Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 discussions

Passcode for unzipping ubuntu 7.2 file
by SJ Heany 16 Aug '22

16 Aug '22

External Email - Use Caution Hello, I am trying to unzip and install FS_7_2_0_ubuntu_18_04_06.ova but it seems I need a passcode for the 7zip step. I was prompted to email this list. Please forward such if possible. Regards, SJ

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transform amygdala mask from FS to native space
by Elizabeth Haris 15 Aug '22

15 Aug '22

External Email - Use Caution Hi Freesurfer Developers, I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask? mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz Many thanks, Elizabeth

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Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur
by fsbuild 15 Aug '22

15 Aug '22

External Email - Use Caution Hello Sara, You could try running bash shell and putting a copy of your license file as license.txt in your home directory and then set the environment variable FS_LICENSE to point to it, e.g. $ bash$ cd $HOME… copy in your license file here as license.txt ...$ export FS_LICENSE=$HOME/license.txt… make sure it is there …$ cat $FS_LICENSE… should see contents of your license file ... … then setup the freesurfer environment as usual …$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreesurfer.sh… output deleted …$ which freeview/Applications/freesurfer/7.3.2/bin/freeview… see if you can just bring up freeview displaying an empty window …$ freeview There are various postings reporting that MacOS BigSur running on machines with dual monitor settings have issues including when they wake up from the screen saver or the machine has goner to sleep - as in the machine crashes. Some reports recommend turning off the screensaver, and making sure the machine energy saver settings are not set to put the machine to sleep. - R. On Aug 15, 2022, at 17:08, Addison, Reuben <RAddison(a)mghihp.edu> wrote:Sara, do you have a double screen by any chance ?Reuben A.  Get Outlook for iOSFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Sara Sanchez-Alonso <sanchez.alonso.sara@gmail.com>Sent: Monday, August 15, 2022 5:07:01 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur         External Email - Use Caution        Hello,I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was successful, but every time I need to open freeview, it quits unexpectedly.The environment seems to be set up correctly and I have also downloaded my license and copied it to the freesurfer directory. I tried downloading version 7.2.0 and I keep having the same issue.Any ideas as to why I am unable to open freeview?Thanks,Sara_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview quits unexpectedly on macOS Big Sur
by Sara Sanchez-Alonso 15 Aug '22

15 Aug '22

External Email - Use Caution Hello, I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was successful, but every time I need to open freeview, it quits unexpectedly. The environment seems to be set up correctly and I have also downloaded my license and copied it to the freesurfer directory. I tried downloading version 7.2.0 and I keep having the same issue. Any ideas as to why I am unable to open freeview? Thanks, Sara

2 1

Parcellation issue
by Addison, Reuben 14 Aug '22

14 Aug '22

I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after In terminal (ASSUMING shell is bash), a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5 b) export SUBJECTS_DIR=`pwd` c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot Reuben A.

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running mri_glmfit with atlas
by Hye Min Shin 14 Aug '22

14 Aug '22

External Email - Use Caution Hello experts, While going through GroupAnalysis tutorial for freesurfer ( https://secure-web.cisco.com/1vsiSpzodxBizvnBXlCu7-xP4XPwjzJ4w3O_H2Phnc0vsq…) I was wondering if there was a way to analyze mri_glmfit by regions from an atlas. So instead of looking at vertex-by-vertex or clusters, I wanted to look at areas that are statistically significant by cortical atlas such as Desikan-Killiany or DK-Tourville atlas. I understand that mri_glmfit has --label option. Can I just use this to tell mri_glmfit to use atlas label file as a mask then? Thank you in advance for your help. Best, Julia Shin

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Large number of false negative MS lesions in SAMSEG
by Martin Kavec 14 Aug '22

14 Aug '22

External Email - Use Caution Hello, I am testing SAMSEG on my group of MS patients. Unfortunately, even when dropping threshold to 0.005 I have large number of false negative lesions left behind by SAMSEG (80% in about 75 cases I tried), which are clearly visible lesions. I ran/checked registration between inputs, which is typically very good to excellent. Images are all 3D acquisitions , mprage, flair, and t2 with ~1 mm3 isotropic voxel. Here is the command, which I ran: run_samseg --input mprage_reg.nii.gz flair.nii.gz t2_reg.nii.gz --pallidum-separate --lesion --lesion-mask-pattern 0 1 1 --threshold 0.005 --output samseg_threshold_0.005 and example of the lesion in occipital white matter in sagittal and axial orientations. [image: image.png] [image: image.png] I would very much appreciate any leads as to how to improve the segmentation. Thanks, Martin

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Passcode Request
by Ryan Olsen 14 Aug '22

14 Aug '22

External Email - Use Caution Hello, I am trying to extract files in the 7zip download for the VurtualBox VM and it requires a passcode. Could you please send me the passcode required for this step. Thanks, Ryan

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FreeSurfer 7Zip archive passcode
by 王馨霈 12 Aug '22

12 Aug '22

External Email - Use Caution Hello, I would like to ask for the passcode for the VM file (FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thank you in advance, Hsin Pei Wang

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Question about WhiteSurfs lh
by 项嵘加 12 Aug '22

12 Aug '22

External Email - Use Caution Dear FreeSurfer exports: When I calculate autorecon3,the problem as shown in the email attachment. This command seems to be executable only when the status is 0, but now the status is 1. I can't find a solution. Please guide me how to operate. Yours sincerely, Ender.

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Freesurfer August 2022