Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

XL defect detected_how to resolve
by Koustav Chatterjee 06 Sep '21

06 Sep '21

External Email - Use Caution Dear Forum members, Could you please help me resolve the following issue? The recon-all.log file is also attached herewith. CORRECTING DEFECT 34 (vertices=29039, convex hull=8209, v0=118726) normal vector of length zero at vertex 121849 with 0 faces vertex 121849 has 0 face XL defect detected... Numerical result out of range Linux research1-HP-280-G3-MT 4.4.0-210-generic #242-Ubuntu SMP Fri Apr 16 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Thank you for your time, Regards, KC

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TOPOLOGICAL DEFECTS
by halil ibrahim AKÇAY 06 Sep '21

06 Sep '21

External Email - Use Caution Hi My name is Halil Ibrahim akçay. I am a neurologist. I have been used FreeSurfer for a while. And I cannot understand some part of troubleshooting process. I am sending a screenshot of my question. How can I understand whether gray zone as marked blue circle is a problem or not in this picture? And Should I fill this zone to fix the problem, if this is a problem? Thanx for your helping. I am looking forward to your answer. Best regards

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Issue with reg-feat2anat and tkregister2
by ChristianBauer 06 Sep '21

06 Sep '21

External Email - Use Caution Hello freesurfer help team! I am using the command reg-feat2anat but I get the error message: tkregister2_cmdl_cmdl: Command not found. Here is my full command Fri Sep 3 17:56:20 CEST 2021 /Users/christianbauer/Desktop/Imogen2bids_copy/freesurfer/my_subjects /Applications/freesurfer/7.1.1/bin/reg-feat2anat --feat /Users/christianbauer/Desktop/Imogen2bids_copy/sub-032/func/motion_run_test_1.gfeat/cope1.feat --subject 032 Darwin Christians-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Tue Jun 22 19:49:55 PDT 2021; root:xnu-6153.141.35~1/RELEASE_X86_64 x86_64 example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2_cmdl_cmdl --targ /Users/christianbauer/Desktop/Imogen2bids_copy/freesurfer/my_subjects/032/mri/brainmask.mgz --mov /Users/christianbauer/Desktop/Imogen2bids_copy/sub-032/func/motion_run_test_1.gfeat/cope1.feat/example_func.nii.gz --reg /Users/christianbauer/Desktop/Imogen2bids_copy/sub-032/func/motion_run_test_1.gfeat/cope1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /Users/christianbauer/Desktop/Imogen2bids_copy/sub-032/func/motion_run_test_1.gfeat/cope1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit tkregister2_cmdl_cmdl: Command not found. Many thanks, Christian

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Question about freesurfer
by hyeyoung park 06 Sep '21

06 Sep '21

External Email - Use Caution Hi, This is hyeyoung Park from Seoul National University in South Korea. I have one question about FREESURFER. I ran recon-all using terminal, and finally I got files such as aseg.stats and aparc.stats. For the next steps, I'd like to extract the measurements like thickness or volume from these files using the terminal or "freesurfer" package in R. But I don't know how should I do for the next steps. How can I get the measurements for several subjects in parallel? I hope you can help me. Thank you, Hyeyoung

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How to remove segments from white and left cerebral white matter and get cerebral white matters without these segments
by Ammar Shujaa 06 Sep '21

06 Sep '21

External Email - Use Caution Hello freesurfer developer, I have extracted the right and left cerebral white matter (label 2, and label 4) I just want to know how I can remove label 4, 43, 28, 60 (brown and purple labels) from the the right and left cerebral matter so that I can get the cerebral white matter without the segments corresponding to the labels 4, 43, 28, and 60. I am looking forward to hearing from you. Best regards,Ammar Shujaa Addin

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Total Brain volume normalization
by Fabiola Macruz 06 Sep '21

06 Sep '21

External Email - Use Caution Hello Free Surfer developers, >From my understanding, the volumes provided in the aseg.stats document is not corrected by the head size. In order to do that, it is recommended to use the ITV and the label ID's: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53 However, I need the corrected volume of the Brain Segmentation Volume without Ventricles, the Total gray matter volume, Left hemisphere cerebral white matter volume, and Right hemisphere cerebral white matter volume, none of which have a label ID. Is there any way to obtain these corrected volumes in free surfer itself? Thanks, Dra. Fabíola Macruz MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo PhD from Faculdade de Medicina do Hospital das Clínicas da USP Former Research Fellow from Stanford University Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham Phone: + 1(650)686-0668 / + 55(11)99571-5906

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Mask Correlation Analysis Area by Yeo Network
by Haley Park 06 Sep '21

06 Sep '21

External Email - Use Caution Hello, I would like to run a correlation analysis but limit the analysis area to three of the seven networks of the Yeo 2011 network parcellations. Would this be possible? Would I do it via a --mask option in mri_glmfit? Thank you, Haley

2 1

SAMSEG esitmation error
by achille.teillac＠chu-lyon.fr 06 Sep '21

06 Sep '21

External Email - Use Caution Dear experts, We are working with a large MRI dataset (FLAIR, T1) and we are performing SAMSEG pipeline to estimate lesion volumes. We computed the registration between the two input images and the resampling as advised in the SAMSEG page (mri_coreg and mri_vol2vol) which worked perfectly. However, when we do the visual chek on the segmentation after running SAMSEG, it is completely wrong for some subjects. By looking at corresponding mode01_bias_corrected.mgz and mode02_bias_corrected.mgz images, they are too cropped (centered on the cerebellum) compared to the original ones (3D_T1 .nii.gz and 3D_FLAIR.nii.gz). We also noticed a < RuntimeWarning: invalid value encountered in true_divide > during the burn-in phase (in the GMM.py code). Do you have any clue of what is happening with this cropping (can it be linked to the bias field estimation ?) and how we can correct it ? Thanks for your help and I can provide some screenshots of the cropped images to help visualize the issue. Best, Achille Teillac

2 1

How to cite Freesurfer
by Camargo, Aldo 03 Sep '21

03 Sep '21

External Email - Use Caution Hi Freesurfer group: How should I cite freesurfer in my manuscript ? Thanks a lot and have a nice day, Aldo

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Python Surface API discussion
by Christopher Markiewicz 03 Sep '21

03 Sep '21

External Email - Use Caution Hi FreeSurfers, I wanted to reach out to this group about plans to create a new Python API for working with surface data in Nibabel. As you are all undoubtedly aware, surface meshes are too large and cumbersome to pack with data sampled on the surface, necessitating something like FreeSurfer's directory structure. We're looking to create a common API that would work with FreeSurfer directories, collections of GIFTI files, CIFTI-2 + WBspec, etc., to allow efficient access to the topology, geometry and sampled data as needed. We need input from users and developers of downstream tools who would like to work with these data. Non-Python developers are also welcome to share their experience and advice! I'd like to plan a meeting in the next couple weeks. I'm (slowly) trying to start discussions over at https://secure-web.cisco.com/18kV2cNFE9uq84UPL5TGr7HSq3wVmYRpi0JhnQnLHwSQ5x…. Please reach out over there or email me directly if you're interested in taking part in these discussions. On behalf of the Nibabel developers, -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University

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