Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 discussions

recon-all: error in creating rh.white.H
by Peled, Noam 14 Jan '22

14 Jan '22

Dear group A colleague of mine was trying to run recon-all on one of her patients and received an error message. After looking at the attached log, I'm not sure what is the source of the problem. The T1 looks quite good. She is using freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b Thanks! Noam From: Gumenyuk, Valentina <vgumenyuk(a)unmc.edu> Sent: Friday, January 14, 2022 10:48 AM To: Peled, Noam <NPELED(a)mgh.harvard.edu> Subject: UNMC error External Email - Use Caution freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b Thanks! -Valia The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Fwd: INS Meeting
by Rosalia Dacosta Aguayo 14 Jan '22

14 Jan '22

External Email - Use Caution FYI!!

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Question about fsaverage
by zhoudongyue＠mail.dlut.edu.cn 14 Jan '22

14 Jan '22

External Email - Use Caution Dear FreeSurfer experts: I am confused how vertex position is determined. Is the vertex's position on surface is determined? And is the distance between each two vertex the same？ Bests， dongyue External Email - Use Caution

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Re: [Freesurfer] Request for the Developer password
by fsbuild 14 Jan '22

14 Jan '22

External Email - Use Caution Sending to your email shortly. - R. On Jan 13, 2022, at 02:31, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear to Whom It may Concern, I am writing the email of request for a Developer password. As I downloaded Freesurfer by following this link, there was a sign-in page that required the password as shown below:<3F84E90C1E1A49C6BDBEE1CBCDE247FF.png>Would you please kindly send it to me? Thanks.  Best regards, Krystal _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Inconsistent contrasts on longitudinal Samseg
by peder lillebostad 13 Jan '22

13 Jan '22

External Email - Use Caution Dear Freesurfer experts, I want to run a multi-contrast longitudinal Samseg (ms lesions), but not all timepoints are consistent with regards to which contrasts are available (some have only T1s, some have both T1 and T2). As stated in the wiki, `run_samseg_long` does not accept such inconsistent input, but is there a natural workaround for it? So far I lean towards running only those timepoints that contain the full set of contrasts, and subsequently running the cross sectional stream on those timepoints that don't. Does that make sense? Thank you very much! - Peder

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Request for the Developer password
by krystaly 13 Jan '22

13 Jan '22

External Email - Use Caution Dear to Whom It may Concern, I am writing the email of request for a Developer password. As I downloaded Freesurfer by following this link<https://secure-web.cisco.com/1fxAaxGHQxN25yymFu6CFok7OB1Y211kRGwYTn6wh4aXkx…>, there was a sign-in page that required the password as shown below: [cid:image003.png@01D80892.7BA70360] Would you please kindly send it to me? Thanks. Best regards, Krystal

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The volume of some hypothalamus subunits is 0
by Xiaotong Zhang 12 Jan '22

12 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, When I used the FS.dev version for hypothalamus segmentation, I have segmented it sucessfully. Tensorflow-CPU has been installed to run this module (hypothalamus_seg). The .sh file was: for subj3 in 111 112 114...and 431 do mri_segment_hypothalamic_subunits --i /run/media/guanliyuan/Elements_Learningmaterials/try3_fs/$subj3/mri/orig/001.mgz --o /run/media/guanliyuan/Elements_Learningmaterials/try3_fs/try3fs_seg/$subj3/ --vol /run/media/guanliyuan/Elements_Learningmaterials/try3_fs/try3fs_seg/$subj3/ --threads 1 --cpu done However, in the .csv file of some subjects, there were no the volume of the left and right anterior-inferior. I don't know the reason for this cese. I am looking forward to your reply. Thanks very much in advance. Please check attachment about the results of hypothalamic_subunits 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev 2) Platform: CentOS 7.9 Sincerely, Zhang

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Re: [Freesurfer] FS installation question ( help )
by fsbuild 12 Jan '22

12 Jan '22

External Email - Use Caution Hello Jamie, If you are using the Windows Subsystem for Linux (WSL), you don't need to download the archive on the windows side and copy it over to Ubuntu linux through the mounted path..  I would try downloading the freesurfer 7.2.0 installer in linux. In Ubuntu linux, run the terminal program, and use these commands to try and directly install freesurfer. (There is also some documentation under https://secure-web.cisco.com/16yf-9jnI1XE2VTPlodTjL4JQ0cg__EgJTUM4KJe7m5QTs… Get the 7.2.0 installer with, $ cd $ wget  https://secure-web.cisco.com/1Axw7MVZbtZg7DWF1xSXkEcIDLIFHbL30xZStvae83fDk2… Then try the install with the .deb file, $ sudo apt-get update $ sudo apt-get install ./freesurfer_7-dev_amd64.deb .... answer Y/yes to prompts .... Do you want to continue? [Y/n] Y ..... if the install succeeds, you should then try the freesurfer environment ... $ bash $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. "Ford, Jamie K" (j.ford(a)imperial.ac.uk) January 12, 2022 at 10:19         External Email - Use Caution         Hi everyone,     Please could someone please help me on some issues I’m having in trying to download FS with Linux (version 7.1.1)?   In Ubuntu 18.04 LTS, I successfully ran: cd /mnt/c/Users/[my Windows username]/Downloadstar -zxvf freesurfer-linux-centos7_x86_64-7.1.1.tar.gzcd Freesurferpwdexport FREESURFER_HOME=$HOME/freesurferexport SUBJECTS_DIR=$FREESURFER_HOME/subjects   However, for “source $FREESURFER_HOME/SetUpFreeSurfer.sh”, I get an error message saying “-bash: /home/[Ubuntu username]/freesurfer/SetUpFreeSurfer.sh: No such file or directory”   I’m really new to Linux, so if someone could explain how to solve this as simply as possible, I would really appreciate it.   Thank you so much!   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/12JAbDZKjArmfIndhqSfwhBs7H9HWTfuWNk96ja7BQ8yWx…

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Postdoctoral Position – Neuroimage Analysis and Deep Learning
by Gang Li 12 Jan '22

12 Jan '22

External Email - Use Caution A postdoctoral fellow position is available in the Department of Radiology and Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current research focuses on the development and dissemination of advanced image processing and deep learning techniques for pediatric neuroimaging data analysis for better understanding the dynamic development of brain structure, function and connectivity in health and disease during the prenatal and early postnatal stages. For more information, please visit: https://secure-web.cisco.com/1Aamh0DrerC5p2EGmmyN9N4bsYM4vuU8fkiSRy4Nydubq-… The successful candidate will support our efforts in advancing pediatric neuroimaging analysis technologies (e.g., reconstruction, parcellation, registration, mapping, prediction, modeling, harmonization, fusion, atlas building, pattern analysis, etc.). We are seeking highly motivated individuals who have extensive research experience in medical image analysis and deep learning and demonstrated academic excellence, including publications in first-class journals or conferences. The candidate should have a Ph.D. (or equivalent) in Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, Neuroscience, or related fields. Good command of programming tools including Python, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. The University of North Carolina at Chapel Hill is an equal opportunity and affirmative action employer. We strongly encourage applications from diverse backgrounds. Interested candidates should email a cover letter and a resume to Dr. Gang Li ( gang_li(a)med.unc.edu)

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FS installation question ( help )
by Ford, Jamie K 12 Jan '22

12 Jan '22

External Email - Use Caution Hi everyone, Please could someone please help me on some issues I'm having in trying to download FS with Linux (version 7.1.1)? In Ubuntu 18.04 LTS, I successfully ran: * cd /mnt/c/Users/[my Windows username]/Downloads * tar -zxvf freesurfer-linux-centos7_x86_64-7.1.1.tar.gz * cd Freesurfer * pwd * export FREESURFER_HOME=$HOME/freesurfer * export SUBJECTS_DIR=$FREESURFER_HOME/subjects However, for "source $FREESURFER_HOME/SetUpFreeSurfer.sh", I get an error message saying "-bash: /home/[Ubuntu username]/freesurfer/SetUpFreeSurfer.sh: No such file or directory" I'm really new to Linux, so if someone could explain how to solve this as simply as possible, I would really appreciate it. Thank you so much!

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Freesurfer January 2022