf variables age eTIV L-ThaVol I have normalized all continuous variables, and have 12 different FSGD files, one for each subcortical area of interest My Contrasts matrix, to test for differences in volume covariance between HC and SZ in either slope or intercept, is the following (16 regressors): 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 Is this the right approach, and if yes is the contrast matrix correct? Or is there a way to do test for structural covariance through FreeSurfer commands? I would appreciate any help! Mariangela

2 1

Pass code
by Santiago Gómez 26 Mar '23

26 Mar '23

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images for my research project and a pass code is needed for this 7z archieve. Would you please send me the pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1MlcuMSSiFoTx0GjyrQW1D_iGKohpLuJFfWKiIEF3BcSo-…> ? I really appreciate it. Greetings, Santiago Gómez Castro, MD Neurosurgeon Universidad Nacional de Colombia Cel. +57 316 623 69 00 -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/1GYOl7UuM7xf4ZhF71VSWMCVhFZCYuelWuXbjcGXGyzHOiT… <http://secure-web.cisco.com/1cYNL9a6ejl6w7JEp3F7zG0n1PylzIv5VwhJqbX6n3ZCuIX…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

1 0

kvlThresholdImage: command not found
by Song, Xinrui 26 Mar '23

26 Mar '23

External Email - Use Caution Hello Dear Developers, I am trying to segment ex vivo hemisphere brains following instructions here "https://secure-web.cisco.com/1yI3dz-T0lQE-jN1p4p6MgEh8QOPQyERm9wL9X_vVhCt5v…". I was just proceeding to the Segment White Matter section and found that none of the kvl commands can be found in my installation. They are also not found in the freesurfer/bin folder. I searched the archive and found that there was one case that's very similar to mine, but it occurred back in 2012 and on a Mac distribution. (https://secure-web.cisco.com/1tVA2ZQl9_YrOUpNZqZ-IA4YxSqzjGL5Mp3wdVgTgftKi5…) Freesurfer version: freesurfer_ubuntu20-7-dev_amd64.deb Platform: WSL-Ubuntu on Windows.

1 0

PETsurfer registration
by Douglas N. Greve 24 Mar '23

24 Mar '23

On the PETsurfer wiki, https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended using mri_coreg to register your PET to the FS anatomical using the following command line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta This works well for PET scans that do not have much activity outside the head (eg, FDG and many neuroreceptor ligands). However, it can be inaccurate for other ligands that do have lots of uptake outside the head (eg, tspo, maybe tau). In these cases I now recommend using mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --ref nu.mgz --no-ref-mask This command will use the whole head MRI (nu.mgz) instead of the brainmasked MRI (brainmask.mgz); this will align better for these types of scans. This is now documented on the PETsurfer website. Remember, you should always check your PET-MR registrations manually. Sorry for any inconvenience this has created. best doug

1 0

Re: [Freesurfer] SAMSEG in MS terminal error
by Cerri, Stefano,PHD 24 Mar '23

24 Mar '23

Hi Gabriel, These messages look like TensorFlow warnings. They just mean that you're running it on a system without GPUs. They should not stop the run. Is this the last message printed by run_samseg, or does the algorithm continues? Can you provide more details on when the run terminates? Stefano External Email - Use Caution Hi, I'm having difficulty with the command to assess WM lesion in MS, using the SAMSEG. I have already installed tensorflow and python3.9, however when typing in the terminal the command "run_samseg --input /home/username/data/t1.nii /home/username/data/flair.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/username/data/samsegOutput", this message appears: "2023-03-24 13:21:04.936769: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-03-24 13:21:04.936787: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7.2.0/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term" -- Att, Gabriel de Deus Vieira _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.

1 0

Postdoctoral Position in Cognitive and Translational Neuroscience at Brown University
by Elizabeth Sharp 24 Mar '23

24 Mar '23

External Email - Use Caution Postdoctoral Position in Cognitive and Translational Neuroscience at Brown University Area: Cognitive Neuroscience of Visual Memory, Aging, and Alzheimer’s disease Depts. of Cognitive, Linguistic, and Psychological Sciences (CLPS) and Psychiatry and Human Behavior Brown University We are seeking a highly motivated postdoctoral researcher to lead an NIH-funded project in the Laboratory for Cognitive and Translational Neuroscience directed by Dr. Hwamee Oh at Brown University. The project is to use fMRI and PET to study visual memory networks in healthy young, cognitively normal older adults, and older adults who are considered as preclinical Alzheimer's disease. Applicants with a Ph.D. degree in cognitive neuroscience, computational neuroscience, biomedical engineering, or a relevant field are encouraged to apply. Prior experience with human neuroimaging, a strong background in cognitive neuroscience and experimental design, and/or familiarity with programming in relevant languages (e.g., Python, MATLAB) are required. Applicants with experience with multivariate analyses on task-fMRI data are especially encouraged to apply. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive neuroscience of visual perception and memory, brain aging or Alzheimer’s disease, and the ability to independently develop research questions and work in collaboration with other team members. An expected start date is early summer or fall 2023. The position is primarily affiliated with Brown CLPS. Interested applicants should email a brief description of research background and career goals, and CV with a list of 3 references to Dr. Hwamee Oh at hwamee_oh(a)brown.edu. Contact Website https://secure-web.cisco.com/1534_IfZK4Xe7CtgB-h6v7DQVDNkwHRBS0xj2cNxbYGHZ3… Twitter @OhLabBrown -- Elizabeth Sharp Research Assistant Oh Lab Brown University

1 0

SAMSEG in MS terminal error
by Gabriel Vieira 24 Mar '23

24 Mar '23

External Email - Use Caution Hi, I'm having difficulty with the command to assess WM lesion in MS, using the SAMSEG. I have already installed tensorflow and python3.9, however when typing in the terminal the command "run_samseg --input /home/username/data/t1.nii /home/username/data/flair.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/username/data/samsegOutput", this message appears: "2023-03-24 13:21:04.936769: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-03-24 13:21:04.936787: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7.2.0/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term" -- Att, Gabriel de Deus Vieira

1 0

negative uptakes after GTM pvc correction
by Federica Di Antonio 24 Mar '23

24 Mar '23

External Email - Use Caution Dear experts, I report an answer you gave about some negative values avatar partial volume correction: "[...] Usually this only happens in small ROIs and/or low uptake regions. Why might the model not be perfect? It could be a number of things: 1. the MRI-PET registration is inaccurate 2. the MRI segmentation is inaccurate 3. the ideal segmentation is not reflected by the MRI segmentation (eg, one of the segmentations has a hot spot)" I wonder if it is possible for you to give me an hint about the reason why an inaccurate registration or segmentation can cause negative uptake values. At first sight it seemed intuitive to me, but on second thought that's not so obvious. I would be very grateful for any help! Federica Di Antonio

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer