Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30065 discussions

SynthSeg QC - Reliable cut-off?
by AmirHussein Abdolalizadeh 15 Sep '23

15 Sep '23

External Email - Use Caution Hi, We're trying SynthSeg on data that has been improved using SynthSR. We are interested in the intracranial volume per se. I am curious how we can approach the QC metrics. Our first guess was to get an average for the QC metric of grey matter, white matter, and CSF (since they make ICV) and put an arbitrary cut-off to include reliable results. However, any comments are welcome. Best, Amir

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Re: [Freesurfer] registration error (reCAPTCHA not checked)
by fsbuild 14 Sep '23

14 Sep '23

External Email - Use Caution  The captcha authentication will not work if javascript is blocked from running in your browser.  Check that you browser preferences are not set to block/filter javascript in its preferences and/or by using some added browser extension.  I’m not aware that a firewall enabled on your machine or your ISP would otherwise block javascript from running. If your current browser does not work, you could do a clean install of some browser you do not currently have installed on your machine (w/o changing its default preference settings).   Choices for chrome based browsers you might not already have installed could be Vivaldi or Opera.  You could search for "download Vivaldi" or "download Opera" and go directly to that vendors web site and download the installer. - R. On Sep 6, 2023, at 09:21, lizhao_du(a)sjtu.edu.cn wrote:        External Email - Use Caution        Hi there,     I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A license is required yet I could not get the license.txt from my e-mail. After filling the form from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/registration.html, a registration error occured (see below).  Is there something wrong for my internet? Or what could I do to get the license?     A few words from you may help me a lot. Thanks in advance.<Catch7EDF(09-06-21-20-21).jpg>Best!Lizhao Du<InsertPic_799C(09-06-21-20-21).png> School of Biomedical Engineering, Shanghai Jiao Tong UniversityLizhao_Du@sjtu.edu.cn _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Password for FS Ubuntu virtual machine
by fsbuild 13 Sep '23

13 Sep '23

External Email - Use Caution The private email notice you received with the VM information explicitly stated NOT TO POST ANY PASSWORDS.   We will look to suspend the VM image and change the login credentials. - R. On Sep 11, 2023, at 17:23, Ynze Hokken <ylhokken(a)gmail.com> wrote:        External Email - Use Caution        Dear Sapere-Aude,The password is: Map.Brain321!Regards,Ynze HokkenOp ma 11 sep. 2023 om 23:21 schreef <sapere-aude@tuta.io>        External Email - Use Caution        Hi,I would like the password for the user "developer" in the FreeSurfer 7.2.0 Ubuntu virtual machine.Thanks!Regards,Sapere-aude_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recon-all completed without error in 10 seconds
by Lauren Stephens 13 Sep '23

13 Sep '23

External Email - Use Caution Hi Freesurfers, I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty. Here is the code we ran: recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz Here is the output message: Started at Wed Sep 13 10:52:44 PDT 2023 Ended at Wed Sep 13 10:52:54 PDT 2023 #@#%# recon-all-run-time-hours 0.003 recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023 done We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2. I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues. Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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recon-all -localGI error
by Alexopoulos, Dimitrios 13 Sep '23

13 Sep '23

External Email - Use Caution Hi all, We have successfully processed a subject through FS7.2 using recon-all -all. We then try to obtain the local GI using recon-all -localGI which produces the following error. What would be causing this issue on this specific subject. Jim [cid:image001.png@01D9E632.5387EAF0] ________________________________ 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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"-atlas" argument and help with multiple errors running recon-all
by Rona Haker 13 Sep '23

13 Sep '23

External Email - Use Caution Dear Free Surfer developers, I have several subjects that are not successful with recon-all. In most cases, the log file looks something like the one attached, with errors in "inflating to sphere" and in "validation": *********************VALIDATION********************* curvature mean = -0.010, std = 0.009 curvature mean = 84.153, std = 7.183 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 11.66, sigma = 23.42 after rotation: sse = 11.66, sigma = 23.42 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 19.34, its var is 27.07 before Erosion-Dilatation 24.37% of inacurate vertices after Erosion-Dilatation 37.82% of inacurate vertices 58.52% of 'positive' inacurate vertices 41.48% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mri_strip_skull: done peeling brain Brain Size = 2625362 voxels, voxel volume = 1.000 mm3 = 2625362 mmm3 = 2625.362 cm3 the /mri output directory is missing aparc+aseg and looks like this: [image: image.png] I tried running the recon-all command with the option '-atlas' as suggested in the log with this command: export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=<path_to_subject> cd $SUBJECTS_DIR recon-all -s 00_FSseg -i 8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all -atlas but: 1. I could not find any documentation on this option, what it means and what arguments to give it. 2. I get the following error: 'ERROR: Flag -atlas unrecognized. -s 00_FSseg -i 8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all -atlas Linux nbelab 4.15.0-206-generic #217-Ubuntu SMP Fri Feb 3 19:10:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 00_FSseg exited with ERRORS at Mon Sep 4 17:02:23 IDT 2023 I would greatly appreciate some help!

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Problem with T1 pial adherence to skull and T1+T2 poor estimation of cortex.
by Jonas Østerhaug Andersen 13 Sep '23

13 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all -i $workdir/$t1folder/${subj}.nii.gz -subjid ${subj} -all -gcut -clean-bm -3T -mprage -T2 $workdir/$t2folder/${subj}.nii.gz -T2pial -all I have added some pictures to highlight my issue. The issue that I am experiencing it that the T1 (red) adheres to what remains of the skull, while the T1+T2 (blue) underestimates the surface of the cortex. Are thee any solutions to this? And if not, would you recommend to use the T1 alone pr the T1+T2 when proceeding further? In advance I'd like to inform that I have tried to run the multistrip with watershed threshholds ranging from 0.1 to 30, but the gcut just worked better for us rather than trying different watershed threshold levels. best, Jonas Østerhaug Andersen

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invalid license
by 黄俊彬 13 Sep '23

13 Sep '23

External Email - Use Caution i ran qdec and clicked on analyze, error occurred. it said the license is invalid. the version is 5.3.0. how to solve this?

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Re: [Freesurfer] ScLimbic issue
by fsbuild 12 Sep '23

12 Sep '23

External Email - Use Caution  If you are getting an “illegal instruction” error running Freesurfer on Linux,  then the hardware (CPU’s) do not have those instructions available in their instruction set to execute.   As far as I know that error only happens with Freesurfer binaries compiled with AVX instructions.  So either you are running on new ARM based processors or you are running on older Intel processors (approx. pre-2011) that do not implement AVX.  There is a list of Intel processors supporting AVX instructions at https://secure-web.cisco.com/1uW45KoTvgWNrFJTk9Lu8MiuKA56yspFlAr2_S…; For Linux machines, the resolution is to run use Intel processors that can execute those instructions. - R. On Sep 12, 2023, at 16:27, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        what problem? There is nothing else in your email and I don't have the previous threads.On 9/12/2023 10:51 AM, Glass, John wrote:        External Email - Use Caution        Hello, I am running into the exact same problem at my local site running version 7.4.1 on a centos 7 machine with a build stamp of: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. Has this issue been resolved? Thank you, John O. Glass, M.S.Signal Processing SupervisorDepartment of Diagnostic ImagingSt. Jude Children's Research Hospital262 Danny Thomas Place, Mail Stop 220Memphis, TN 38105-3678john.glass(a)stjude.org(901) 595-3276MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1zIIZtAoXKf8myf-KWBMwne7yPoUAd7Qy1jEcPW… Disclaimer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Q1uNU-pDdKZt3c2gJvRAX-e_HCj8f2TfRXbDL5… Disclaimer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YLtpOgLUGV6rBo4lpwcQb-p3mwycbu6cy2hqQt… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1banHDx6NgdG-lM1NRwrxZmZ6Z41zC38nEpucEeSW4wG4k… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] ScLimbic issue
by Glass, John 12 Sep '23

12 Sep '23

External Email - Use Caution Hello, I am running into the exact same problem at my local site running version 7.4.1 on a centos 7 machine with a build stamp of: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. Has this issue been resolved? Thank you, John O. Glass, M.S. Signal Processing Supervisor Department of Diagnostic Imaging St. Jude Children's Research Hospital 262 Danny Thomas Place, Mail Stop 220 Memphis, TN 38105-3678 john.glass(a)stjude.org<mailto:john.glass@stjude.org> (901) 595-3276 http://secure-web.cisco.com/1cDTV5tT9Oa6ZugGCMbS5sM9mmuOcH5ETeAFbpyv_6rsfu-…<http://secure-web.cisco.com/1BpeOmGNdiCKRYBgOZ6T6GstDeTtB_1HTpS5klyKFrwc5_Q…> ________________________________ Email Disclaimer: http://secure-web.cisco.com/1uykVz0BTSeYpAi1ACN5eHA5oADlYO8HITenLBX1I7NWhN-… Consultation Disclaimer: http://secure-web.cisco.com/18gCvDjdTqEs3ScUYn27xadymDMR0ucfW9MF2xyg_dkrN2c…

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