Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

watershed, saving issue
by Kirill Elin 14 Feb '20

14 Feb '20

External Email - Use Caution Hallo everybody, I am not entirely sure whether this is FreeSurfer error actually. I am doing first recon all which completes without errors. Then I need to create BEM surfaces using the FreeSurfer watershed algorithm for MEG data analysis using MNE-Python. So the next command in the terminal is: mne watershed_bem --subject subjectname And it runs e.g. till: mri_watershed ru_nivcsw 12490 mri_watershed done and quits with errors like: File "/work/modules/Ubuntu/14.04/amd64/common/anaconda3/latest/envs/neuroimaging/lib/python3.6/site-packages/mne/utils/check.py", line 143, in _check_fname raise IOError('Destination file exists. Please use option ' OSError: Destination file exists. Please use option "overwrite=True" to force overwriting. Now, it is unclear what file destination file is meant. This happens on several machines for all participants. --overwrite option does not help. The correct outcome should include bem folder with resulting files and also watershed subfolder with resulting files. Here and the files in bem folder are missing and there are files only in watershed subfolder. FreeSurfer 6.0.0., Ubuntu Thank you in advance. Sincerely yours, Kirill

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Systematically Navigating .sphere vertices
by Mcnorgan, Christopher 14 Feb '20

14 Feb '20

External Email - Use Caution I’m interested in working with data mapped to the .sphere icosohedrons. I understand from a response from Doug back in 2017 that: waveforms = fast_vol2mat(MRIread('waveform.nii.gz')); will give me a v x time matrix of values from my functional values. In the case of fsaverage, I believe I can expect somewhere around 160K rows, 1 per vertex, for each hemisphere. I was wondering how I might be able to determine the neighbors (i.e., vertices connected by an edge) for any vertex v? Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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study design flair T1
by Renew Andrade 14 Feb '20

14 Feb '20

External Email - Use Caution Dear FreeSurfer experts: I am dealing with a crossectional retrospective case control study where I don't have all subjects with the same inaging protocols. I do have T1 for all of them although some have T2 others FLAIR others T2+FLAIR (besides T1 for all of them). My question is regarding VBM can I do inference on images with different characteristics? Or should them all have T1 + T2 or T1 + FLAIR. I guess this is the case that is all subjects should be processed with the same protocols. This is in Multiple Sclerosis by the way just in case it matters. Sincerely, Andrade. Sent from my iPhone

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FSAVERAGE and LabelROI
by Faizan Anwar 14 Feb '20

14 Feb '20

External Email - Use Caution Hello, My name is Faizan Anwar. I am currently a undergraduate student at UCLA. I had two questions regarding freesurfer: - Is FSAVERAGE file a universal template that could be used with any set of subject data, or is it a specific file created during recon all. If yes, how can I recreate fsaverage file with a freesurfer processed dataset (i.e. recon all was already done on this dataset and I have moved the FS data to a different computer without the FSAVERAGE file - Also, I wanted to ask if there is a way to extract LabelROI of multiple subject at the same time alike aseg2stats command? and If there is a way to do a group analysis and visualize the difference within that specific region? Any assistance in these two questions would be extremely helpful. Looking forward to your reply Thank you, Sincerely, Faizan Anwar

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converting mgh to gii
by Lara Foland-Ross 14 Feb '20

14 Feb '20

External Email - Use Caution Hello Freesurfer experts, I'd like to convert my subjects' thickness mgh files to gii format for use in an analysis with a separate software package. Could you please confirm whether the following command is appropriate? Will this provide thickness maps that are in alignment? mris_convert -c lh.thickness.fwhm15.fsaverage.mgh fsaverage/surf/lh.white lh.thickness.fwhm15.fsaverage.gii Many thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Volume to 5th order icosahedron tesselation Surface (with PET images)
by Marina Fernández 14 Feb '20

14 Feb '20

External Email - Use Caution Hi experts, This is a question related to PetSurfer steps. I would like to know if it is correct to sample the mgx volume onto the surface of the average subject of my dataset (created with 5th order icosahedron tesselation) instead of the fsaverage (created with 7th order icosahedron tesselation) or if there is any problem in the next steps following this procedure. We would like to do that because the volume PET resolution is more proportional to this number of vertex (10242). Do you think it is correct? Best wishes, Marina.

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Re: [Freesurfer] Problem with registration (PetSurfer)
by Marina Fernández 14 Feb '20

14 Feb '20

External Email - Use Caution The error was shown after running tkregisterfv. Marina.

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Question re: hippocampal/amygdala subfields
by Tegan Hargreaves 14 Feb '20

14 Feb '20

External Email - Use Caution Hi all, I am fairly new to FreeSurfer and am implanting the hippocampal/amygdala subfields script in our participants. As there are two versions of the hippocampal script (i.e., version 10 that is only hippocampus and version 21 which is both), I wanted to confirm that I should be using FS v6.0 (stable) for recon-all, and then running only the hippocampal/amygdala (v21) script through the dev version of FS. I don't believe that I should be running the exclusively hippocampal script anymore, as the guide states it is now obsolete, but I just wanted to confirm. Thank you so much! Best, Tegan Tegan Hargreaves, MSc Research Assistant Peter Boris Centre for Addictions Research | St. Joseph's Healthcare Hamilton 100 West 5th Street, Hamilton, ON L8P 3P2 P: 905-522-1155 ext. 36368 | E: thargrea(a)stjoes.ca<mailto:thargrea@stjoes.ca> ________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and/or privileged information. Any unauthorized review, use, copying, saving, disclosure, re-transmission or distribution is strictly prohibited. If you are not the intended recipient or this information has been inappropriately forwarded to you, please contact the sender by reply e-mail or the Privacy Office via privacy(a)stjoes.ca. Thank you. ________________________________

2 1

Thickness group normalization
by Vyacheslav Yarkin 14 Feb '20

14 Feb '20

External Email - Use Caution Hello Freesurfer Team, Would you be so kind to provide freesurfer steps to implement warping fsaverage mean thickness data on individual subject inflated brains ? I am using expert opts to disable cortical thickness restriction, and set mris_thickness -max 20 as I want to find fcd to cortical surfaces. The reason i need normalization is that there is zones like sulci orbitales have bigger thickness accross subjects group ( control ) and have red LUTs on inflated thickness map. So i would like to normalize thickness over control group, to use it on patients to exclude "normal" thickness excedings to include only increased FCD zones. The main issue I faced is how to warp fsaverage mean thickness data on individual subject's inflated brain as they have vertices number missmatch. Steps I tried: 1) make_average_subject 2) mri_concat --mean to create mean thicknesses over group? Thank you

2 4

recon-all -make all
by Benjamin Ineichen 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer experts, I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s <subject>" on all 100 subjects and it will only recon-all the manually edited ones or do I need to run it individually for the 20 subjects? 2.) Do I need to add the flags which I used for the original recon-all command to the "recon-all -make all- s <subject>, e.g. -qcache -T3 -hippocampal subfields etc? Many thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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