Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] Virtual Machine password
by fsbuild 10 Oct '22

10 Oct '22

External Email - Use Caution I sent you an email earlier today with that and some other info - you might want to check your spam filters. - R. On Oct 10, 2022, at 02:49, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom it may concern,I am currently installing the Virtual Machine to run Freesurfer. I was prompted with a password and was wondering if anyone could share with me the password.Thank you for your help and time.Sincerely,Justina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Virtual Machine password
by Justina Lee 10 Oct '22

10 Oct '22

External Email - Use Caution To whom it may concern, I am currently installing the Virtual Machine to run Freesurfer. I was prompted with a password and was wondering if anyone could share with me the password. Thank you for your help and time. Sincerely, Justina

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Re: [Freesurfer] mkdir: /Applications/freesurfer/7.3.2/subjects/sub01: Permission denied
by fsbuild 09 Oct '22

09 Oct '22

External Email - Use Caution Hello Padma, The freesurfer installation under /Applications on MacOS, like most applications installed there, does not expect users to write their own data into what is installed there.  Or the example subjects that  are part of the freesurfer installation - pointed to by the environment variable SUBJECTS_DIR - is not meant to be written to with user data. So just change SUBJECTS_DIR to point to a directory where you have normal write permissions.  One location would be your home directory, e.g., $ echo $HOME /Users/padma $ cd $HOME $ mkdir subjects $ export SUBJECTS_DIR=$HOME/subjects $ echo $SUBJECTS_DIR /Users/padma/subjects Then put your subjects data there to process, etc.Here are some links with some additional info,https://secure-web.cisco.com/1whAZMfyHZ4FLyVo5f2kazK_sVsLOEt4UrO4idC_8… https://secure-web.cisco.com/1J0Gr93Wou3vnAj2gdII49F94CdlmxnssGDtUMKvrvolLz… R. On 10/9/22 01:40, priya padma (priya(a)phenomx.ai) wrote:         External Email - Use Caution         Hello Team, Thanks for the help before I successfully opened freeview. now i am trying to run recon-all for a nifti file. After setting the path  export FREESURFER_HOME=/Applications/freesurfer/7.3.2 export SUBJECTS_DIR=$FREESURFER_HOME/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh My data is in downloads so I navigated to Downloads and then gave  $ recon-all -s sub01 -i sub-AD003S1059S61129_0000.nii.gz -all but I always get permission error mkdir: /Applications/freesurfer/7.3.2/subjects/sub01: Permission deniedfs-check-version --s sub01 --o /var/folders/j3/plp0z25j1j969hgspftsz2fm0000gp/T//tmp.gqzbloERROR: cannot find sub01recon-all: version check failed fs-check-version --s sub01 --o /var/folders/j3/plp0z25j1j969hgspftsz2fm0000gp/T//tmp.gqzblo so I did it with sudo then also I get error which I learnt that the environment changes with sudo so we shouldn't use sudo. I tried keeping the data in the subjects folder and still the same error  Could you help me with this? Thank you  -- Best RegardsPadma PriyaAI Developer  PhenoMx, Inc.priya(a)phenomx.ai | (+82)10-5405-2685 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1xxWxLDmeEoiQxOKYuarVzAWD0Lk8txTO_wg4j3isHNR3F… 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/1ntTHUGAr4gWDwxykf07vXvYCcviwTHjgLiZaY7LnN10Jf… <https://secure-web.cisco.com/1yIuYSKuUR-U8QRGcTHvftWNx5rXOcpSoGeZln_Zrt_6qTw32NhBoF3g0dyBrkioAByqPvz_1_pMXRjkYPmSVEvujPEwwuiJgZsXeBROHmvwa_-_uWo05GfP8vgIY7GSA9NCttRqE9-d9MnYO0n2_KunotTSoTugcmhzWNbHTmK3D5QtFkBdEujVCTOisETRO9LAJhKxBC0Ytf_YIftc3snjiHHM7FyEVb-Prh1t_9hk5UsTOKVTkcRp0sybasQVtS6pqFOOoMlRsgBjjjYn2vhVz41qSXqv-pMeOlCpRX82ElQgwdj14UAE6s8zoHrMt/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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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mkdir: /Applications/freesurfer/7.3.2/subjects/sub01: Permission denied
by priya padma 09 Oct '22

09 Oct '22

External Email - Use Caution Hello Team, Thanks for the help before I successfully opened freeview. now i am trying to run recon-all for a nifti file. After setting the path export FREESURFER_HOME=/Applications/freesurfer/7.3.2 export SUBJECTS_DIR=$FREESURFER_HOME/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh My data is in downloads so I navigated to Downloads and then gave $ recon-all -s sub01 -i sub-AD003S1059S61129_0000.nii.gz -all but I always get permission error mkdir: /Applications/freesurfer/7.3.2/subjects/sub01: Permission denied fs-check-version --s sub01 --o /var/folders/j3/plp0z25j1j969hgspftsz2fm0000gp/T//tmp.gqzblo ERROR: cannot find sub01 recon-all: version check failed fs-check-version --s sub01 --o /var/folders/j3/plp0z25j1j969hgspftsz2fm0000gp/T//tmp.gqzblo so I did it with sudo then also I get error which I learnt that the environment changes with sudo so we shouldn't use sudo. I tried keeping the data in the subjects folder and still the same error Could you help me with this? Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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SynthSR
by AJ 08 Oct '22

08 Oct '22

External Email - Use Caution Can SynthSR be used on MRI scans of subjects with T2 lesions, such as MS? If yes, is their a way to save the masks of lesions that were Inpainted or their volume? For the output files, what are their image parameters such as TR, TE, TI? Thank you, AJ

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matlab 2019b and brainstem substructures analysis
by tulu＠ms36.hinet.net 08 Oct '22

08 Oct '22

External Email - Use Caution Dear Freesurfer experts, I will analysis brainstem structure and I use Freesurfer 7.2 version and maltab 2019b. I wonder if I need to install Matlab R2014b runtime or how to run hippocampal subfield/brainstem module by matlab2019b Thanks your help Jung Lung Hsu

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pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Shen Vivien 08 Oct '22

08 Oct '22

External Email - Use Caution Dear freesurfer developer: Thank you for your great tool and communication platform. I am writing to ask for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z, as I failed to find it anywhere. Could you kindly provide it? Many Thanks! Wenwen

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Parcellating Individuals using Yeo17Networks Atlas
by Remiszewski, Natalie 07 Oct '22

07 Oct '22

External Email - Use Caution Hi all, I have a dataset of structural MRIs that I have previously used FS on to parcellate into the DKT and Destrieux atlases. I am interested in parcellating and getting cortical thickness values using the yeo17networks atlas. Is there a way to modify recon-all so that i can get individual yeo17 data for each subject? Thank you! Best, Natalie Remiszewski Graduate Student Trainee University of Alabama at Birmingham Kraguljac Lab

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Re: [Freesurfer] Freeview does not show images
by fsbuild 07 Oct '22

07 Oct '22

External Email - Use Caution Did it say the driver was installed successfully?   I’m wondering if the driver did not install because it does not support your machines hardware for some reason.  But it should tell you if it cannot be installed. You can tell if the DCH driver is installed by following the instructions here,https://secure-web.cisco.com/1C5iHX14FwFkb0bd5IYlzilnGkZNKBRhHFB5E1e8V… There is more info about it here,https://secure-web.cisco.com/1OnUvmRVhRWfRd2WCZXsandn42tB-a7ROvNPXbkZS… - R. On Oct 7, 2022, at 06:05, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        Hi  Ruopeng,I tried to run the glxgears command in the WSL Ubuntu subsystem, but it doesn't show me the gears. I am having the same issue as this thread linked here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NxVL-emVuHw_jOzG4gXfcbpKLhoo9hS4C5IwC… I followed the advice and downloaded the latest Intel Graphics Driver, but this did not seem to fix the issue for me. I also looked at the corresponding debian package installer in accordance with my ubuntu version, and the same error occurs. How can I add a 3D accelerator or GPU acceleration so that the glxgears command can show me the gears?Thanks for your help and time.Sincerely,JustinaOn Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Are you able to run glxgears command? Do you see spinning gears?RuopengOn Oct 6, 2022, at 4:28 AM, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom this may concern and can help, I am currently trying to run Freeview under the Windows Subsystem Linux System. I can successfully download and open images, but nothing seems to be showing on my end (see image attached at the end). In order to find out what is preventing the X-server from correctly displaying graphics, I have tried to run the $ xeyes command and the eyes pop up, meaning that the X-windows server is working fine.Upon checking the WSL Version, I am currently using the WSL version 2.I have entered the two commands as follows:$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrcThen I exited Ubuntu, and tried to run freeview again (attempting to open a data file T1.mgz.) This still did not produce any image in freeview, although it opened it up. I tried changing the window, contrast, and brightness but to no avail. Is there another solution?Terribly sorry and thank you so much for your time.Sincerely,Justina <Freeview image display.png>_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1x2O2S2I-mf4HqnIK9_KstdCRE_wrCYlZRAFyk… mailing listFreesurfer@nmr.mgh..harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1TH-a_ARr0KQ1PoZEkN8WQN8Bk3ci8v4cWfSc3… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11TjdGy9B7gzRP3B7lBnlaCwFqv13mfF9heyLn… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HcGt3lm_5mwfaxmqwtlQ5ekQZRDmp28yuUB4e…; ._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview does not show images
by Justina Lee 07 Oct '22

07 Oct '22

External Email - Use Caution To whom this may concern and can help, I am currently trying to run Freeview under the Windows Subsystem Linux System. I can successfully download and open images, but nothing seems to be showing on my end (see image attached at the end). In order to find out what is preventing the X-server from correctly displaying graphics, I have tried to run the $ xeyes command and the eyes pop up, meaning that the X-windows server is working fine. Upon checking the WSL Version, I am currently using the WSL version 2. I have entered the two commands as follows: $ *echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc* $ *echo "export DISPLAY=:0" >> $HOME/.bashrc* Then I exited Ubuntu, and tried to run freeview again (attempting to open a data file T1.mgz.) This still did not produce any image in freeview, although it opened it up. I tried changing the window, contrast, and brightness but to no avail. Is there another solution? Terribly sorry and thank you so much for your time. Sincerely, Justina

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