Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

segmentation fornix with mri_cc
by Mostafa Fakhri 27 Jun '22

27 Jun '22

External Email - Use Caution Hello to all of you I ran recon-all: $ recon-all -sd /share/users/mfakhri/FS/subjects -subject 102109 -i T1w.nii.gz -all Then I tried segmentation fornix and I used -f on the mri_cc command: $ mri_cc -f -force -sdir /share/users/mfakhri/FS/subjects 102109 including fornix in segmentation processing regardless of existence of cc in input volume using /share/users/mfakhri/freeSurfer-analys/subjects as SUBJECTS_DIR... reading aseg from /share/users/mfakhri/freeSurfer-analys/subjects/102109/mri/aseg.mgz reading norm from /share/users/mfakhri/freeSurfer-analys/subjects/102109/mri/norm.mgz 128569 voxels in left wm, 173189 in right wm, xrange [111, 140] MRIprincipleComponents: unsupported input type 1 searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot 5.8 global minimum found at slice 128.0, rotations (-0.50, -1.00) final transformation (x=128.0, yr=-0.500, zr=-1.000): 0.99981 0.01745 -0.00873 0.02437; -0.01745 0.99985 0.00015 130.23384; 0.00873 -0.00000 0.99996 126.88302; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping There was no fornix.mgz in mri directory and this error file has been created: $ cat error.log MRIprincipleComponents: unsupported input type 1 I used an HCP 3T preprocess image. Thanks for the help! Mostafa

2 1

selxavg3-sess out of memory error
by Caspar M. Schwiedrzik 27 Jun '22

27 Jun '22

External Email - Use Caution Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that. I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2. This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory. Any advice would be appreciated! Caspar

2 4

change the $SUBJECTS_DIR
by Mostafa Fakhri 25 Jun '22

25 Jun '22

External Email - Use Caution Hello to all, I am new to FreeSurfer. By executing recon-all I get the permission error. Is there a way to change the $SUBJECTS_DIR, such as /share/users/my user/subject name ? $ recon-all -subject 102109 -i T1w.nii.gz -all mkdir: cannot create directory `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109': Permission denied mkdir: cannot create directory `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109': Permission denied mkdir: cannot create directory `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109': Permission denied cp: cannot create regular file `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109/scripts/build-stamp.txt': No such file or directory cat: /share/Application/FreeSurfer/Install/freesurfer/subjects/102109/scripts/build-stamp.txt: No such file or directory /share/Application/FreeSurfer/Install/freesurfer/subjects/102109/scripts/patchdir.txt: No such file or directory. Thanks for the help! Mostafa

2 1

ERROR : mri_ca_register with non-zero status 15
by 김다운 24 Jun '22

24 Jun '22

External Email - Use Caution Hello FreeSurfer Develops, I'm attempting to run recon-all on two single subject with T1. However, I got the following error message for subject respectively: ================================================================ ERROR : mri_ca_register with non-zero status 15 but continuing despite the error ... ERROR : cannot find or read transform/talairach.m3z I have attached the recon-all.log in case it's of any use. ================================================================= my commend code #!/bin/bash #SBATCH -N 1 # Number of Nodes required #SBATCH -c 8 # Number of threads #SBATCH -t 0-10:00:00 # Amount of time needed DD-HH:MM:SS #SBATCH -p shared # Partition to submit to #SBATCH --mem-per-cpu=8GB #Memory per cpu export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK module load freesurfer export FS_LICENSE=$HOME/license.txt export SUBJECTS_DIR=~/DWKIM/T1/00sample recon-all -i s3001.nii -s s3001 -parallel -openmp 8 -all -qcache ================================================================== FreeSurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform : CentOS Linux ver.7 uname -a : Linux holylogin04.rc.fas.harvard.edu 3.10.0-1160.36.2.e17.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86 64 x86_64 GNU/Linux

2 3

Visualizing and interpreting vertex-wise GLM analysis
by Julian Macoveanu 24 Jun '22

24 Jun '22

External Email - Use Caution Dear Freesurfers, I have a simple design with patients and controls and would like to find regions showing group differences in cortical volume and thickness. I also remove the effect of age, sex and ICV. Running the GLM group analysis by the book I get a few clusters showing significant differences in intercept. 1. I interpret this like patients have smaller “predicted” regional volume at age 0, or at mean age of the group (if demeaned age covariate) compared to controls. How can this finding be described in a more clinically meaningful way? 2. Related to the above, how do I visualize what is going on in the significant clusters? The extracted values from these clusters (ocn.dat) show no group differences in volume when displaying the group means in SPSS (using either age/sex/ICV adjusted or non-adjusted values). Maybe I am misunderstanding something, how can there be differences in intercept but no differences between group means? (slopes not significantly different). How do I best describe and visualize this group difference in a paper? Julian

2 1

recon-all -s exited with ERRORS
by Wang, Yu 24 Jun '22

24 Jun '22

External Email - Use Caution Hi, FreeSurfer Developers, I am attempting to use the recon-all to reconstruction, I successfully run this command in some subjects, but it also failed in around 1/3 of subjects. And after running the recon-all of this 1/3 subjects. It will show “mri_watershed error:GLOBAL region of the brain empty” and I already solve this with the command “recon-all -skullstrip -no-wsgcaatlas -s smwrc1NT816”. And after working with this, I tried to use the command “recon-all -autorecon2 -autorecon3 -s smwrc1NT816” and it shows the output as without given some detailed reasons: recon-all -s smwrc1NT816 exited with ERRORS at Mon Jun 13 13:54:10 CDT 2022 For more details, see the log file /Applications/freesurfer/7.2.0/subjects/smwrc1NT816/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1iPjG6_yDpeRBXccjdFdxifv54y1GvmJtNQuC-KaFzx3NzA… I’ve searched over the internet and did not find the reasons and solutions of my problems. And I will attached the recon-all.log in case it's of any use. I try to work out on two machine, and they show the same problems : 1. FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b and freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2. Platform: MacOs 11.4 and ubantu 20.04.4 3. uname -a:Darwin WANGs-MBP.attlocal.net 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:31 PDT 2021; root:xnu-7195.121.3~9/RELEASE_ARM64_T8101 arm64 or: Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 1. recon-all.log: see attached (this one is run by macOS) I will be appreciated if you can give me a hand with these problems. And looking forward to your reply. Sincerely, Yu

2 3

How to interpret vertex-wise findings?
by Julian Macoveanu 24 Jun '22

24 Jun '22

External Email - Use Caution <This is an updated repost> Dear Freesurfers, I have a simple design with patients and controls and would like to find regions showing group differences in cortical volume and thickness. I also remove the effect of age, sex and ICV. Running the GLM group analysis by the book I get a few clusters showing significant differences in intercept. 1. I interpret this like patients have smaller “predicted” regional volume at age 0, or at mean age of the group (if demeaned age covariate) compared to controls. How can this finding be described in a more clinically meaningful way? 2. Related to the above, how do I visualize what is going on in the significant clusters? The extracted values from these clusters (ocn.dat) show no group differences in volume when displaying the group means in SPSS (using either age/sex/ICV adjusted or non-adjusted values). Maybe I am misunderstanding something, how can there be differences in intercept but no differences between group means? (slopes not significantly different). How do I best describe and visualize this group difference in a paper? Going through the studies I found on Pubmed that used Freesurfer with vertex-wise GLM, so far, I only found e.g. the “lower thickness” interpretation in one group vs the other and not “lower intercept”. In my case at least I cannot say this since the extracted values between groups show no group difference. Julian

1 0

Request for 7z VM passcode
by Chuang, Tzu-Chao 24 Jun '22

24 Jun '22

External Email - Use Caution Hello, I need the passcode to expand the VM file (FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thank you!

1 0

aseg.stats - eTIV volume space
by Katie Rose Jobson 23 Jun '22

23 Jun '22

External Email - Use Caution Hi FreeSurfer experts, I apologize if this question has been addressed, but I was unable to find a definitive answer elsewhere. I am using the aseg.stats file to extract the estimated Total Intracranial Volume (eTIV) value to be used as a correction to my anatomical data. I just want to confirm what space this data is in. I had previously assumed this data was in native anatomical space. But I read on the wiki that this statistic is calculated using the Talairach transform file (talairach.xfm), which is the conversion from MNI305 to Talairach. I just want to ensure I am correct in the assumption that this data is represented in native anatomical space. Thank you so much for your help in this matter. Best Wishes, Katie -- Katie Jobson, M.S. PhD Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/15mzkkYt-HVv32ujlEOwH-7Z0bKXddWNX6mHpHztqONWIe…> Department of Psychology and Neuroscience | Temple University [cid:dcfe96a7-bf68-4d92-8c1e-61f5814893fa]

2 2

freeview and dmri_trk2trk
by Juan 23 Jun '22

23 Jun '22

External Email - Use Caution Hello freesurfer experts, I have been using TRACULA to analyze my group of images and I have noticed a bug or not. But I would like to comment it so that you can help me to solve it. I embed the two files with the dmri_trk2trk function. - perm.th20.pos.sig.voxel.mgh - z.mgh I visualize them with the freeview image viewer and when I try to exchange the files to see them, only one of the two is reflected, that is to say, they don't change, the same map is maintained at all times. This is an error of my computer, or maybe my freesurfer could be wrongly installed. Thank you very much for the clarification. Juan

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Freesurfer June 2022