Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Database of longitudinal freesurfer subjects
by KennethSPrice 08 Mar '23

08 Mar '23

External Email - Use Caution Hello all, Is there a database of longitudinal data anywhere that have already been processed? There are some databases with longitudinal data but to run recon-all on them would take an entire month! Thanks, Ken

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SynthSeg with CT images.
by Gonzalo Rojas Costa 08 Mar '23

08 Mar '23

External Email - Use Caution Hi: I tried SynthSeg using CT images, but I got very bad results... CT images must have some specific characteristics? I tried with axial acquisition and volumetric one.... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/124lTzPUFk2g93tIiOP_RZIKtO7aB_xIAzR3n-NFnpRUBD… https://secure-web.cisco.com/1j0ISp47eIFtrb1e8T61MHEGaGOjjkY7X7EP3tl6QI9uUy… https://secure-web.cisco.com/1Y56xwcQwRV4t77xO4h4FW-bL40P_UtP-sWKcOdTY6xL_b… http://secure-web.cisco.com/1jDmtFL__LFuOoeWvIVy_NxznOAMBVzwNnvweeEquHeNDvB… https://secure-web.cisco.com/1zOogV6Olu-Gbu6J9GAYf7iYCLr5rTveKf3HrLVn5jSdNR…

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Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation
by Zollei, Lilla,Ph.D. 08 Mar '23

08 Mar '23

Hi Inga, Could you share some screenshots and the age-at-scan of your subjects? Thanks, Lilla ________________________________ From: Harting, Inga <Inga.Harting(a)med.uni-heidelberg.de> Sent: Wednesday, March 8, 2023 10:18 AM To: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: AW: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation External Email - Use Caution Hi Lilla, I got infant_recon_all to run through, but the segmentation did not produce the subcortical results I was hoping for. Looking stepwise at results it seemed as if the registration process “bloated” the central structures = basal ganglia, internal capsules (email and your answer below). I’d be happy if you have any suggestions looking at the label fusion step. Best regards, Inga Von: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu<mailto:LZOLLEI@mgh.harvard.edu>> Gesendet: Montag, 6. März 2023 17:18 An: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Harting, Inga <Inga.Harting(a)med.uni-heidelberg.de<mailto:Inga.Harting@med.uni-heidelberg.de>> Betreff: Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation Hi Inga, Sorry, I missed this message on the mailing list. This is a new issue to me, so I will take a look at the label fusion step. And yes, we are working on including T2w images in the pipeline as at the newborn stage it would help with the GM/WM segmentation accuracy. Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Inga Harting <inga.harting(a)gmx.de<mailto:inga.harting@gmx.de>> Sent: Monday, October 31, 2022 3:11 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Inga_klinik <inga.harting(a)med.uni-heidelberg.de<mailto:inga.harting@med.uni-heidelberg.de>> Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation External Email - Use Caution Hello experts, I've begun using infantFS for neonates and I'am interested in the subcortical segmentation. I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards. Is there a way to preserve the subcortical anatomy? Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast? Best regards, Inga. -- Dr.med. Inga Harting Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de<mailto:inga.harting@med.uni-heidelberg.de> Mühltalstr. 124b 69121 Heidelberg inga.harting(a)gmx.de<mailto:inga.harting@gmx.de> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1s0ysBlCft27Tx_i8N73qUOkTNobR8v2yZnptqd2cp5sgb…> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1LI_y60Z9xdsi_MfBPpNQMIcMItnhcFBE7Wa4lwhsnZXS2…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Fwd: infant Freesurfer - subcortical/white matter segmentation
by Inga Harting 08 Mar '23

08 Mar '23

External Email - Use Caution Gesendet: Mittwoch, 8. März 2023 16:17 An: 'Zollei, Lilla,Ph.D.' <LZOLLEI(a)mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu Betreff: AW: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation Hi Lilla, I got infant_recon_all to run through, but the segmentation did not produce the subcortical results I was hoping for. Looking stepwise at results it seemed as if the registration process “bloated” the central structures = basal ganglia, internal capsules (email and your answer below). I’d be happy if you have any suggestions looking at the label fusion step. Best regards, Inga Von: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu> Gesendet: Montag, 6. März 2023 17:18 An: freesurfer(a)nmr.mgh.harvard.edu Cc: Harting, Inga <Inga.Harting(a)med.uni-heidelberg.de> Betreff: Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation Hi Inga, Sorry, I missed this message on the mailing list. This is a new issue to me, so I will take a look at the label fusion step. And yes, we are working on including T2w images in the pipeline as at the newborn stage it would help with the GM/WM segmentation accuracy. Best, Lilla From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Inga Harting <inga.harting(a)gmx.de> Sent: Monday, October 31, 2022 3:11 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Inga_klinik <inga.harting(a)med.uni-heidelberg.de> Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation External Email - Use Caution Hello experts, I've begun using infantFS for neonates and I'am interested in the subcortical segmentation. I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards. Is there a way to preserve the subcortical anatomy? Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast? Best regards, Inga. -- Dr.med. Inga Harting Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de Mühltalstr. 124b 69121 Heidelberg inga.harting(a)gmx.de _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/15NZRlEJ1Qw9lqmqqp06dT_F-2aqPXLCySzGHdV_Dsc1ul… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1P3TaHH8y3URhhJQ9UaC-mXSbCjguz_m-Zg7wcruNhxGgF… . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Freeview Edit options restricted
by Carlos Alcocer 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, When I try to do recon-edit, it does not let me click on certain options ie. changin the brush size. It additionally doesnt let me exit out of or minimize it. I am running the most recent version of freesurfer (7.3.2) on linux (wsl). I reinstalled/updated freeview but this did not resolve the issue. I have attached screen shot below. You cant see cursor but if i were to hover over brush size for example, the cursor would be a light gray and not let mec change any of the options. [image: image.png] Thank you, Carlos

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password
by Tsai, Perry 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, I would like to get the password for unzipping FS_7_2_0_ubuntu_18_04_06.ova.7z, thank you. *********************EMAIL DISCLAIMER********************* This email and any files transmitted with it may be confidential and are intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient or the individual responsible for delivering the e-mail to the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. If you have received this e-mail in error, please delete it and notify the sender or contact Privacy Office 312.355.5650.

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pass code for FS 7.2.0 archive
by lzagorch＠gmail.com 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, Could you please send me the pass code for extracting the archive of FS 7.2.0 (FS_7_2_0_Ubuntu_18_04_06.ova.7z)? Thanks, Lyubomir

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ERROR: cannot find or read transforms/talairach.m3z
by Fraser Aitken 07 Mar '23

07 Mar '23

External Email - Use Caution Hi all I have upgraded to 7.3.2 and i seem to be having issues running recon all after unto recon1. Basically, auto recon completes but after I have checked the brain masks and go to run auto recon 2 and 3 i get the following error reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transformCommand exited with non-zero status 255 @#@FSTIME 2023:03:07:14:29:54 mri_ca_label N 10 e 15.23 S 0.25 U 14.96 P 99% M 498868 F 9 R 123462 W 0 c 42 w 348 I 1568 O 0 L 1.48 1.71 1.24 @#@FSLOADPOST 2023:03:07:14:30:10 mri_ca_label N 10 1.37 1.67 1.24 Linux bioeng342-pc 5.4.0-144-generic #161-Ubuntu SMP Fri Feb 3 14:49:04 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Freesurfer exited with ERRORS at Tue Mar 7 14:30:10 GMT 2023 This is the command I am using to run the skull strip reconAllCommand = sprintf('recon-all -i %s -subjid ''Freesurfer'' -autorecon1 -multistrip -cw256 -cm',T1File); and these are the other commands % run autorecon2 reconAllCommand = 'recon-all -subjid ''Freesurfer'' -autorecon2 -cm'; unixCommand = sprintf('%s\n%s',subjectDirCommand,reconAllCommand); unix(unixCommand); % run autorecon3 reconAllCommand = 'recon-all -subjid ''Freesurfer'' -autorecon3 -cm'; unixCommand = sprintf('%s\n%s',subjectDirCommand,reconAllCommand); unix(unixCommand); % copy Freesurfer output to rootDir sourceDir = fullfile(Freesurfer,'Freesurfer'); targetDir = fullfile(rootDir,'Subject_data',subjects{iSubj}); unixCommand = sprintf('cp -r %s %s',sourceDir,targetDir); unix(unixCommand); Greatful for any suggestions of a fix

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VirtualBox pass code
by Jennifer Kilmer 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, Is it possible to have the virtual box passcode sent to me? Thank you in advance! Jennifer

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MRI image quality metrics
by MANSON ERIC NAAB 06 Mar '23

06 Mar '23

External Email - Use Caution Dear FreeSurfer experts, Please, I need your assistance and guidance on calculating the contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White matter, Gray matter, and CSF of the brain after recon-all. Thank you

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