Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Request FSF VM password
by 최형진 16 Jun '22

16 Jun '22

External Email - Use Caution Hi, May I ask the password for extracting FS_7_2_0_ubuntu_18_04_06.ova.7z that was downloaded yesterday? Thanks Jin M.D./Ph.D. 네이버 메일앱에서 보냈습니다.

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Hippocampal Subfield Segmentation with a T2: Warnings in the log file
by Kaya, Batu 16 Jun '22

16 Jun '22

External Email - Use Caution Hi all, I recently ran the hippocampal subfield segmentation script with a T2 scan. The subfield outputs make sense, however, when I was reviewing the log, I noticed this warning: makeIsotropic WARNING: not different enough, won't reslice! I also noticed four other warnings of the same kind: WARNING: Registration did not converge in 5 steps! Problem might be ill posed. Please inspect output manually! I reviewed the freesurfer email archive and found one thread where the firstwarning was discussed. I checked that my T1 and T2 are roughly aligned. Should I be concerned about the first and second warnings, or can they be ignored if: a. the outputs make sense; the script ran successfully otherwise? Specs: FreeSurfer Version: 7.1.1 Platform: Centos7 Thank you for your time! Batu Kaya PD Clinical Research Coordinator Toronto Western Hospital Neuropsychology Research Lab https://secure-web.cisco.com/1L7Dxdru2GBABYsjkqMvqWksEYscEYwKfxO6U9fKRNUW2L… This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following: (1) Follow any unsubscribe process the sender has included in their email (2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page. Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists. Patient Consent for Email: UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here<https://secure-web.cisco.com/1ScRcgXx1SCThEg82u6mmqhJMDzFnyTkGAc7PMhBicE4_e…> to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

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Postdoctoral Fellow Positions in Brain Development
by Anqi Qiu 16 Jun '22

16 Jun '22

External Email - Use Caution Postdoctoral Fellowship Positions in Brain Development Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort longitudinal study over the world. The GUSTO mothers were recruited during pregnancy between 2009 and 2010. We have followed the GUSTO family since then. The GUSTO study collects the unique data on cognitive functions, children behaviors, psychopathology, brain imaging, genetic and epigenetic data at multiple points from birth to 8 years of age. For instance, we acquired executive functions and behaviors in the first day, 3, 6, 12, 18, 24, 36, 48, 60, 72, and 84 months of life. The neuroimaging data were acquired at 0, 4, 6, 7, 9 years of age. The GUSTO has become a Singapore national platform to study developmental origins of mental illness and cross-generational transmission of mental illness. In addition, our laboratory has the public datasets of HCP, ABCD, PNC, ADHD, and Autism. The lab has great computing capacity, including multiple M40 and V100 GPU systems for deep learning, and computing clusters for large data set processing. We have 4000T neuroimage data that allow deep learning and machine learning exploration. We are looking for postdoctoral fellows who are interested in exploring longitudinal trajectories of brain, cognitive and behavioral development from birth onwards. How do environments and gene regulate such developmental trajectory? Qualification: 1. PHD in Neuroimaging, or Cognitive Neuroscience; 2. Experience with MRI-based neuroimage techniques; 3. Knowledge in statistical analysis; 4. Good communication and writing skills in English. If you are interested in the job listed above, please send your CV to Anqi Qiu, (bieqa(a)nus.edu.sg) Deputy Head for Research & Enterprises, Department of Biomedical Engineering, National University of Singapore Lab Website: https://secure-web.cisco.com/1sH5Vv7ZWsoknS3iff2uhMHygibEIDLyzb_90RXtvVkKgf…

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about the errors running TRACULA using tutorial data
by Xin Qi 16 Jun '22

16 Jun '22

External Email - Use Caution Hi FreeSurfer Support Team: I downloaded the FreeSurfer tutorial data ( https://secure-web.cisco.com/1OLGwSqYzgPPULXgJdbA3a6aEYR7c20U5gEp1Sz7adYYB2… <https://secure-web.cisco.com/1zEifGNLods-S-bcomvrPp9jUsIhuK0u0TYzTpvu0xdWZs…>) and tried to test TRACULAR. In the preprocessing step by running $trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial, I got the following error messages. ERROR: length of pathway list (lh.cst_AS rh.cst_AS lh.ilf_AS rh.ilf_AS lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.atr_PP rh.atr_PP lh.cab_PP rh.cab_PP lh.ccg_PP rh.ccg_PP lh.slfp_PP rh.slfp_PP lh.slft_PP rh.slft_PP) and endpoint label ID list ERROR: () do not match There may be something wrong with the demo dmrirc.tutorial configuration file, which is attached to the email. Please help me with how to fix the problem. Thank you very much and looking forward to hearing from you. Best regards Xin

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Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors
by fsbuild 16 Jun '22

16 Jun '22

External Email - Use Caution If you have not run fsck with the -y option from the intramfs prompt, you could try the instructions in this post - which shows the error (on a different version of Ubuntu),  https://secure-web.cisco.com/1G_OxjZo0eZ-YJ0rw8-xiLxDsmlEKgBMgmEnSsywbnbejd… You could revert the VM image back to your most recent snapshot, i.e., select the most recent snapshot in the list prior to the “current state” and then hit the restore button at the top (see screenshot). If the current state of the VM cannot be repaired and boot, then you can run, copy or retrieve the versions of the files from the most recent snapshot that boots, e.g., to otherwise backup or use in a new clone or fresh copy of the VM.   I think it is possible to have a persistent mapping of paths to the Windows side, but I would not bother with that until you have a VM running again. - R.

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Freesurfer Password
by Sean Amormino 15 Jun '22

15 Jun '22

External Email - Use Caution Hello! I need the password to expand the archive for Freesurfer 7.2.0 release in Ubuntu 18.04.06. Thanks!

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Re: [Freesurfer] FSL Password
by fsbuild 15 Jun '22

15 Jun '22

External Email - Use Caution Try, $ sudo  python3  fslinstaller.py … then enter password for developer.  The sudo command will use admin privileges which may allow install to occur. - R. On Jun 15, 2022, at 20:54, Rachel Wagner <rwagne2(a)uwo.ca> wrote:        External Email - Use Caution        Hello,  I am downloading FSL into ubuntu freesurfer VM, and have gotten the following prompt: developer@developer-VirtualBox:~/Downloads$  python3 fslinstaller..py--- FSL Installer - Version 3.2.3 ---[Warning] Some operations of the installer require administative rights,    for example installing into the default folder of /usr/local.    If your account is an 'Administrator' (you have 'sudo' rights)    then you will be prompted for your administrator password    when necessary.When asked a question, the default answer is given in square brackets.Hit the Enter key to accept this default answer.Where would you like the FSL install to be (including the FSL folder name)? [/usr/local/fsl]:Downloading...Checking FSL package        [OK] File downloadedInstalling FSL software version 6.0.5.2...We require your password to continue...password:  When I try to type in the password, I am unable to type at all, for some reason I can’t write anything in the terminal. Is there any way for me to troubleshoot? Thanks very much!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FSL Password
by Rachel Wagner 15 Jun '22

15 Jun '22

External Email - Use Caution Hello, I am downloading FSL into ubuntu freesurfer VM, and have gotten the following prompt: developer@developer-VirtualBox:~/Downloads$ python3 fslinstaller.py --- FSL Installer - Version 3.2.3 --- [Warning] Some operations of the installer require administative rights, for example installing into the default folder of /usr/local. If your account is an 'Administrator' (you have 'sudo' rights) then you will be prompted for your administrator password when necessary. When asked a question, the default answer is given in square brackets. Hit the Enter key to accept this default answer. Where would you like the FSL install to be (including the FSL folder name)? [/usr/local/fsl]: Downloading... Checking FSL package [OK] File downloaded Installing FSL software version 6.0.5.2... We require your password to continue... password: When I try to type in the password, I am unable to type at all, for some reason I can’t write anything in the terminal. Is there any way for me to troubleshoot? Thanks very much!

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Nii to Img file
by Rachel Wagner 15 Jun '22

15 Jun '22

External Email - Use Caution Hello, Thank you for your assistance! I am trying to convert an nii nifti file to an img file within free surfer. I’ve used the mri convert function and did create the img file, but I’m getting an error message in SPM when I try to co-register it to another img file. Is there a particular way I should be converting an nii file? My only other thought is that potentially I’m not exporting properly. I am using ubunu VM on a windows computer, and need to export the two img files from ubuntu to my windows files so I can upload them in matlab. Is there a preferred way to export files out of the ubuntu VM? Thanks very much again, Rachel

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Re: [Freesurfer] SPM to FreeSurfer
by fsbuild 15 Jun '22

15 Jun '22

External Email - Use Caution Hello Rachel, SUBJECTS_DIR is preset in the terminal window to point to the example subjects already provided with the freesurfer distribution under /usr/local/freesurfer/7.2.0/subjects.  You will see subject names under that directory like “bert”.  That SUBEJCTS_DIR setting is printed out when you start a new terminal window. But it is not intended you process your own subjects there.  You don’t have permission to copy data into that location unless you use the “sudo” command. It’s preferable to set SUBJECTS_DIR to point to a subdirectory where you have permission to read and write your own subject data files such as /home/developer   If you put your data under there, then you can set SUBEJCTS_DIR to instead be, $ export SUBJECTS_DIR=/home/developer/subjects… under which you would presumably have directories referenced by subject name. To see the value of SUBEJCTS_DIR in the terminal window,$ echo $SUBJECTS_DIR To see the value of all environment variables in the terminal window,$ env | sort You can change what SUBJECTS_DIR is set to in the terminal window by editing the file /home/developer/.bashrc  I would put any export command to change SUBJECTS_DIR from the subejcts provided with freesurfer at the end of that file. - R. On Jun 15, 2022, at 17:04, Rachel Wagner <rwagne2(a)uwo.ca> wrote:        External Email - Use Caution        Hello,  I am trying to take my SPM images and cortically project them with free surfer (SpmPainting - Free Surfer Wiki (harvard.edu) As it might be quite obvious, I have very little experience using these softwares. I am typing in the suggested code as follows: developer@developer-VirtualBox:~$ mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.imgmri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz brain.imgreading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, -1): could not open filedeveloper@developer-VirtualBox:~$ ^Cdeveloper@developer-VirtualBox:~$ Is there something I am doing incorrectly? Thank you!Rachel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer