Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Calculate cortical thickness of a volumetric ROI
by Carlos Alcocer 07 Jun '23

07 Jun '23

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using https://secure-web.cisco.com/1SRB1kl1prYOxcV3133JRM9O5Bj21w9M9aZYfcod7MM5GH… as a guide. Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels. Thank you, Carlos

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Volume files for clinical pipeline
by KennethSPrice 06 Jun '23

06 Jun '23

External Email - Use Caution Hello Freesurfers! I'd like to compare volumetric changes in two groups and visualize the difference on an overlay of fsaverage. But there are no volume files to concatenate and compare. How do I run a volumetric analysis using FSGD or QDEC without the volume files from recon-all_clinical? Thanks, Ken

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Password Freesurfer VirtualBox Image
by Michael 06 Jun '23

06 Jun '23

External Email - Use Caution Hello! I kindly ask for the VM_67 VirtualBox Image password. Thank you so much! Best, Michael

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Request for Password to unzip FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Kazuki Sakakura 05 Jun '23

05 Jun '23

External Email - Use Caution Dear developers, I kindly request a passcode to unzip FS_7_2_0_Ubuntu_18_04_06.ova.7z. Sincerely, Kazuki Sakakura, MD, PhD Research Scholar, Wayne State University Address: 3901 Beaubien Street, Detroit, Michigan, 48201, USA.

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Re: [Freesurfer] cannot find freesurfer folder
by fsbuild 04 Jun '23

04 Jun '23

External Email - Use Caution Please check your email/spam filters as you were sent the info for the VM earlier today. The freesurfer_7.2.0_amd64.deb file will install 7.2.0 as /usr/local/freesurfer/7.2.0, but there is no need to that in the VM because it should already be installed there. - R. On Jun 4, 2023, at 11:31, Pedro henrique barradas <phbarradas(a)hotmail.com> wrote:        External Email - Use Caution        HelloI tried installing freesurfer through ubuntu but I can not understand where it has been instaled nor  can I find the source file. can anyone help please?

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cannot find freesurfer folder
by Pedro henrique barradas 04 Jun '23

04 Jun '23

External Email - Use Caution Hello I tried installing freesurfer through ubuntu but I can not understand where it has been instaled nor can I find the source file. can anyone help please? I am trying to install with a virtualbox but I need a passcode to unzip the file pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'freesurfer' instead of './freesurfer_7.2.0_amd64.deb' freesurfer is already the newest version (7.2.0). The following packages were automatically installed and are no longer required: efibootmgr libefiboot1 libefivar1 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ cd freesurfer -bash: cd: freesurfer: No such file or directory pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ pwd $FREESURFER_HOME /mnt/c/Users/phbar/Desktop pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ echo $FREESURFER_HOME pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb [sudo] password for pedro: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'freesurfer' instead of './freesurfer_7.2.0_amd64.deb' freesurfer is already the newest version (7.2.0). The following packages were automatically installed and are no longer required: efibootmgr libefiboot1 libefivar1 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ [https://secure-web.cisco.com/1b-Yh_XBB5RIegXXHi7o45IHWi1ofOMHmN79tn6_xj3GCj…]<http://secure-web.cisco.com/19tyssBrpamrK0eOnbMfTrJ66_s4XP0-581Fw-9rA_kIhY9…> Sem vírus.http://secure-web.cisco.com/15e5A5-l5iw1W96sl0rIE2bIKpt8EjCXtYl0e3OPo…<http://secure-web.cisco.com/19tyssBrpamrK0eOnbMfTrJ66_s4XP0-581Fw-9rA_kIhY9…>

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Pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Pedro henrique barradas 04 Jun '23

04 Jun '23

External Email - Use Caution Hi I would like to request a passcode to unzip FS_7_2_0_ubuntu_18_04_06.ova.7z Thank you Pedro Barradas

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7.4.0 Recon-all_Clinical - error in computing lh.BA_exvixo.annot
by NicolasNorton 02 Jun '23

02 Jun '23

External Email - Use Caution Hey Devs, I'm experimenting with recon-all_clinical in FS 7.4.0. I'm wondering how to pass the --qcache option to recon-all. I also wanted to give you a heads up that recon-all_clinical is calling for a colortable in the dev build which is resulting in an error. I don't think this will affect my analysis but it may someone else's. Here is the error message: " ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt computing statistics for each annotation in ./lh.BA_exvivo.annot. " Its the same for RH.BA_exvivo.annot, and continues: error: No such file or directory error: could not read annot file ./rh.BA_exvivo.annot error: No such file or directoryerror: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.annot Please let me know if this will affect thickness or volume analysis. Thanks, Nic

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Freesurfer installation
by Stefan Rampp 02 Jun '23

02 Jun '23

External Email - Use Caution Dear Freesurfer developers, For the installation of Freesurfer, I'd need a pass code to extract the zip file. Best regards Stefan

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Re: [Freesurfer] Sourcing freesurfer
by fsbuild 01 Jun '23

01 Jun '23

External Email - Use Caution Hello Pedro, It does not look like you are using a standard installation of freesurfer given the path you list below as /root/freesurfer. We have information available about how to use either WSL (Windows Subsystem for Linux) to host Ubuntu Linux in order to run Freesurfer on Windows, https://secure-web.cisco.com/1kqIIthfElwIFp4xfRtH02uxDl8MR86sRRP-ugqp0vSmGT… - or you can install VirtualBox on your Windows machine to run a VM we provide for download with freesurfer already installed and setup to run (see https://secure-web.cisco.com/1v32HavIAAMjouxecLl5yEhLk0tyE2hxIHnDGZC-o-FlJl…) For WSL, once you have Ubuntu Linux running, we recommend using one of the debian (.deb) package installers listed on the Freesurfer 7 download page that matches your Ubuntu system (https://secure-web.cisco.com/1q0Hyt7h01b-vvXLm4oWRsX0bWB4JcKCG1QCz9R_lYE6XH… So for Ubuntu 22 running in WSL, you would download one of the freesurfer_ubuntu22-7.X.X_amd64.deb files into Ubuntu linux and install it.  That would install freesurfer as /usr/local/freesurfer/7.x.x in the Ubuntu Linux image running in WSL.    In the VM, freesurfer 7.2.0 is already installed as /usr/local/freesurfer/7.2.0 We recommend you verify you are using (or try) one of the setups above. - R. On 6/1/23 11:38, Pedro henrique barradas (phbarradas(a)hotmail.com) wrote:         External Email - Use Caution         Hello! I'm having a couple problems with the final installation steps When I attempt to export $FREESURFER_HOME=$HOME/freesurfer it tells me: bash: export: ´#HOME/freesurfer=root/freesurfer`: not a valid identifier When I source it, it now says it cannot find the directory and gives back the following answers: bash: /root/freesurfer/SetUpFreeSurfer.sh: No such file or directory I also tried doing "source SetUpFreeSurfer.sh" from the freesurfer directory and I got this response: bash: /root/freesurfer/FreeSurferEnv.sh: No such file or directory Also, When I type echo $FREESURFER_HOME I get root/freesurfer But when I type pwd $FREESURFER_HOME it gives me c/mnt/Users/ASUS/Downloads/freesurfer I greatly appreciate any advice. Thank you Best wishes _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1rCsMjiZIFhaEwoY93DEQzlsfPXVd-HIQ12aABmwCyfvS7… 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/118-9oU96FBuN-fAsM44xOA0MwIfhdZwbjRCeoLflO_wr8… <https://secure-web.cisco.com/1dNhjMyd4TYc8nsrgllD7hrTFSK1vGTJjsNEAy5RvBAj2dcZVIqKezDjWV9AEXSi_Zgf1TS6Sm0FM6GmczEq96Yp_42KH1GvUHTqu2ym0RhSRt9ZU7QGgxTSzAxbuwuWkZjcb0MjUZOnrMEeDrLeod_AOz610_wNhQuA0380mlMtXwof-BUBefkW8mBPiB785MTI_PkZWIz2iKb4YOD6jr7ql3lCnJ0oV63_Nzg4UZH9lEPP9v-1l11BZH-fuIMFAjV-BP-Jup0HYvlzF7dOMUrdXWtYzPeiUALcojMg5ZKSF4Za0hRjEw2KQjIGez0fTFFN8xZ3LtGigUpUHU485Pw/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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