Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Question on EasyReg package syntax
by Codrin Mironiuc 16 Mar '23

16 Mar '23

External Email - Use Caution Hi, I have tried to use EasyReg. I have tried to use the following syntax to generate the output of EasyReg and it didn't seem to work: mri_easyreg --ref structural1.nii.gz --flo structural2.nii.gz --ref_seg segmentation_reference --flo_seg segmentation_float --ref_reg deformed_ref_image --flo_reg deformed_flo_image --fwd_field forward_field --bak_field backwards_field Do you know what may be the issue?Thanks so much!

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(no subject)
by Ömer Faruk Cihan 16 Mar '23

16 Mar '23

External Email - Use Caution Hello, Is it feasible to get the password to access the FreeSurfer VirtualBox VM's FS 7 2 0 Ubuntu 18 04 06.ova.7z image? I sincerely appreciate it.

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Re: [Freesurfer] WM edits, prevent surface from cutting sulcus
by Chris Adamson 15 Mar '23

15 Mar '23

External Email - Use Caution Hi Bruce, It was a topological defect. I found it after looking harder. My bad. Hi Chris It sounds like a topological defect, but hard to say without seeing it. Can you post some images? Or follow Doug's instructions about visualizing the defects and see if there is one in the sulcus you mention below? Cheers Bruce Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia http://secure-web.cisco.com/1fOd32XG6hsKdPSy4dFk5NcN7OVhbNu4K_XoSxYMMrFXhgY…<http://secure-web.cisco.com/1dFcCNj7lLcwZic2NNYxeDhYghneJ0e0yh3OEitswMBLHrG…> E chris.adamson(a)mcri.edu.au T 03 9936 6780 Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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EasyReg usage
by fidel vila 15 Mar '23

15 Mar '23

External Email - Use Caution Hi, I checked the archive for any pointers about specific use instructions for EasyReg and read the wiki page. I would like to register three T1w acquisitions on three planes (Axial, Cor, Sagittal). This was my first attempt: *mri_easyreg --ref [myimageAXIAL.nii] --flo [myimageCOR] --ref_seg [filename_tobecreate_seg_not_runpreviously] --flo_seg /[filename_tobecreate_seg_not_runpreviously] --ref_reg /[filename_tobecreate]* The command run and did generate the segmentation files but froze here: Deforming and writing to disk Computing backward field Deforming reference image Saving deformed reference image I could not find a log file. Any suggestions? My plan was to use EasyReg on this registered image and register it to the Saggital acquisition, but maybe there is a way to do that registration at once? thanks for any pointers and for putting together such amazing tools, Fidel

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WM edits, prevent surface from cutting sulcus
by Chris Adamson 15 Mar '23

15 Mar '23

External Email - Use Caution Freesurfer experts, I have a subject where the WM surface is cutting across a sulcus despite the WM segmentation correctly labelling the GM. Is there a way of putting a "barrier" value in the wm.mgz to prevent the white matter surface from cutting across the sulcus? Thank you. Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia http://secure-web.cisco.com/1d6ZfS-gj9LtrRXTrQsFAWc7vS2Not3rs0nohUS6oyiIY0L…<http://secure-web.cisco.com/1giMGY4fn9dwYvilfpFRhVhRx3qCzn553ez9a38OZIgqEmC…> E chris.adamson(a)mcri.edu.au T 03 9936 6780 Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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VM Password
by Christian Owen 15 Mar '23

15 Mar '23

External Email - Use Caution Hi, Would you mind sending the password to unzip FS_7_2_0_ubuntu_18_04_06.ova. 7z? Christian

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Freeview error
by tsengyuheng1999＠gmail.com 15 Mar '23

15 Mar '23

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Unable to Run Recon-all on T1 Image
by Annie Cooper 15 Mar '23

15 Mar '23

External Email - Use Caution Hi there, I am trying to run recon-all using the Agave Supercomputer at ASU. When I try to run recon-all, these error messages pop up prohibiting me from running recon-all on my T1 image. Here is the error message I received: [asurite@agave2:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all mkdir: cannot create directory '/packages/freesurfer-5.0.0/subjects/ATN001v1': Permission denied mkdir: cannot create directory '/packages/freesurfer-5.0.0/subjects/ATN001v1': Permission denied cp: cannot create regular file '/packages/freesurfer-5.0.0/subjects/ATN001v1/scripts/build-stamp.txt': No such file or directory cat: /packages/freesurfer-5.0.0/subjects/ATN001v1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /packages/freesurfer-5.0.0/subjects Actual FREESURFER_HOME /packages/freesurfer-5.0.0 /packages/freesurfer-5.0.0/subjects/ATN001v1: No such file or directory. I’m curious if the issue is that in order to run recon all and put subject “ATN001v1” into the subjects folder, I have to have the necessary permissions to edit a folder that isn’t under my username in the supercomputer. Please let me know if there are any solutions to this problem. Thanks! Best, Annie

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HELP (I don't have the password to unzip on Winrar/7zip)
by Juan Felipe Gaitan Nocua 14 Mar '23

14 Mar '23

External Email - Use Caution Hello In this email I request help to acquire the password that the freesurfer requests when wanting to unzip the file. I have followed the steps for the installation and this problem does not let me continue. I add that the reason why I will use the program is for research that we are doing at the National University of Colombia for the biomedicine and artificial intelligence research seedbed. Thanks you. *--* *Juan Felipe Gaitan Nocua* *Ingenieria Electronica* *Estudiante de la Universidad Nacional de Colombia* -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/15qd3FEE_9QR8rTmC4t6iMVtYrajvwHFVh-lK8fSxWhU-Eh… <http://secure-web.cisco.com/14bpKla3JrDHA9RQKrCaHTWEImO7wk8P6tcsn2DyTPxVbPq…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Hypothalamus segmentation using hypothalamic subunits vs ScLimbic
by Asmin Alam 13 Mar '23

13 Mar '23

External Email - Use Caution Dear FreeSurfer Experts, I have a question regarding how the hypothalamus volumes are calculated using the hypothalamic subunits function, as opposed to the ScLimbic deep learning tool which is only currently available in the dev version of Freesurfer. My project consists of measuring the volume of the hypothalamus, so I thought of running both algorithms and comparing results to ensure they were consistent. However, they are quite different and I was wondering if there are certain flags/options I should be adding to ensure that the results will relate to each other and why that is the case. What is the key difference in how the hypothalamus is calculated by both these methods? How do I ensure my results are robust/trustworthy? What does noMB mean in the ScLimbic results? I have tried running the ScLimbic function using the original T1 and the --conform flag to make sure that the voxels were isotropic, and then retried by using the nu.mgz as input (as that's what the hypothalamus subunits function uses). Here are the results (also attached): HYPOTHALAMIC SUBUNITS subject left anterior-inferior left anterior-superior left posterior left tubular inferior left tubular superior right anterior-inferior right anterior-superior right posterior right tubular inferior right tubular superior whole left whole right test 19.88 25.155 136.715 145.785 131.879 20.078 29.209 134.882 161.009 133.293 459.414 478.471 SC LIMBIC (T1-W and --conform) # Subcortical Limbic Volumetric Stats # Created by mri_sclimbic_seg # NRows 12 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 26 469 471.6122 Left-Nucleus-Accumbens 2 58 460 459.8144 Right-Nucleus-Accumbens 3 819 588 571.3680 Left-HypoThal-noMB 4 820 631 586.4990 Right-HypoThal-noMB 5 821 667 707.3562 Left-Fornix 6 822 631 700.7991 Right-Fornix 7 843 58 60.5358 Left-MammillaryBody 8 844 57 64.1979 Right-MammillaryBody 9 865 414 396.2163 Left-Basal-Forebrain 10 866 448 450.1535 Right-Basal-Forebrain 11 869 165 170.6947 Left-SeptalNuc 12 870 151 157.4303 Right-SeptalNuc SC LIMBIC (nu.mgz input) # Subcortical Limbic Volumetric Stats # Created by mri_sclimbic_seg # NRows 12 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 26 513 519.7247 Left-Nucleus-Accumbens 2 58 526 537.3985 Right-Nucleus-Accumbens 3 819 575 570.7261 Left-HypoThal-noMB 4 820 613 604.3893 Right-HypoThal-noMB 5 821 657 675.3337 Left-Fornix 6 822 663 691.8721 Right-Fornix 7 843 51 53.4853 Left-MammillaryBody 8 844 58 61.4891 Right-MammillaryBody 9 865 473 483.7591 Left-Basal-Forebrain 10 866 487 496.4204 Right-Basal-Forebrain 11 869 145 153.3073 Left-SeptalNuc 12 870 138 142.8245 Right-SeptalNuc I'm also not sure exactly what the flag "--crop" means for the hypothalamic subunits function. I left it to the default value of 184 but how will changing this affect my final result? Below are also my codes for all three functions: mri_segment_hypothalamic_subunits --s ${subjid} --sd ${sd} --crop 184 mri_sclimbic_seg --i ${sd}/${subjid}/mri//T1.mgz --o ${sd}/${subjid}/mri/sclimbic.mgz --write_volumes --conform mri_sclimbic_seg --i ${sd}/${subjid}/mri//nu.mgz --o ${sd}/${subjid}/mri/sclimbic.mgz --write_volumes Any help is appreciated. Thank you, Asmin UCL Queen Square Institute of Neurology

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Freesurfer March 2023