Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30129 discussions

Re: [Freesurfer] mri_synthSR on a virtual machine. Graph execution error
by fsbuild 08 Feb '25

08 Feb '25

External Email - Use Caution  I would try using the recent freesurfer 8.0.0 beta release package installer which you can download from, https://secure-web.cisco.com/1v5XAdUiYIVEywZIISJkv2IIJr0bRqNKwWZFAR92C5eeuq… The links for those are at the top of the page. I would first uninstall the current freesurfer package, e.g. $ sudo apt remove freesurfer .... and then install the .deb package for the 8.0.0 beta release - R. On 2/7/25 03:27, Zito Giuseppe (giuseppe.zito(a)paraplegie.ch) wrote:         External Email - Use Caution         Dear experts,   I just installed freesurfer on a windows virtual machine. It is a windows virtual machine, in the sense that I have a windows machine, on which is installed a virtual windows machine, in which is installed Ubuntu with WSL2 (nested virtual machine). I have then installed FreeSurfer by following the instructions on this page FS7_wsl_ubuntu - Free Surfer Wiki   When I tried to use mri_synthsr to convert a Flair image into a T1, I get the following error. No T1 file is then generated. Does anyone have an idea of what could go have gone wrong?   Thank you very much, Giuseppe   My command line mri_synthsr --i 3D_FLAIR.nii --o 3D_T1converted.nii     Output from the software Using general model from January 2023 (version 2) /usr/local/freesurfer/7.4.1/models/synthsr_v20_230130.h5 using 1 thread predicting 1/1 Prediction without flipping   the following problem occured when predicting output for image /mnt/c/AIR_Software/SynthSR/3D_FLAIR.nii : Graph execution error:   Detected at node 'unet/unet_merge_8/concat' defined at (most recent call last):     File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 1227, in <module>       main()     File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 88, in main       predict(     File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 151, in predict       pred1 = np.squeeze(net.predict(image))     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler       return fn(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2382, in predict       tmp_batch_outputs = self.predict_function(iterator)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2169, in predict_function       return step_function(self, iterator)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2155, in step_function       outputs = model.distribute_strategy.run(run_step, args=(data,))     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2143, in run_step       outputs = model.predict_step(data)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2111, in predict_step       return self(x, training=False)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler       return fn(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 558, in __call__       return super().__call__(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler       return fn(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__       outputs = call_fn(inputs, *args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler       return fn(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/functional.py", line 512, in call       return self._run_internal_graph(inputs, training=training, mask=mask)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/functional.py", line 669, in _run_internal_graph       outputs = node.layer(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler       return fn(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__       outputs = call_fn(inputs, *args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler       return fn(*args, **kwargs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/layers/merging/base_merge.py", line 196, in call       return self._merge_function(inputs)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/layers/merging/concatenate.py", line 134, in _merge_function       return backend.concatenate(inputs, axis=self.axis)     File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/backend.py", line 3581, in concatenate       return tf.concat([to_dense(x) for x in tensors], axis) Node: 'unet/unet_merge_8/concat' OOM when allocating tensor with shape[1,192,256,256,72] and type float on /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu          [[{{node unet/unet_merge_8/concat}}]] Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info. This isn't available when running in Eager mode. [Op:__inference_predict_function_2117]   resuming program execution   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1MclApZSk9sjn4ROiQE-j_E5ZWBtCVot54njMy9BF_jS3G… 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/1nErkJ5uaRkwjymT0wW_gYlu9rc3nZmn3vqO7G0vu_ZiwM… <https://secure-web.cisco.com/1L9K25muKzdk2zS6tDY4-DhZ7Ff87PF5_uTSiOugetgh2jw17ElukrTLLEUbGu4GKHADXQg2DZ9Pyp5uMAcHTXj7F8sgziXgMMcpl_bPZgk4ONLNVOan-uF-vnGgS2xhhprmWbuOTrIR8WyqIFjG6mQC6drgpY_PqQdLNfpdLy9iURyFt_u1Q3ddkb1oj2IiKrqD2Dtbucy9DSN0S6sTYWaqkb3McKl6t9UmXQmfAmJ8VBIVajSEDYyAHFL4KkvMIf9lY9Ry_Wu_uFNZHgwKn8rHq9CHml_ZRs79HMhFo-jNXv1tk9ktdgK4fCVphgXeKP6illQwP8l5My0qG_-_Eog/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. 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Re: [Freesurfer] Problem with FreeSurfer 8.0
by fsbuild 07 Feb '25

07 Feb '25

External Email - Use Caution   Have you tried running freeview from the command line after setting up the environment? - R. $ export FREESURFER_HOME=/Applications/freesurfer/8.0.0-beta $ source $FREESURFER_HOME/SetUpFreeSurfer.sh .... then try running freeview without any arguments to check it opens an empty window ... $ freeview On 2/7/25 14:24, Sahil Bajaj (sahil.brain(a)gmail.com) wrote:         External Email - Use Caution         Greetings, I am trying to use the latest FreeSurfer version 8.0 (beta version) on my Mac Book Pro. But somehow I am struggling to resolve the following issue when I try to open FreeView. When I checked the FreeSurfer directory - I can see that /Applications/freesurfer/bin/freeview exists but /Applications/freesurfer/Freeview.app/Contents/MacOS/freeview: does not exist.. Any help would be greatly appreciated. Best, Sahil sbajaj@XJ6RDJF6Y9 ~ % export FREESURFER_HOME=/Applications/freesurfer  source $FREESURFER_HOME/SetUpFreeSurfer.sh  -------- freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer FSFAST_HOME       /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/subjects MNI_DIR           /Applications/freesurfer/mni FSL_DIR           /Users/sbajaj/fsl sbajaj@XJ6RDJF6Y9 ~ % freeview & [1] 15056  /Applications/freesurfer/bin/freeview: line 2: /Applications/freesurfer/Freeview.app/Contents/MacOS/freeview: No such file or directory _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1gXDVdC-uo76VCgZjMTGoXYmkO-vhDL2daaqcrdfrGJESP… 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/1nBhwOq4-b4wTkpXe5R_C3IR8MS_FVpkNPu8mQY4GCKGY6… <https://secure-web.cisco.com/18eF4_RBcos-H0-vARQaECITiLJ_CS7wKyWW8ti2L6NxGAd7ZyIQAAZOG0EkZhfs0kRZzoDZKipoVOyMfJhoic17dGPtBlt3r5lTSxZJpjKDEQkIEus4kWKjwn-xtu9s16dsGWPv2e5TfIsKOT69YGjDdwTJwqM1gnvyut_DK3zaeQiUXy3bV9YqoGQVlswlkDJj_Ny5fcZdugS5CrIvKxPqcpvSNnB4jDo1S2WwyUnKmO3t_P5d2IxUX5w9U59ggx68Q7-4KALpRVltEoaY2obZvihyu4gzIH1MeplTr7ORXy4wXgnE0kJyebJbRQ-Hplc0cTdKSBjdMGt-Ms9OnPw/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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Problem with FreeSurfer 8.0
by Sahil Bajaj 07 Feb '25

07 Feb '25

External Email - Use Caution Greetings, I am trying to use the latest FreeSurfer version 8.0 (beta version) on my Mac Book Pro. But somehow I am struggling to resolve the following issue when I try to open FreeView. When I checked the FreeSurfer directory - I can see that /Applications/freesurfer/bin/freeview exists but /Applications/freesurfer/Freeview.app/Contents/MacOS/freeview: does not exist. Any help would be greatly appreciated. Best, Sahil sbajaj@XJ6RDJF6Y9 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Users/sbajaj/fsl sbajaj@XJ6RDJF6Y9 ~ % freeview & [1] 15056 /Applications/freesurfer/bin/freeview: line 2: /Applications/freesurfer/Freeview.app/Contents/MacOS/freeview: No such file or directory

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mris_pmake for calculating surface distances between peak vertices and creating vertex ROIs
by Fanton, Silvia 07 Feb '25

07 Feb '25

Dear FreeSurfer experts, I am reaching out to kindly ask for some clarification on how to set up mris_pmake to achieve the following: 1. Calculate the distance between pairs of peak vertices on the inflated fsaverage surface using the Dijkstra's algorithm 2. Create fixed-radius ROIs around peak vertices to plot them on the inflated fsaverage surface in Freeview After reviewing the FreeSurfer mail archive, I understand that mris_pmake should be able to address both tasks. However, I am finding the argument structure a bit challenging to interpret. For point 1), would the following command be appropriate? mris_pmake --subj fsaverage --hemi lh --surface inflated --mpmOverlay distance --mpmProg pathFind --mpmArgs vertexStart:{start_vertex},vertexEnd:{end_vertex} Could you please elaborate on the available options in mris_pmake, particularly in relation to --mpmOverlay and --mpmProg? For example, I have noticed that the total path cost remains unchanged whether I use “distance” or “euclidean” in –mpmOverlay. As for point 2), could you please provide some guidance on how to set up mris_pmake? Or, more simply, would it be possible to save a number of peak vertices and plot them on the inflated fsaverage surface in Freeview.? I am using FreeSurfer version 7.1.1. Thank you in advance for your time, Silvia

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mri_synthSR on a virtual machine. Graph execution error
by Zito Giuseppe 07 Feb '25

07 Feb '25

External Email - Use Caution Dear experts, I just installed freesurfer on a windows virtual machine. It is a windows virtual machine, in the sense that I have a windows machine, on which is installed a virtual windows machine, in which is installed Ubuntu with WSL2 (nested virtual machine). I have then installed FreeSurfer by following the instructions on this page FS7_wsl_ubuntu - Free Surfer Wiki<https://secure-web.cisco.com/12twtudy3gB_NJlsrHFZDE-M9SwSDMGFINdPbZcIDLWt1E…> When I tried to use mri_synthsr to convert a Flair image into a T1, I get the following error. No T1 file is then generated. Does anyone have an idea of what could go have gone wrong? Thank you very much, Giuseppe My command line mri_synthsr --i 3D_FLAIR.nii --o 3D_T1converted.nii Output from the software Using general model from January 2023 (version 2) /usr/local/freesurfer/7.4.1/models/synthsr_v20_230130.h5 using 1 thread predicting 1/1 Prediction without flipping the following problem occured when predicting output for image /mnt/c/AIR_Software/SynthSR/3D_FLAIR.nii : Graph execution error: Detected at node 'unet/unet_merge_8/concat' defined at (most recent call last): File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 1227, in <module> main() File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 88, in main predict( File "/usr/local/freesurfer/7.4.1/python/scripts/mri_synthsr", line 151, in predict pred1 = np.squeeze(net.predict(image)) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2382, in predict tmp_batch_outputs = self.predict_function(iterator) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2169, in predict_function return step_function(self, iterator) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2155, in step_function outputs = model.distribute_strategy.run(run_step, args=(data,)) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2143, in run_step outputs = model.predict_step(data) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 2111, in predict_step return self(x, training=False) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/training.py", line 558, in __call__ return super().__call__(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/functional.py", line 512, in call return self._run_internal_graph(inputs, training=training, mask=mask) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/functional.py", line 669, in _run_internal_graph outputs = node.layer(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/layers/merging/base_merge.py", line 196, in call return self._merge_function(inputs) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/layers/merging/concatenate.py", line 134, in _merge_function return backend.concatenate(inputs, axis=self.axis) File "/usr/local/freesurfer/7.4.1/python/lib/python3.8/site-packages/keras/backend.py", line 3581, in concatenate return tf.concat([to_dense(x) for x in tensors], axis) Node: 'unet/unet_merge_8/concat' OOM when allocating tensor with shape[1,192,256,256,72] and type float on /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu [[{{node unet/unet_merge_8/concat}}]] Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info. This isn't available when running in Eager mode. [Op:__inference_predict_function_2117] resuming program execution

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Re: [Freesurfer] recon-all failed with FreeSurfer v8.0.0 (beta) on Mac
by fsbuild 06 Feb '25

06 Feb '25

External Email - Use Caution  The fix for the error you posted when running the 8.0.0 beta release - which has to do with how some python code is run - will be fixed in the forthcoming 8.0.0 release; it’s unrelated to your environment setup. The commands that run the recon-all pipeline in the 8.0.0-beta 2024 release have changed since the older 7.2.0 release from 2021, so 7.2.0 does not reproduce that error.  You could try setting the environment variable listed below on your 8.0.0-beta recon-all command line (bash shell example) to revert to the older recon-all behavior. $ export FS_V8_XOPTS=0 && recon-all <your arguments here> - R. On Feb 6, 2025, at 01:02, Lee Lin <lee.kevin.lin(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer developers, running the 8.0.0-betaRecently, I attempted to run FreeSurfer on my new work computer (MacBook Pro, Apple M3 Max, macOS 14.6). I found that v8.0.0 beta is the only compatible version, and the installation appeared to be successful. However, when running recon-all on my 7T anatomical data using the following command:recon-all -i <path_to_anatomy_nii_file> -s <subject_initials> -allI encountered an error during subcortical segmentation (see attached "7T_recon-all.log" and screenshots). It looks like the deep learning model used by mri_sclimbic_seg was reporting an input dimension mismatch.  To diagnose the issue, I tested the following possibilities:1. Is the error specific to this data?I ran recon-all on other 7T anatomical data, but the same error occurred.2. Is the error specific to 7T data?I tested recon-all with 3T data, but in this case, the process was killed even earlier, and no useful error message was provided (see "3T_recon-all.log"). I’m unsure whether these two issues are related..3. Is the issue related to the FreeSurfer version or my work environment?I ran recon-all on an older MacBook Pro (Apple M1, macOS 12.6) using FreeSurfer 7.2.0, and the process completed successfully. This suggests that the issue is specific to FreeSurfer v8.0.0 beta or my work environment rather than the dataset itself. Do you have any suggestions on this issue? Additionally, I noticed that FreeSurfer v8.0.0 beta uses a deep learning model for segmentation, which differs from previous versions. Is there a way to switch back to the traditional segmentation method? I would greatly appreciate any insights or troubleshooting suggestions. Best regards,Lee Lin<7T_recon-all.log><7T_recon-all_error-msg2.png><7T_recon-all_error-msg1.png><3T_recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1vJ3hkJcbeBmkSfHBn3idEPYXvTCSXvkeUXnJa1D_GXnUv…

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recon-all failed with FreeSurfer v8.0.0 on Mac
by Lee Lin 06 Feb '25

06 Feb '25

External Email - Use Caution Dear FreeSurfer developers, Recently, I attempted to run FreeSurfer on my new work computer (MacBook Pro, Apple M3 Max, macOS 14.6). I found that v8.0.0 beta is the only compatible version, and the installation appeared to be successful. However, when running recon-all on my 7T anatomical data using the following command: recon-all -i <path_to_anatomy_nii_file> -s <subject_initials> -all I encountered an error during subcortical segmentation (see attached "7T_recon-all.log" and screenshots). It looks like the deep learning model used by mri_sclimbic_seg was reporting an input dimension mismatch. To diagnose the issue, I tested the following possibilities: 1. Is the error specific to this data? I ran recon-all on other 7T anatomical data, but the same error occurred. 2. Is the error specific to 7T data? I tested recon-all with 3T data, but in this case, the process was killed even earlier, and no useful error message was provided (see "3T_recon-all.log"). I’m unsure whether these two issues are related. 3. Is the issue related to the FreeSurfer version or my work environment? I ran recon-all on an older MacBook Pro (Apple M1, macOS 12.6) using FreeSurfer 7.2.0, and the process completed successfully. This suggests that the issue is specific to FreeSurfer v8.0.0 beta or my work environment rather than the dataset itself. Do you have any suggestions on this issue? Additionally, I noticed that FreeSurfer v8.0.0 beta uses a deep learning model for segmentation, which differs from previous versions. Is there a way to switch back to the traditional segmentation method? I would greatly appreciate any insights or troubleshooting suggestions. Best regards, Lee Lin

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Re: [Freesurfer] Regarding Freesurfer for Ubuntu 24.01
by fsbuild 05 Feb '25

05 Feb '25

External Email - Use Caution  We are aware that changes to the system libraries in Ubuntu 24 prevent installing packages that installed and ran fine in Ubuntu 22.  We hope to have a development build available for Ubuntu 24 in the near future.    Ubuntu 22.04 LTS was made generally available in April of 2022 with the standard 5 year support cycle from Canonical - which means it has support until 2027.   Some users will not be eager to switch to the latest version of an OS if for example they started processing their subjects on Ubuntu 22 given that upgrading to Ubuntu 24 could change their results. - R. On Feb 5, 2025, at 04:47, Debika Ghosh <debika.2023phd(a)iimu.ac.in> wrote:        External Email - Use Caution        Dear team, I need to use Freesurfer and I am on Ubuntu version 24.01. Since I could not find the specific installation file for this version of Ubuntu, I tried installing the .deb file for Ubuntu 22. The installation process is not working because it is showing somy dependency related error. Could you please suggest what can be done in such an instance? Best regards,Debika Ghosh  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1VTbjASPeJpyBz8jnUW5skvvU-7OQD1y4_18-nynPuMULa…

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Re: [Freesurfer] mri_TumorSynth: command not found
by fsbuild 05 Feb '25

05 Feb '25

External Email - Use Caution  I think that command is no longer/not supported and its wiki page is out of date; it has not been in any 7.X or 8.X  freesurfer distribution dating back to at least 2020. - R.On Feb 5, 2025, at 12:40, Zapaishchykova, Anna <azapaishchykova(a)bwh.harvard.edu> wrote:mri_TumorSynth

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Fw: mri_TumorSynth: command not found
by Zapaishchykova, Anna 05 Feb '25

05 Feb '25

Hi, Hope this email finds you well. Just wanted to report that https://surfer.nmr.mgh.harvard.edu/fswiki/TumorSynth package gets "mri_TumorSynth: command not found" on freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc and on 7.4 Best, Anna

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