Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Re: [Freesurfer] Running Freeview from Ubuntu (on WSL)
by fsbuild 19 Sep '24

19 Sep '24

External Email - Use Caution   It would be good to know what version of Ubuntu you are running in WSL.   You can see that in the Ubuntu linux terminal window with the command below, and you should see something like the following ... $ cat /etc/os-release PRETTY_NAME="Ubuntu 22.04.5 LTS" NAME="Ubuntu" VERSION_ID="22.04" VERSION="22.04.5 LTS (Jammy Jellyfish)" VERSION_CODENAME=jammy ID=ubuntu ID_LIKE=debian HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" UBUNTU_CODENAME=jammy - which in this case indicates Ubuntu 22. I would also check you used the Ubuntu 22 .dev installer package from, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubu… - and installed it from wherever you downloaded it to on the Ubuntu system with the command, $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb If you didn't use that installer, then the system may be missing xcb related files it needs to run Qt, etc. If you got that Qt error even after the freesurfer .deb package install completed with no errors, then you could try the commands, $ xhost +local: $ sudo apt-get install --reinstall libxcb-xinerama0 Please note you need a license.txt file for freeview to find.  You can put that in your $HOME directory on linux and set the environment variable FS_LICENSE to point to it $ export FS_LICENSE=$HOME/license.txt $ head -1 $FS_LICENSE you(a)somewhere.com    <-----  email address you used to reigster via the form, Then try running freeview again (with no arguments to see if it can open an empty window).  $ freeview - R. On 9/19/24 17:31, Barsotti, Ercole (john-barsotti(a)uiowa.edu) wrote:         External Email - Use Caution         Just re-upping this message in case anyone has any ideas. :) Hi all, I've successfully downloaded Freesurfer version 7.4 and can run its commands, with the exception of Freeview. I downloaded and installed Xming, like the FreeSurfer instructions tell you (https://freesurfer.net/fswiki/FS7_wsl_ubuntu) but this does not seem to work, either. I am using Ubuntu on a Windows computer. I get the following error when I run the freeview command : This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted Best, John From: Barsotti, Ercole <john-barsotti(a)uiowa.edu> Sent: Thursday, September 19, 2024 12:21 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Running Freeview from Ubuntu   Hi all, I've successfully downloaded Freesurfer version 7.4 and can run its commands, with the exception of Freeview. I downloaded and installed Xming, like the FreeSurfer instructions tell you (https://freesurfer.net/fswiki/FS7_wsl_ubuntu) but this does not seem to work, either. I am using Ubuntu on a Windows computer. I get the following error when I run the freeview command : This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted Any ideas? Best, John _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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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Running Freeview from Ubuntu
by Barsotti, Ercole 19 Sep '24

19 Sep '24

External Email - Use Caution Hi all, I've successfully downloaded Freesurfer version 7.4 and can run its commands, with the exception of Freeview. I downloaded and installed Xming, like the FreeSurfer instructions tell you (https://freesurfer.net/fswiki/FS7_wsl_ubuntu) but this does not seem to work, either. I am using Ubuntu on a Windows computer. I get the following error when I run the freeview command : This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted Any ideas? Best, John

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BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
by Sambamoorthy, Sowmya 19 Sep '24

19 Sep '24

External Email - Use Caution Hello Freesurfer support, We have freesurfer/7.3.2 on CentOS7. This installation is working fine and the recons (recon-all -autorecon-pial -s $SUBJECT -parallel) run to completion. What we are trying to do: Upgrade OS to ROCKY Linux 8.10. and trying to make freesurfer/7.3.2 work to completion.The reason we are keeping 7.3.2 is to not add variance to the current project. What issue we are facing: <<snippet of the last few lines of the log below>> Reporting on 45 segmentations Using PrintSegStat mri_segstats done /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss/fmri102_005_rocky/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss; ln -s /opt/freesurfer/7.3.2/freesurfer/subjects/fsaverage; cd - ln: failed to create symbolic link './fsaverage': File exists #-------------------------------------------- #@# BA_exvivo Labels lh Wed Sep 11 17:06:02 CDT 2024 ------------------------------------------------------------------------- ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version ------------------------------------------------------------------------- Linux rocky8-sg.cvl.utdallas.edu 4.18.0-553.8.1.el8_10.x86_64 #1 SMP Tue Jul 2 17:10:26 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fmri102_005_rocky exited with ERRORS at Wed Sep 11 17:06:02 CDT 2024 More Context: 1. The same brain on Centos7 has no issues finishing recons. If needed, we can share logs for this. 2. We have tried adding some fsaverage switches as seen on a few support groups. "recon-all -autorecon-pial -s $SUBJECT -parallel --fs-subjects-dir $SUBJECTS_DIR". This does not seem to help and does not get past the initial phases of the run. Hope this helps in giving the picture of what we are attempting to accomplish. Please let me know if you have any questions. --Sowmya Sowmya Sambamoorthy Research Assistant (972) 883-3746 Functional Neuroimaging of Memory Laboratory [cid:image001.png@01DB0A8B.4D12C810] T H E U N I V E R S I T Y O F T E X A S A T D A L L A S

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Re: [Freesurfer] FreeSurfer License Error
by fsbuild 18 Sep '24

18 Sep '24

External Email - Use Caution  Since the last release of freesurfer 5.X in 2014, the encryption libraries on linux systems have changed such that the licenses downloaded for the current 7.X releases,https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads- cannot work with 5.X. If you were previously using 5.X on an old linux system, then you could run it with the license file that worked for you on that system in a container or VM running whatever that OS was - hosted on a current version of Linux like Rocky8, Ubuntu 22, etc. Otherwise, I suggest you download and install the 7.4.1 release via the link above.  The license file you downloaded should work with that. - R. On Sep 18, 2024, at 20:25, Barsotti, Ercole <john-barsotti(a)uiowa.edu> wrote:        External Email - Use Caution        Hi all, I've downloaded Freesurfer version 5.3 and signed up for a license. However, when I try to run the example: mri_convert sample-001.mgz sample-001.nii.gz I get the following error: ERROR: Invalid FreeSurfer license key found in license file /home/john/freesurfer/license.txt I'm not sure what to do here as I have the license file in the correct place and thought that I had obtained it correctly. Best, John_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer License Error
by Barsotti, Ercole 18 Sep '24

18 Sep '24

External Email - Use Caution Hi all, I've downloaded Freesurfer version 5.3 and signed up for a license. However, when I try to run the example: mri_convert sample-001.mgz sample-001.nii.gz I get the following error: ERROR: Invalid FreeSurfer license key found in license file /home/john/freesurfer/license.txt I'm not sure what to do here as I have the license file in the correct place and thought that I had obtained it correctly. Best, John

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Error in dt_recon
by Ramesh Babu 17 Sep '24

17 Sep '24

External Email - Use Caution Dear All, I am new to dti analysis. I am trying analysis in a single subject. I set the environment as mentioned below. export DTI_DATA=export DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis export SUBJECTS_DIR=$DTI_DATA/subjects/t1_data/ In the last step, I received this error. dt_recon --i dti_data.nii --b bvals.txt bvecs.txt --s $SUBJECTS_DIR/t1_SPGR.nii --o dtioutput2 error: mghRead(/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis/subjects/t1_data//t1_SPGR.nii/mri/brainmask.mgz, -1): could not open file How to get this brain mask? Should it be from subject T1 image or bo map? I attached the full error report as a text file. I kindly request you to provide me with a solution. Thanks in advance Ramesh

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Question on lateral ventricle segmentation
by Necati Emre Şahin 17 Sep '24

17 Sep '24

External Email - Use Caution Dear FreeSurfer Developers, I hope this message finds you well. I am currently working with FreeSurfer 7.4.1 and I have encountered a situation that I would like your guidance on. Specifically, I have noticed that FreeSurfer outputs the lateral ventricle in two parts for sides, namely "Left-Lateral-Ventricle" and "Left-Inf-Lat-Vent" for left. However, from an anatomical perspective, I am interested in obtaining the results for the four parts of the lateral ventricle separately: the anterior horn, central part, posterior horn, and inferior horn. I understand that the "Left-Inf-Lat-Vent" might correspond to the inferior horn. Is FreeSurfer capable of providing the segmentation for the lateral ventricle in these specific sub-regions? If not, could you recommend any method or workaround that would allow me to obtain these detailed segmentations? Additionally, if it is not possible to directly obtain these sub-regional volumes, is there a way to derive the ventricle volumes within each lobe (e.g., frontal, parietal, occipital, temporal) using FreeSurfer or any other tool? Your assistance in this matter would be greatly appreciated. Thank you for your time and support. Best regards, Necati Emre Sahin.

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(no subject)
by Matthew Lynch 17 Sep '24

17 Sep '24

External Email - Use Caution I run this command: mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test and it fails with the following (partial) error message: Node: 'model_3/unet_conv_downarm_0_0/Conv3D' DNN library is not found. which I assume means it cannot access the appropriate the CuDNN library. I have installed GPU: nvidia geforce RTX 3050 Ti (4Gb) WSL2 Linux kernel: 5.15.153.1-microsoft-standard-WSL2 (after recent wsl --update) CUDA Version 12.6 Windows Nvidia Driver version 560.94 CuDNN Version 9.4.0 installed in WSL, with libraries located in /lib/x86_64-linux-gnu However, freesurfer's tensorflow seems to point to its own cudnn libraries in: /usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/nvidia/cudnn/lib including libcudnn.so.8 which I assume is CuDNN version 8, and may not be compatible with CUDA 12.6? Is there a way I can get freesurfer's script to use the CuDNN 9.4.0 that are installed globally on the WSL system? Any other suggestions on what might be causing this error and how to fix it?

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Hippocampus Subfields Stats (FreeSurfer v7.3.2)
by Boa Sorte Silva, Narlon 16 Sep '24

16 Sep '24

Hi there, I have searched the archive and couldn't find information relating to this issue. I am running longitudinal analysis in FreeSurfer v7.3.2 in and using the segmentHA_T1_long.sh. The subfields segmentation works as expected, however the stats files are outputted to the “mri" folder instead of to the “stats" folder. Consequently, the attempts at concatenating these files using “asegstats2table” or “ConcatenateSubregionsResults.sh” won’t work. I was able to get around the issue of concatenation using a customized script. My question is whether there are any concerns with the outputs for this version that I should be aware of? Or should I trust that the stats outputs are correct, despite being in the “mri” instead of “stats” folder? I also noticed that the Wiki shows examples with files tagged as “v21”, while the version I am using outputs “v22” text files. Please find attached is a sample log file for a participant with details about OS etc. These are the files listed in the “mri" folder: Text files: lh.amygNucVolumes-T1.long.v22.txt lh.hippoSfVolumes-T1.long.v22.txt rh.amygNucVolumes-T1.long.v22.txt rh.hippoSfVolumes-T1.long.v22.txt Volumes: lh.hippoAmygLabels-T1.long.v22.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.CA.mgz lh.hippoAmygLabels-T1.long.v22.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.FS60.mgz lh.hippoAmygLabels-T1.long.v22.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.HBT.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.HBT.mgz lh.hippoAmygLabels-T1.long.v22.mgz rh.hippoAmygLabels-T1.long.v22.CA.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.CA.mgz rh.hippoAmygLabels-T1.long.v22.FS60.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.FS60.mgz rh.hippoAmygLabels-T1.long.v22.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.HBT.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.HBT.mgz rh.hippoAmygLabels-T1.long.v22.mgz Thanks for your help! Nárlon External Email - Use Caution

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using easy_reg to build unbiased template: separating linear and non linear components
by Joshua K Lee 16 Sep '24

16 Sep '24

External Email - Use Caution apologies if this is a duplicate, I seem to be having some trouble with the listserv. [cid:5208cb3b-161c-4601-9f9c-1dd8840a03da] I've really impressed with mri_easy_reg and I was hoping to use it in a similar way as ANTs built_template scripts, which requires separation of affine from nonlinear transforms for their unbiased template updating algorithm. However, mri_easy_reg only returns a single transform object, combining affine and nonlinear components. I added an argument as an option for producing separate transforms ``` def main(): parser.add_argument("--separate_transforms", default=None, help="(optional) Produce Affine and NonLinear Fields Separately, if 'a' produce combined transform too. If 'b', do not produce combined transform") ``` then include ``` if args.separate_transforms is not None: sepAII3 = II2 sepAJJ3 = JJ2 sepAKK3 = KK2 sepAaffine = torch.tensor(np.matmul(Mflo, atlas_aff), device='cpu') sepARAS_X = affine[0, 0] * sepAII3 + affine[0, 1] * sepAJJ3 + affine[0, 2] * sepAKK3 + affine[0, 3] sepARAS_Y = affine[1, 0] * sepAII3 + affine[1, 1] * sepAJJ3 + affine[1, 2] * sepAKK3 + affine[1, 3] sepARAS_Z = affine[2, 0] * sepAII3 + affine[2, 1] * sepAJJ3 + affine[2, 2] * sepAKK3 + affine[2, 3] ``` and ``` if args.separate_transforms is not None: #create separate nonlinear naked field ndepth, nheight, nwidth, _ = f2r_field.shape # Create meshgrid indices for each dimension nII, nJJ, nKK = np.meshgrid(np.arange(ndepth), np.arange(nheight), np.arange(nwidth), indexing='ij') # Convert numpy arrays to PyTorch tensors nII2 = torch.tensor(nII, dtype=torch.float32, device='cpu') # or device='cuda' if using GPU nJJ2 = torch.tensor(nJJ, dtype=torch.float32, device='cpu') nKK2 = torch.tensor(nKK, dtype=torch.float32, device='cpu') # Now use these tensors as inputs to your interpolation function nFIELD = fast_3D_interp_field_torch(f2r_field, nII2, nJJ2, nKK2) nII3 = nII2 + nFIELD[:, :, :, 0] nJJ3 = nJJ2 + nFIELD[:, :, :, 1] nKK3 = nKK2 + nFIELD[:, :, :, 2] ``` ``` and saves them if args.separate_transforms is not None: print("args.separate_transforms is not None") # Correctly combine the prefix with the filename fwd_field_dir = os.path.dirname(args.fwd_field) fwd_field_basename = os.path.basename(args.fwd_field) nonlinear_fwd_field = os.path.join(fwd_field_dir, nonlinear_prefix + fwd_field_basename) print(f" Saving nonlinear field to: {nonlinear_fwd_field}") try: nonlinear_field = torch.stack([nII3, nJJ3, nKK3], axis=-1) print(f" Nonlinear field shape: {nonlinear_field.shape}") save_volume(nonlinear_field, Raff, Rh, nonlinear_fwd_field, n_dims=3) print(" Nonlinear field saved successfully") except Exception as e: print(f" Error saving nonlinear field: {str(e)}") # Do the same for the affine field affine_fwd_field = os.path.join(fwd_field_dir, affine_prefix + fwd_field_basename) print(f" Saving affine field to: {affine_fwd_field}") try: save_volume(torch.stack([sepARAS_X, sepARAS_Y, sepARAS_Z], axis=-1), Raff, Rh, affine_fwd_field, n_dims=3) print(" Affine field saved successfully") except Exception as e: print(f" Error saving affine field: {str(e)}") ``` full python file attached. but it doesn't work. When I try applying them to floating image one at a time, the images go haywire. On the left is after applying the affine transform my code generated, on the right is applying the nonlinear transform onto the image on the left. Josh Lee Assistant Professional Researcher Department of Psychiatry and Behavioral Sciences University of California, MIND Institute jkilee(a)ucdavis.edu

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