Freesurfer

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21 participants
30070 discussions

Skullstripping
by priya padma 16 Oct '22

16 Oct '22

External Email - Use Caution Hello Team, I am trying to do only Skull stripping for my image and get the output. is there any command of freesurfer, when it executes only the first step- skull stripping. My objective is to get whole brain segmentation where only the brain tissues should remain and all the skull has to be removed. I searched through the internet but haven't got anything. Does anyone know any solution? Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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somatosensory cortex (S1)
by Eszter Boros 16 Oct '22

16 Oct '22

External Email - Use Caution Dear FreeSurfer Team, I would like to do a ROI analysis focusing on the primary somatosensory cortex (S1) using Freesurfer and see the potential alterations after a (behavioral) treatment . I am wondering how I can do that? First, I picked and looked at the postcentral gyrus and sulcus, but I am specifically interested in the face area. Is there a way to make my analysis more accurate? I am using Freesufer 7.1.1 Thank you for your answer! I greatly appreciate it. All the best, Eszter Boros

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Pass code to unzip VM
by Allesha Eman 16 Oct '22

16 Oct '22

External Email - Use Caution Dear Researchers, I am emailing to request the pass code to unzip the FS_7_2_0_ubuntu_18_04_07.ova.7z file to use FreeSurfer on Windows. Thank you. Allesha Get Outlook for iOS<https://secure-web.cisco.com/1LtOdy3dE2mITbmcYnYqCazSDK21IfZF4a2GTuYxS23Zak…>

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Creating a seed sphere using MNI coordinate
by Addison, Reuben 16 Oct '22

16 Oct '22

1. I am planning to add a seed sphere 6mm cortical and 4 millimeters subcortical and I want to do this with Fsfast using given MNI coordinates from a previous study. I am wondering if there is a command on fsfast to achieve that, I have gone through the connectivity analysis but couldn't quite figure a way to do that. 1. Also I want to add a covariate (behavioural score) to my second level connectivity map. I want to use fsfast for consistency sake. If I can be pointed to the command it will be very helpful. Thanks, Reuben N. Addison Postdoctoral Fellow Brain Recovery Lab MGH Institute of Health Professions<https://www.mghihp.edu/> Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129 Get Outlook for iOS<https://aka.ms/o0ukef>

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fft
by Proulx, Jean Sebastien 16 Oct '22

16 Oct '22

Hello, Is there an easy way to perform fast fourier transform (fft) or other fancier spectral analysis with freesurfer tools (e.g. with mris_calc)? Thanks and Have a good day! Sebastien

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Specify random seed with recon-all
by Elizabeth Kenneally 16 Oct '22

16 Oct '22

External Email - Use Caution Hi FreeSurfer Developers, I’m trying to run FreeSurfer with a specified random seed with recon-all. I found the -rng-seed flag, but it seem to have been deprecated. I also found the -randomness flag, but I was hoping to specify the random seed myself for testing purposes. Is there a way to do this in the newer versions? I searched the mail archives and didn’t find anything recent. Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: OSX Monterey Thanks for your help! Elizabeth Kenneally Assistant Research Engineer Computational Neuroimaging Laboratory Child Mind Institute 917.472.1812 childmind.org<http://secure-web.cisco.com/1NFHUQ9u0R9_V3v6SHV7fVhQQ59J34BHwuVu635hIarQk28…> | Location<https://secure-web.cisco.com/1gABeb_5rSD3SPHRFC1-gDfs_uSvEujbgodCtMz86CHALX…> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error, please notify the sender by return email and delete the original message.

2 1

Creating a lobar atlas
by James Brown 16 Oct '22

16 Oct '22

External Email - Use Caution Dear colleagues Freesurfer experts, I would like to create an atlas (my atlas) for the white matter like "wmparc.mgz" so I can generate statistics. I would like this atlas to be limited to the following structures (frontal lobe, parietal lobe, occipital lobe and temporal lobe). I reviewed Freesurfer tutorials and Q&A in Freesurfer forum then ran the following commands: mri_annotation2label --subject subject --hemi lh --lobesStrict lobes mri_annotation2label --subject subject --hemi rh --lobesStrict lobes mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz --annot lobes --base-offset 200 Then, mris_ca-train -t ./color.tab lh ../surf/lh.sphere.reg ../label/lh.lobes.annot SUBJECT_TEST lh.my_atlas.gcs mris_ca-train -t ./color.tab rh ../surf/rh.sphere.reg ../label/rh.lobes.annot SUBJECT_TEST rh.my_atlas.gcs I would like to use mri_segstats with “my atlas” to generate statistics in lobes not in parcellates. How can I convert lh.my_atlas.gcs and rh.my_atlas.gcs to myatlas.mgz ? Thanks for your help James

2 1

mri_glmfit error
by fernanda rohrsetzer 16 Oct '22

16 Oct '22

External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C Contrasts/LR-HR_testcov.mtx --C Contrasts/LR-MDD_testcov.mtx --C Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir lh.groupteste.thickness.glmdir --eres-save But it gives me an error (attached below) indicating a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. The design matrix (examining difference in thickness after controlling for effects of age, sex and Average thickness) 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx Could someone please help me resolve it? Thanks for your time.

2 1

Quality control of longitudinal recon-all output for >500 participants
by Blujus, Jenna 16 Oct '22

16 Oct '22

External Email - Use Caution Hi all, I am processing a large longitudinal dataset of T1-weighted anatomical images through the recon-all pipeline (N=680). I know that the gold standard for quality control following recon-all is visual inspection of the output surfaces and parcellations. However, given the large sample size, I was writing to see if the community has any recommendations for automatic QC pipelines. I read a few papers discussing the use of Euler numbers to detect outlier datasets for exclusion (see citations below). Does anyone have any other recommendations? Thank you in advance! Best, Jenna References: 1. Rosen, A. F., Roalf, D. R., Ruparel, K., Blake, J., Seelaus, K., Villa, L. P., ... & Satterthwaite, T. D. (2018). Quantitative assessment of structural image quality. *Neuroimage*, *169*, 407-418. 2. de Lange, A. M. G., Kaufmann, T., Quintana, D. S., Winterton, A., Andreassen, O. A., Westlye, L. T., & Ebmeier, K. P. (2021). Prominent health problems, socioeconomic deprivation, and higher brain age in lonely and isolated individuals: A population-based study. *Behavioural Brain Research*, *414*, 113510.

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