Freesurfer March 2025

freesurfer@nmr.mgh.harvard.edu

49 participants
63 discussions

freesurfer course
by Sikah, Kevin (BIDMC - Neurology) 25 Mar '25

25 Mar '25

External Email - Use Caution Hello, Sorry to message the wider list; I emailed the fscourse address previously but did not hear back. Is there a course planned for this spring, and if so, is the timing known? Thank you! Best, Kevin ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1QDxtk6PFb9zuBLlWWwdrTv1EM9Dw99G1f9rL-P9WVOCHa0… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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xhemi fsaverage_sym rh backward mapping
by Dr. Cornelius Kronlage 24 Mar '25

24 Mar '25

External Email - Use Caution Dear freesurfer team, in the wiki (https://secure-web.cisco.com/1WbYcGgb3srAnGYyZARo_Jad7UgANe_5pADqErCcDyQA2U…) the following is used to map surface data from an individual subject's right hemisphere to fsaverage_sym's left hemisphere: mris_apply_reg --src rh.map.mgh --trg rh.map.lh.fsaverage_sym.mgh --streg $SUBJECTS_DIR/subject/xhemi/surf/lh.fsaverage_sym.sphere.reg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg How would you recommend to perform the inverse mapping from fsaverage_sym's left hemisphere to an individual subject's right hemisphere? I would suspect the --streg arguments need to be swapped like so: mris_apply_reg --src rh.map.lh.fsaverage_sym.mgh --trg rh.map.mgh --streg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg $SUBJECTS_DIR/subject/xhemi/surf/lh.fsaverage_sym.sphere.reg Is that correct? Or would you need to first map to fsaverage_sym's right hemisphere? Thank you! Cornelius

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Cortex thickness
by Feruza Turdialieva 22 Mar '25

22 Mar '25

External Email - Use Caution Can anyone explain how to use FreeSurfer (Freeview) to measure cortical thickness? I would really appreciate any help! please dm feraata4(a)gmail.com

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Voxel editing
by Yoel HALIMI 22 Mar '25

22 Mar '25

External Email - Use Caution Hello, I have a problem with the tool: Voxel editing. When I open the window, it appears correctly but I can't modify it or enter values. I'm using WSL 2 and I've followed the tutorial. When I move my mouse over it, the cursor is transparent. Here an image to describe my problem : [cid:442d656e-f59b-46db-a88f-5154ebafb784] Thanks to reply, Best regards, Yoel

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thresholding advice for probabilistic subfield amygdala atlas in MNI 152 space
by Stephanie Williams 20 Mar '25

20 Mar '25

External Email - Use Caution Hello, When I threshold the new probabilistic maps amygdala subnuclei in MN152 space at a threshold of 0.8 I see that only 5 amygdala subnuclei survive (AAA, Basal nucleus, Corticoamygdaloid transition, Lateral nucleus, Accessory Basal nucleus). Is this perhaps overly strict threshold? Are there any general consensus guidelines for picking a reasonable threshold to use with these probabilistic maps? When I use a lower threshold of 0.35 there is still one nuclei that does not survive (medial nucleus). Thank you!! Location of maps: https://secure-web.cisco.com/1uhXMhTQwjvX1lxAZWJI1ov3nuo7OX-qQSRwkAXWXvSpar… HippoAmygProbs.MNIsymSpace.right.nii.gz 2025-03-03 11:28:52 13506796 HippoAmygProbs.MNIsymSpace.names.txt 2025-02-28 15:52:58 581 HippoAmygProbs.MNIsymSpace.left.nii.gz 2025-02-28 18:02:02 13506619

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Recon-all-clinical pipeline
by Lieshout, P.B. van (Pauline) 20 Mar '25

20 Mar '25

External Email - Use Caution Dear sir/madam, I am implementing the recon-all-clinical pipeline on clinical MRI scans. I have done a test-run of around 70 T1-w clinical MRI scans. Processing of 9 out of 70 scans have failed. In almost all the failed processing scans, the pipeline stopped at the corpus callosum segmentation step. I was curious as to why this might happen, do you have any ideas? error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping Best, Pauline van Lieshout [A blue and white logo Description automatically generated] Promovendus | Divisie Hersenen, Zorglijn NMZ | Universitair Medisch Centrum Utrecht De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Re: [Freesurfer] Human connectome workbench
by Glasser, Matthew 18 Mar '25

18 Mar '25

External Email - Use Caution 1. A 512*512*90 dataset is likely a long way from an isotropic resolution dataset of 1mm isotropic or better that works best with FreeSurfer. 2. What Connectome Workbench command were you trying to run? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Ni, Zhen (NIH/NINDS) [C]" <zhen.ni(a)nih.gov> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 18, 2025 at 5:40 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Human connectome workbench Hello, I used the command “recon-all -all -subjid $SUBJECTNAME”. There was no error for Freesurfer, but it was slow at certain time points with a lot of corrections (sometimes with large defects, our initial imaging was a 512*512*90 slices T1 axial imaging set). The outputs for this were used in HCP workbench to downsample the size of the cortical sheet. When I run the workbench script, it showed an error: While running >>>>/workbench/sub-001.L.sulc.native.shape.gii CORTEX_LEFT ERROR: NAME OF FILE: sub-002.L.sulc.native.shape.gii PATH TO FILE: >>>>/sub-002/workbench File does not exist I don’t think this is a problem with workbench but should be missing some components (cortical mesh) when the initial cortical sheet was made by Freesurfer. I wonder if you have any ideas. Thanks Zhen ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Human connectome workbench
by Ni, Zhen (NIH/NINDS) [C] 18 Mar '25

18 Mar '25

External Email - Use Caution Hello, I used the command "recon-all -all -subjid $SUBJECTNAME". There was no error for Freesurfer, but it was slow at certain time points with a lot of corrections (sometimes with large defects, our initial imaging was a 512*512*90 slices T1 axial imaging set). The outputs for this were used in HCP workbench to downsample the size of the cortical sheet. When I run the workbench script, it showed an error: While running >>>>/workbench/sub-001.L.sulc.native.shape.gii CORTEX_LEFT ERROR: NAME OF FILE: sub-002.L.sulc.native.shape.gii PATH TO FILE: >>>>/sub-002/workbench File does not exist I don't think this is a problem with workbench but should be missing some components (cortical mesh) when the initial cortical sheet was made by Freesurfer. I wonder if you have any ideas. Thanks Zhen

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Unusual Cortical Thickness Measurements
by hmarzban＠student.ubc.ca 17 Mar '25

17 Mar '25

External Email - Use Caution Hello, I hope you are well. I was wondering if there is an easy way to correct for missegmentation of the grey matter parcellation. For example, would it be possible to correct for the overestimation of the pre-postcentral gyri (see picture below)? Since it seems as if the parcellation is extending into the meninges. Warmly, Hengameh

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Hippocampal Subfield Hierarchies
by Erin L Ratliff 17 Mar '25

17 Mar '25

External Email - Use Caution Hi FS experts, We are running the segmentHA_T2.sh script, and we get the .mgz files for the 3 hierarchies (CA, FS60, and HBT), but when we run either concatenatesubregions or asegstats2table, we get the fine grain hippocampal subfield volumes. Is it possible to extract the volumes (as .txt) from the hierarchy .mgz files? We are interested in using the CA hierarchy, and we are not sure how to calculate this with the output we receive from either concatenatesubregions/asegstats2table. Any help is appreciated! Erin

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Freesurfer March 2025