Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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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Visualizing brain features
by Banerjee, Tania 16 Sep '24

16 Sep '24

External Email - Use Caution Hello, I have a quick question regarding my pial analysis, which, after feature selection, includes regions such as lh_G_temp_sup-G_T_transv_area and lh_S_interm_prim-Jensen_area, among others. Is there a method or tool available to visualize these specific brain areas? If not, I would appreciate any guidance to locate these areas in a standard brain structure. Thank you, Tania Banerjee

2 1

mri_synthseg on Mac M3
by Valerian Altersberger 15 Sep '24

15 Sep '24

External Email - Use Caution Dear Freesurfer Community, I am new to using Freesurfer and obtained version 7.4.1 to try white and grey matter segmentation with the help of mri_synthseg. I am running it on an Apple M3 chip under Sonoma 14.5. However, if I try to run mri_synthseg I get the error “illegal instruction”. I also tried to run Freesurfer 7.4.1 in Docker using the x86 (amd64) architecture but when trying the command mri_synthseg I still receive the error “illegal instruction”. Also, opening the terminal using Rosetta did not change the outcome. I would very much appreciate your help and avice. Kind regards, Valerian Altersberger

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Re: [Freesurfer] Ongoing issue with Mac
by fsbuild 13 Sep '24

13 Sep '24

External Email - Use Caution I mistkamely put the .tgz archive for the Intel Mac instead of its ,pkg file in the red box in the screenshot. - R. On Sep 13, 2024, at 22:35, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         When you navigate in a browser to,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/- you choose to download the installer package for either an Intel processor Mac (freesurfer-macOS-darwin_x86_64-dev.pkg) or a Silicon Mac with an M1, M2, M3 chip (freesurfer-macOS-darwin_arm64-dev.pkg). My browser preferences are set to ask whether or not to download a file when clicking on a link (see screenshot).  You may not see that if your browser is set to block pop-up windows, or you might have some other setting blocking downloads, but I can download either package file.  Those files can be refreshed periodically, so you may have to reload the web page in your browser if you have not looked at it recently. But the link should always work. After you have downloaded the .pkg installer and clicked on it to install as described in the previous maill, you should check freeview can open an empty window from the terminal, i.e., don’t try to display and volumes or surfaces. You should see something like what’s listed below when setting up the freesurfer environment in the terminal window. $ bash$ export FREESURFER_HOME=/Applications/freesurfer/dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh———— freesurfer-macOS-darwin_x86_64-dev-20240909-9ca95c6 ————    <—— this is from the install of the Intel Mac .pkgSetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME.       /Applications/freesurfer/devFSFAST_HOME                /Applications/freesurfer/dev/fsfastFSF_OUTPUT_FORMAT    nii.gzSUBJECTS_DIR                 /Applications/freesurfer/dev/subjectsMNI_DIR                          /Applications/freesurfer/dev/mni $ which freeview/Applications/freesurfer/dev/bin/freeview$ freeview                                                       <—— this should open an empty freeview window If you get the empty window, then freeview is basically working. - R. On Sep 13, 2024, at 20:24, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:       External Email - Use Caution         Hello, I sent an email regarding issues with not being able to get the newest version (or any version, really) of freesurfer to run on my Mac due to the fact that no update can handle MacOS version 14.5. I just received another email from Henry that was sent to an individual having a similar issue, and the link for the download does not work for me yet again. I keep receiving messages that the server cannot be found. I can get the download onto my Mac, but every time I open an MRI, the program immediately crashes. Im not sure if there is another link to try or one with a server that can be found, but any help would be appreciated! Cheers, Alisha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard..edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <mac_pkg_download.png>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Ongoing issue with Mac
by fsbuild 13 Sep '24

13 Sep '24

External Email - Use Caution  When you navigate in a browser to,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/- you choose to download the installer package for either an Intel processor Mac (freesurfer-macOS-darwin_x86_64-dev.pkg) or a Silicon Mac with an M1, M2, M3 chip (freesurfer-macOS-darwin_arm64-dev.pkg). My browser preferences are set to ask whether or not to download a file when clicking on a link (see screenshot).  You may not see that if your browser is set to block pop-up windows, or you might have some other setting blocking downloads, but I can download either package file.  Those files can be refreshed periodically, so you may have to reload the web page in your browser if you have not looked at it recently. But the link should always work. After you have downloaded the .pkg installer and clicked on it to install as described in the previous maill, you should check freeview can open an empty window from the terminal, i.e., don’t try to display and volumes or surfaces. You should see something like what’s listed below when setting up the freesurfer environment in the terminal window. $ bash$ export FREESURFER_HOME=/Applications/freesurfer/dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh———— freesurfer-macOS-darwin_x86_64-dev-20240909-9ca95c6 ————    <—— this is from the install of the Intel Mac .pkgSetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME.       /Applications/freesurfer/devFSFAST_HOME                /Applications/freesurfer/dev/fsfastFSF_OUTPUT_FORMAT    nii.gzSUBJECTS_DIR                 /Applications/freesurfer/dev/subjectsMNI_DIR                          /Applications/freesurfer/dev/mni $ which freeview/Applications/freesurfer/dev/bin/freeview$ freeview                                                       <—— this should open an empty freeview window If you get the empty window, then freeview is basically working. - R. On Sep 13, 2024, at 20:24, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:       External Email - Use Caution         Hello, I sent an email regarding issues with not being able to get the newest version (or any version, really) of freesurfer to run on my Mac due to the fact that no update can handle MacOS version 14.5. I just received another email from Henry that was sent to an individual having a similar issue, and the link for the download does not work for me yet again. I keep receiving messages that the server cannot be found. I can get the download onto my Mac, but every time I open an MRI, the program immediately crashes. Im not sure if there is another link to try or one with a server that can be found, but any help would be appreciated! Cheers, Alisha _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Ongoing issue with Mac
by Alisha Davis 13 Sep '24

13 Sep '24

External Email - Use Caution Hello, I sent an email regarding issues with not being able to get the newest version (or any version, really) of freesurfer to run on my Mac due to the fact that no update can handle MacOS version 14.5. I just received another email from Henry that was sent to an individual having a similar issue, and the link for the download does not work for me yet again. I keep receiving messages that the server cannot be found. I can get the download onto my Mac, but every time I open an MRI, the program immediately crashes. Im not sure if there is another link to try or one with a server that can be found, but any help would be appreciated! Cheers, Alisha

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