Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

run recon-all with already skull-stripped data
by June Kang 22 Nov '23

22 Nov '23

External Email - Use Caution Hello,According to the FAQ for earlier version of Freesurfer (maybe 6.x), the instruction is below.First you must run only -autorecon1 like this:recon-all -autorecon1 -noskullstrip -s <subjid>Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all:recon-all -autrecon2 -autorecon3 -s <subjid>The autorecon1 step works good, however, second step ends with error repeatedly in 7.4.1516 voxels in left wm, 1068 in right wm, xrange [124, 129]searching rotation angles z=[-7 7], y=[83 97]searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)final transformation (x=0.0, yr=90.000, zr=-0.000):-0.00000 0.00000 1.00000 128.00000; 0.00000 1.00000 0.00000 128.00000;-1.00000 0.00000 -0.00000 127.99999; 0.00000 0.00000 0.00000 1.00000;error: No such file or directoryerror: mri_cc: no WM voxels found with norm > 40 -- check skull strippingBests,J.

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Unable to add FGATIR during thalamic segmentation
by Pal, Amrita 22 Nov '23

22 Nov '23

External Email - Use Caution Hi I am unable to add an additional scan FGATIR during thalamic segmentation. For example I have a subject in the freesurfer/subjects directory that does thalamic segmentation without adding the additional scan but not with the attached code. I tried different flags but that didn't work. Can you please help? [cid:image001.png@01DA1D2E.1672BBD0] Thanks Regards Amrita

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freesurfer results QC
by yunus soleymani 22 Nov '23

22 Nov '23

External Email - Use Caution Hi Freesurfer users, I have recently used the FSQC algorithm (https://secure-web.cisco.com/1EzTQr-pZpN3NDVSECe0dGNYNhra0JW3OGYIpwSTpVNT4v…) to check the quality of my Freesurfer volumetric results. However, I am having trouble understanding the meaning of the output numbers. What is the acceptable threshold number of SNR? I would appreciate any help you can provide. Thank you, Yunus

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Help
by Xincen Wu 22 Nov '23

22 Nov '23

External Email - Use Caution Hi, I am using freesurfer. I have gone through with the installation and diagnostics and everything works fine. FOr example, using the command recon-all --help in terminal yields a bunch of directions. Yet, when I enter something like: recon-all -s bert -autorecon1 an error pops up saying my python3 is problematic. However, I regularly use python3 and redownloaded it after. Please advise on the issue at hand. Thanks, Lucas

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How many regions does "aparc.DKTatlas+aseg.mgz" have?
by Kei Nishimaki 21 Nov '23

21 Nov '23

External Email - Use Caution Hello FreeSurfer Developers, We ran recon-all on a 3D T1-weighted image, by default. ls *.nii | parallel -–jobs 2 recon-all -s {.} -i {} -all -qcache Our question is very simple. How many regions does "aparc+aseg.mgz" and "aparc.DKTatlas+aseg.mgz" and "aparc.a2009s+aseg.mgz" have in each? We checked the links below. And we want to renumber the region index from 0 as shown in the photo below. https://secure-web.cisco.com/1fBJMEihMTm8S1YZKy0FxnEoJxLOAxKaZC0-l90ulKxJmi… However, the number of regions varies slightly depending on the subjects (103~106 in aparc.DKTatlas+aseg.mgz). Therefore, we want to know the number of regions in three parcellation map. 1) FreeSurfer version: freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz 2) Linux ~~~ 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux [cid:2d03e569-3221-4f8d-b86f-c8d38cf75b2e] Thanks, Kei

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Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1
by Marawi, Tulip 21 Nov '23

21 Nov '23

External Email - Use Caution Dear FreeSurfer developers, Our research group used the FreeSurfer's recon-all tool to reconstruct 74 anatomical images from cognitively healthy older individuals and parcellate the cortex based on the Desikan-Killiany atlas. However, we are running into a consistent issue with the perirhinal volumes on the annot stats from BA_exvivo_thresh.stats, where there is a large discrepancy between the left and right hemispheres (larger left hemisphere). Upon visual and numerical investigation, it appears that this could be due to mis-labelling the right perirhinal vertices as entorhinal, resulting in an unusually small right perirhinal cortex, and unusually large right entorhinal cortex. Could you please clarify why this could be happening, and advise on next steps? We have used FreeSurfer 7.1 for this analysis. Sincerely, Tulip Marawi This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Re: [Freesurfer] Doubts about GLM contrasts
by Laura Willers de Souza 21 Nov '23

21 Nov '23

External Email - Use Caution Great, thanks so much! But I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and cortisol significant regressing out the effect of sex, age, APOE_carrier, abeta and ptau?" It seems like the contrast would be the same as before.. Can you help me with this? Thanks again! Laura Willers de Souza PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil ----- Douglas N. Greve<https://secure-web.cisco.com/1yYgRLzmOCtuh8UFLaxt4ucohab6Ii9cqIDNXc9_tUgQIT…> Wed, 15 Nov 2023 06:54:36 -0800<https://secure-web.cisco.com/1YP7c0yUfORmuLGAmHVodnKa9al2_Y0u_TMgwZ8HHpNLBo…> Yes, that looks right (assuming that cortisol is your first variable) ---- On 11/7/2023 3:49 PM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, Following the FSGD examples on the website, I built the following test: Question: Is there an association between cortisol and cortical thickness regressing out the effect of sex, age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, diagnosis (CU and CI)? Regressors: 2 factors (sex, diagnosis) with 2 levels each, 5 covariates (age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, cortisol) >> 24 regressors Contrast: 0 0 0 0 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 FSGD: GroupDescriptorFile 1 Title CSF_semgrupos Class MaleCU Class MaleCI Class FemaleCU Class FemaleCI Variables Cortisol Age ABETA ptau APOE4_carrier Input 098_S_4003_I224603 MaleCI 11 81.3 741.5 22.83 1 Does this feel right to you? I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and cortisol significant regressing out the effect of sex, age, APOE_carrier, abeta and ptau?" It seems like the contrast would be the same as before.. Can you guys help me with this? Thanks in advance! *Laura Willers de Souza * PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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recon-all error
by Carlos Alcocer 21 Nov '23

21 Nov '23

External Email - Use Caution Reposting due to issue with email bouncing. I am receiving following error on my subjects. Recon-all still continues after error and finishes "without error" I have attached the recon-all log as well. mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz reading from /path/to/anat_t1.nii... NaN found at voxel (0, 0, 244, 0) error: No such file or directory error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii... Thank you, Carlos

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Running autorecon2-wm after wm edits makes no difference in final surface
by Fernanda Hansen P. de Moraes 21 Nov '23

21 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran *recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3* nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Here attached is the complete recon-all log file from the beginning, including all steps attempted. I would be very glad if you could help me overcoming this error to include as much subjects as possible in my project. Best regards, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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recon-all error
by Carlos Alcocer 20 Nov '23

20 Nov '23

External Email - Use Caution Hi, For some of my subjects I get the following error at the beginning of recon-all: mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz reading from /path/to/anat_t1.nii... NaN found at voxel (0, 0, 244, 0) error: No such file or directory error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii... However, recon-all will keep running and then later finish without error. What exactly is going on? This is only happens on some subjects. Thank you, Carlos

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Freesurfer November 2023