Freesurfer October 2022

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Virtual Machine Passcode
by marie 11 Oct '22

11 Oct '22

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password
by Agustina Fragueiro 11 Oct '22

11 Oct '22

External Email - Use Caution Hello, I am installing FreeSurfer 7.2.0 on a virtual box in Windows. How could I get the password to unzip the file? Thank you, Agustina -- Agustina Fragueiro, Ph.D. Postdoctoral researcher EMPENN research unit INRIA - National Institute for Research in Digital Science and Technology Rennes, France

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Virtual machine password
by Daphné Rimsky-Robert 10 Oct '22

10 Oct '22

External Email - Use Caution Hello, I understand I need a password to be able to use the freesurfer virtual machine. I hope this is the correct place to request it ? Best regards, Daphné Rimsky-Robert

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Thalamic nucleus segmentation 3D export
by Paulk, Angelique C.,PHD 10 Oct '22

10 Oct '22

Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview. Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique

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Hemisphere in Yellow
by Jun Yeon Won 10 Oct '22

10 Oct '22

External Email - Use Caution Dear Freesurfer experts, I am running a linear regression analysis and found a significant result showing below (cache.th20.abs.sig.cluster.summary file). [image: image.png] I ran the below script to get this result. Right hemisphere was focused for this analysis. mri_glmfit-sim --glmdir rh.thickness.10.glmdir \ --cache 2 abs \ --cwp 0.05 But, when visualizing the cache.th20.abs.sig.cluster.mgh file, it shows below - the hemisphere is in yellow. [image: image.png] The below is a visualization of sig.mgh. The underlay should be gray but I am not sure why the underlay looks yellow when overlaying the thresholded result. [image: image.png] I saw somebody posted the same issue here ( https://secure-web.cisco.com/1OHcN_bRSEDk0roNAjIAfufCwrh4xf7rzgQtoclY3flDVp…) but I was not able to find the solution from here. Could you please let me know what is an issue and how to resolve this? Best, Jun

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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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Freesurfer October 2022