Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Transparency issue in FreeView
by Wighton, Paul 16 Mar '23

16 Mar '23

Hi All, I have a colleague who is trying to use FreeView on Red Hat Enterprise Linux 8, and there seems to be a transparency issue where windows behind the viewer are being displayed. See attached screenshot. This only happens when using FreeView on the desktop. When using freeview over `ssh -X` everything looks good. Any ideas, or debugging info we could pass along? Thanks, -Paul

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request
by Isra RM 16 Mar '23

16 Mar '23

External Email - Use Caution Dear FS team I would like to request the passcode to the VM FS_7_2_0_ubuntu_18_04_06.ova.7z I have just downloaded Thanks in advance Isra RM

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Question on EasyReg forward field
by Codrin Mironiuc 16 Mar '23

16 Mar '23

External Email - Use Caution Hi, I am trying to shift the statistical maps that I obtained from a second-level fMRI analysis (meaning across multiple sessions for one subject). My plan is to use EasyReg to align the functional data to the structural data. Based on the resulting field then I intend to use it to shift the statistical maps using mri_easywarp. I know that for EasyReg, it doesn't matter the order in that I provide the arguments, e.g. Order 1: mri_easyreg --ref <structural_image> --flo <functional_image> Would produce the same result as Order 2: mri_easyreg --ref <functional_image> --flo <structural_image> Nevertheless, I believe that depending on whether I choose 'Order 1' or 'Order 2', I would need a different field to allign the statistical maps, would this be correct? I think that if I choose Order 1, then the backward field is needed, whereas if I choose Order 2, I would need the forward, field, right? Or would it be the forward field for both Orders that is needed in order to allign the statistical maps from the second level (across runs for a single subject)? Many thanks!Codrin

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Question on easy reg
by Codrin Mironiuc 16 Mar '23

16 Mar '23

External Email - Use Caution Hi, I have tried to use the EasyReg package to obtain the forward field by registering a functional slab to the structural (with skull) of a subject.This doesn't seem to work, do you know what may be the issue? Many thanks,Codrin

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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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