Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Infant FreeSurfer: volumes
by k3ops＠free.fr 21 Jun '21

21 Jun '21

External Email - Use Caution Hi FreeSurfer team, I using the latest version of Infant FreeSurfer to assess brain volumes on very young kids. When looking at the brain volume (aka 'BrainSegVolNotVent') extracted from the aseg statistical file I got a very different volume than doing the pixel count (weighted by pixel resolution). For example: - BrainSegVolNotVent: 1174.5 - PixelCount: 1250.8 With standard FreeSurfer (on adults) I was used to get similar volumes when comparing aseg stat file and pixel count. Is that expected? Why there is a discrepancy between the two way of assessment? I know some other structures are not based on pixel count based on FreeSurfer documentation, but looks like brain volume called 'BrainSegVolNotVent' was not impacted: https://secure-web.cisco.com/1K0DiBqkK6tza56FKjGAoo4Gw5DWfMbyfEne1V4rxz67RM… Thanks. Florent

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Finding equivalent vertices on fsaverage_sym lh and rh surfaces
by Tim Schäfer 20 Jun '21

20 Jun '21

External Email - Use Caution Dear FreeSurfer experts, for the 'fsaverage_sym' template that comes with FreeSurfer, I would like to find a mapping between equivalent vertices (i.e., vertices in the same anatomical position) between the left and right hemispheres. By "equivalent" I mean identical anatomical positions. I noticed, for example, that vertex 500 in the file fsaverage_sym/surf/lh.white and vertex 500 in the file fsaverage_sym/surf/rh.white are not at equivalent anatomical points. I feel this mapping must be documented somewhere or there is an obvious way to get it that I am currently overlooking, so I thought I'd ask here. Thanks in advance, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Problem with rca-config when running recon-all
by Juan Felipe Quinones Sanchez 20 Jun '21

20 Jun '21

External Email - Use Caution Dear Freesurfer team, I am new to Freesurfer. I installed it on my WSL (ubuntu 18.04) following the instructions at: https://secure-web.cisco.com/19NPylFTZm62HJK1A_0s-94uhHZebqqpw9Sitxzpx_bTWo…. I believe that the installation was successful because I get documentation whenever I type a function on the command line. I wanted to run recon-all on a T1 image using the following call: $FREESURFER_HOME/bin/recon-all -s subx -i $t1_img -all where $t1_img = /mnt/c/Users/...../t1.nii.gz Unfortunately I got the following error: rca-config: Command not found. I read a thread (https://secure-web.cisco.com/1H4D7loaV8UEB6OJaKKwdNSc3rqTSamNp7b7KUKBFFvTH3…) addressing this topic and followed the suggested solution. I typed everything manually. I also ran the code directly from the console and from a bash script, both with the $t1_img variable and the original file path but the error persists. I found this code (https://secure-web.cisco.com/1rA78FG6F2-U9A7bR00W9v_d5uE-voxX7qbpwkAvn5xBbo…) supposedly running recon-all and there is a line where the command "rca-config" is used. However, it seems to be not recognized even though the file is indeed located at $FREESURFER_HOME/bin/. I would appreciate any sort of guidance. Thank you, Juan

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a query on gray volume from parcellating data
by Koustav Chatterjee 20 Jun '21

20 Jun '21

External Email - Use Caution Dear Sir/Madam, Could you please tell what does it mean by 'Gray volume' and 'avg thickness' of various structures while we are parcellating cortical surfaces through FreeSurfer and getting 'aparcstats2table'. Thank you for your help. Regards, KC [image: image.png]

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mri_glmfit with pvr
by stdp82＠virgilio.it 20 Jun '21

20 Jun '21

External Email - Use Caution Thanks If I have 4 groups GroupDescriptorFile 1 Title XXX Class G1 Class G2 Class G3 Class G4 Input subj1 G1 Input subj2 G3 Input subj3 G2 Input subj4 G2 Input subj5 G4 .... Are the contrasts below corrected? G1_only_thick 1 0 0 0 G2_only_thick 1 0 0 0 G3_only_thick 1 0 0 0 G4_only_thick 1 0 0 0 G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5 G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5 G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25 Thanks Stefano Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, this thread https://secure-web.cisco.com/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2one… 6/3/2021 10:22 AM, std...(a)virgilio.it wrote: > External Email - Use Caution Hi, how can I perform vertex by vertex (surface) analysis of covariance between functional connectivity data (FS-FAST) and cortical thickness, regressing out the effect of groups?My mean concern is how buid the fsgd file. Stefano > Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N Greve" <gr...(a)nmr.mgh.harvard.edu> wrote: >Hi Aga, what you have done is correct, no need to include the pvr in the >fsgd. >doug > >Burzynska, Aga wrote: >> Dear all, >> I am trying to make group level analysis of functional data on the >>surface and add per-vertex regressors (PVR, here: cortical thickness) >>into the design. When I view the results I have the feeling that the PVR >>is not really included in the model: >> >> I am using the command: >> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd >>Group1versusGroup2.fsgd --pvr lh.thickness.10.mgh --C >>Group1only_thickness.mat --C Group2only_thickness.mat --C >>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C >>Group1plusGroup2_thickness.mat >> >> where >> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed >>level analysis (combining the runs) for each participant >> fsgd file contains: >> GroupDescriptorFile 1 >> Title Group1versusGroup2 >> Class Group1 >> Class Group2 >> Input 1109 Group1 >> Input 1110 Group1 >> Input 1111 Group1 >> Input 1112 Group1 >> ... >> Input 2280 Group2 >> Input 2282 Group2 >> Input 2283 Group2 >> Input 2284 Group2 >> >> The PVR is a file containing thickness maps for each participant, >>concatenated in the same order as for the functional data. >> >> So there are 2 main regressors (1 factor, 2 levels), but the contrast >>files contain 3 regressors (the third one is the PVE), for instance: >> Group1minusGroup2_thickness.mat contains 1 -1 0. >> >> Does it look correct? >> Should the pvr regressor be included in the fsdg file? How can I do it? >> >> Thank you very much for your help, >> Cheers, >> Aga >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ES… >> >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: http://secure-web.cisco.com/1C61OSNwGFU8-MmX4hWZetUP6ivnpYMPZsypGZ1hSjsNzy-… > > > >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 Partners Compliance >HelpLine at >http://secure-web.cisco.com/1SUkt2fsByhbVkrjyleWea7U8vPw7dJUUjO3n73A05t_91l… . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ES…

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Running Freesurfer in the Desktop
by Rosalia Dacosta Aguayo 19 Jun '21

19 Jun '21

External Email - Use Caution Dear Freesurfer's team, I am trying to run FreeSurfer recon-all -all in a folder placed *on my Desktop* and I am having some trouble. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject sub-003_ses-BSL_T1w.nii -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/patchdir.txt: No such file or directory. I would greatly appreciate your help. Kind regards, Rosie

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External 3D View Issue
by Harriet Cornwell 18 Jun '21

18 Jun '21

External Email - Use Caution Hello, We thought we had finished manually editing a T1 scan and so opened it in the external 3D view to perform final checks and it looks incredibly messy (see attached screenshot). Are you able to advise whether this is an issue? If so, is it possible to fix it and, if it can be fixed, how we should go about doing so? Also, do you have any idea what might have caused this to happen? Thank you in advance! Harriet Cornwell

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Problem with Anatomicts in Freesurfer
by Yuqian Chen 17 Jun '21

17 Jun '21

External Email - Use Caution Dear Sir or Madam, Hope you are doing well! Thank you very much for your contribution to the freesurfer software which offers great help to research in the neuroimaging area. However, I met a problem when using it and I hope you can help me with it. The freesurfer version I use is freesurfer-linux-centos7_x86_64-7.1.1.tar.gz. I hope to implement AnatomiCuts with my own data which is tractography data (.vtk) reconstructed from HCP dataset with ukf tractography method. When I tried to run the dmri_AnatomiCuts command (the complete command is: dmri_AnatomiCuts -s wmparc.nii.gz -f 100307_ukf_pp.vtk -c 100 -n 14 -e 50 -o output -d s), the following messages appears: ups ups ups ups ups ups ... queue emplace 3894 queue emplace 0 It seems that the algorithm is running. But it just stays here and I cannot get the final results even with input data of only 100 fibers divided into 2 clusters. I am really confused what is going on here. Are there any special requirements for the input data? Your help will be greatly appreciated. Regards, Yuqian

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matching .label file from left to right hemisphere using a group template (fsaverage6)
by Xiaoxuan Yan 17 Jun '21

17 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to define the anatomically homotopic vertices between the left and right hemispheres on the fsaverage6 template. To do this, I am planning to map a .label file from the left hemisphere to the right hemisphere. I intend to follow the instructions on this wiki page https://secure-web.cisco.com/1dNutup50lUjZBRwKC0jge2QUROar1Y3UGcZEu3ZCD5VUF… to do it. However, at step 1.2, when I try to use surfreg to perform surface registration from fsaverage6 to fsaverage_sym with the command surfreg --s fsaverage6 --t fsaverage_sym --lh surfreg --s fsaverage6 --t fsaverage_sym --lh —xhemi I encountered an error “canot find norm”. I reckon that this occurs since I am using the fsaverage6 template which does not have a corresponding norm.gz file. May I know if there is any way to get around this issue? Best wishes Matilda

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Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years
by Alexandru Hanganu 16 Jun '21

16 Jun '21

External Email - Use Caution Dear All, The PCAN lab: http://pcanlab.ca has a two-year funded postdoctoral research fellow position under the supervision of Dr. Oury Monchi starting immediately to work on the following project: *Neuroimaging and other predictors of cognitive and neuropsychiatric evolution in Parkinson’s disease using multi-modal MRI imaging techniques and machine learning.* The project is funded by the Canadian Institutes of Health Research (CIHR) . It involves longitudinal analyses of cortical thickness, tractography and BOLD resting-state fMRI analyses and will benefit from collaborations with Dr. Alexandru Hanganu at the Department of Psychology of the University of Montreal. Other collaborators include Dr. Nils Forkert head of the Medical Imaging Processing and Machine Learning laboratory. A special focus will be given to the neural origins and predictors of Mild Behavior Impairment (MBI) in Parkinson’s disease in collaboration with Dr. Zahinoor Ismail who has led the development of the MBI-checklist. The project will make use of an existing longitudinal study containing structural, diffusion weighted imaging and functional MRI, neuropsychological and behavioural assessment, and genotyping at three time points. The PCAN lab has been a pioneer in using different neuroimaging techniques to study the origins and evolution of cognitive more recently neuropsychiatric deficits in Parkinson’s disease with the ultimate goal of early prediction of dementia in the disease. Other interests include the function and application of neuromodulation techniques such as transcranial magnetic stimulation, Transcranial direct stimulation and low intensity focused ultrasound. The PCAN Lab is located in the Healthy Brain Aging labs of the Hotchkiss Brain Institute part the Foothills Campus of the University of Calgary. The Foothills campus is home to the Seaman Family MR Research Centre which host a General Electric 3T research dedicated MRI scanner. Requirements of the position include a PhD in Neuroscience, biomedical engineering, biomedical sciences, or Psychology with experience in the analysis of one or multiple MRI neuroimaging techniques such as cortical thickness/volumetry (e.g. *Freesurfer, FSL*), functional connectivity (e.g. *PPI, ICA, graph theory*), diffusion weighted imaging (e.g. *Dipy, MRTrix, FSL*). Some fluency in computer programming (e.g. *Linux, Unix, MATLAB, or Python)* is also required as well as the ability to write scientific peer-reviewed manuscripts. Please send applications (Cover letter, CV, and the name of 2 references including current supervisor) to Oury Monchi: oury.monchi(a)ucalgary.ca

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