Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

MacOS Catalina
by Chantal Miller 11 Dec '19

11 Dec '19

External Email - Use Caution Dear all, I keep getting a warning on my Mac that Freesurfer will not be compatible with the latest update to MacOS Catalina. Does anyone have any information about how critical this issue is/ if Freesurfer will be updated to be compatible with this? Thank you for the help, CM

1 0

tkregisterfv problems
by Vicky Yang 10 Dec '19

10 Dec '19

External Email - Use Caution Dear Freesurfer experts, I am using bbregister to register my functional template image into T1 image. The bbregister is running fine. But when I tried to view registration using tkregisterfv, the window opened and closed quickly with an error message: Warning: Transformation can only apply to volumes for now. If your data includes ROI/Surface/Way Points, please do not use this feature yet. INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. LTAchangeType: src geometry must be valid terminate called after throwing an instance of 'int' Abort (core dumped). My command: bbregister --s subj_ID --mov template.nii --reg bbr_template_T1.reg --bold --init-fsl tkregisterfv --mov template.nii --reg bbr_template_T1.reg --surfs Can anyone help me with this? Thank you so much! VY

2 1

Using pre-segmented results
by Jordi Huguet 10 Dec '19

10 Dec '19

External Email - Use Caution Hi there, I wonder if its somehow possible to feed FreeSurfer's recon-all with pre-existing segmented maps (based on prior segmentation procedure e.g. SPM or ANTs) to "improve" FreeSurfer results. For some images I am working with the FreeSurfer's WM segmentation output is not optimal so I am looking for alternatives to improve the final results on such specific cases without requiring any manual intervention. Any comments, examples or shared reflections on this regard are kindly welcome. Thanks in advance, Jordi Huguet

3 7

Problem for cortical thickness analysis
by Gwang-Won Kim 10 Dec '19

10 Dec '19

1 0

Is subcortical segmentation reliable when cortical segmentation fails?
by Fredrik 10 Dec '19

10 Dec '19

External Email - Use Caution Hi FreeSurfer experts, In our data, we have a sample of older people with brain athrophy. This influences the cortical segmentation, where it can take into consideratin the skull, and/or leave out grey matter. My question regards the subcortical segmentation in such cases: Is it reliable to use the subcortical segmentation when the cortical segmentation clearly fails? Thanks, Fredrik Magnussen

2 1

intensity map
by a Chinese reader 10 Dec '19

10 Dec '19

External Email - Use Caution Dear Freesurfer experts,I have some questions about intensity map: 1. If I would like to get intensity maps of WM, which were created at 1 mm below the white surface, and the GM were taken at half of the thickness of the cortex. which commands I can use. 2. How to use the command line to get the Grey-matter tissue intensity at 10% up to 60% of the distance from the white matter to the pial surface. 3. Then, how to get the WM/GM intensity maps use the above values. Best regards, Zhang Xia

2 1

TRACULA question: Preprocessing exited with ERRORS
by Miguel Ángel Rivas Fernández 09 Dec '19

09 Dec '19

External Email - Use Caution Dear Freesurfer experts, I am a beginner in the use of TRACULA. I tried to run the preprocessing step of the trac-all command and it seems that all have worked fine. However, at the end of the command TRACULA finished with an error. This is the final output tkregister2 --mov /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat_orig.nii.gz --targ /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anatorig2anat.mat --reg /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Dec 9 22:00:14 CET 2019 You can find the configuration file and the trac-all.log file in attached. Best regards, -- *Miguel Ángel Rivas Fernández*

1 0

Recon-all
by Gwang-Won Kim 09 Dec '19

09 Dec '19

2 1

"Bad CPU type in executable" error
by Abhi Jaywant 09 Dec '19

09 Dec '19

External Email - Use Caution Hi, I am trying to run the tkregister2.bin script and receive the following error: Bad CPU type in executable. I see that this question was asked some time back and it sounded like it might be a Mac OS version issue? I am running macOS Catalina 10.15.1 and Freesurfer version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) Thank you, Abhi -- Abhishek Jaywant, Ph.D. Assistant Professor of Neuropsychology, Weill Cornell Medicine Assistant Attending Psychologist, NewYork-Presbyterian Hospital

3 2

Vertex-wise ROI extractions on the surface
by DeCross, Stephanie N. 09 Dec '19

09 Dec '19

Hi, How can I extract functional data (percent contrast) from an aparc ROI on the surface on a vertex-wise basis (i.e. not one value averaged across the whole ROI, but one value per vertex inside the ROI for a given contrast)? Funcroi-config/funcroi-sess/funcroi-table-sess seem to only provide values averaged across the whole ROI. In other analysis pipelines, for a voxel-wise extraction it looks like I would use $ fslmeants -i <input 4D nii> -o <output.txt> -m <3D mask nii> --showall but I’m not sure how to do this on the surface. Thank you, Stephanie DeCross

2 1

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