Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Re: [Freesurfer] [EXTERNE-EMAIL] Re: mri_synthSR on a virtual machine. Graph execution error
by fsbuild 11 Feb '25

11 Feb '25

External Email - Use Caution Sorry I did not see this before, but the message OOM means that you are out of memory, i.e., you need to allocate more memory for WSL to use from the Windows host in order for tensor processing in mri_synthsr to work.  Offhand I don’t know how that is done in WSL, but I suggest that between physical and/or virtual RAM, you end up allocating at least 32G of memory to the WSL VM running Ubuntu Linux. -R. On Feb 8, 2025, at 05:06, Zito Giuseppe <giuseppe.zito(a)paraplegie.ch> wrote:        External Email - Use Caution        Thank you for your comment. I did as you suggested: I first uninstalled freesurfer 7.4.1 and then installed the beta 8.0.0.The installation was successful, but the problem remained, with the same error message. Does any other solution come to your mind? Thank you again,Giuseppe From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of fsbuild Sent: 08 February 2025 02:39 To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNE-EMAIL] Re: [Freesurfer] mri_synthSR on a virtual machine. Graph execution error EXTERNE-EMAIL: Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge! Es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist.         External Email - Use Caution         I would try using the recent freesurfer 8.0.0 beta release package installer which you can download from, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsThe 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 pageFS7_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 linemri_synthsr --i 3D_FLAIR.nii --o 3D_T1converted.nii  Output from the softwareUsing general model from January 2023 (version 2)/usr/local/freesurfer/7.4.1/models/synthsr_v20_230130.h5using 1 threadpredicting 1/1Prediction 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 listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1e_dlk8QpDQcLKIX3cR_GGivsdkQvQuH9fqBKaFLCcwSz_… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Z9AQ8J4gg14Kjd4uzB_Ir8UBZWXOB-eB5rgA8u3s5Q30u… <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Hd7SomgcnZFvBQG9usOUoyVt-08NStvVxwY55Qt6UMZEX…; .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.  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

convert aal3 into .annot file
by Vianney Salvi 10 Feb '25

10 Feb '25

External Email - Use Caution Dear all, To have the best use of freesurfer, I would like to convert the aal3 atlas ( [ https://secure-web.cisco.com/1Lqm9IW7wIlcxFf6HBv0-tMARacY0dOCxDHqgYcxMjc9ee… | https://secure-web.cisco.com/1Lqm9IW7wIlcxFf6HBv0-tMARacY0dOCxDHqgYcxMjc9ee… ] ) into an .annot file. This particular topic has already been answered in the archive: [ https://secure-web.cisco.com/1N6iTTI7fxUa9y78B1gTfYeDCfDE5qyKqLLwhgdQTdpja7… | https://secure-web.cisco.com/1N6iTTI7fxUa9y78B1gTfYeDCfDE5qyKqLLwhgdQTdpja7… ] Or in the Github: [ https://secure-web.cisco.com/1AIwRVtOcHlEGoAfLLunpFibQhBh4kbs13b_zeN2_tPumR… | https://secure-web.cisco.com/1AIwRVtOcHlEGoAfLLunpFibQhBh4kbs13b_zeN2_tPumR… ] However, I'm not used to that field and the documentation found online on the different functions to use isn't sufficient for me to achieve my goal. Is it possible to have a more detailed answer than the one already linked? Thank you in advance for the help, Kind regard -- Vianney Salvi Doctorant équipe MOCOCO, Laboratoire INCIA

1 0

Cortical Thickness Extraction after Dura Correction with Multi-echo MPRAGE
by KEITH JONES 10 Feb '25

10 Feb '25

External Email - Use Caution Hello Freesurfer experts, I am interested in using Freesurfer 7.3.2 to extract cortical thickness values from multi-echo MPRAGE data. I ran recon-all using the T1 RMS and T2 images, and then I ran dura correction using the four T1 echo images to create updated pial surfaces (examples of code below). Next, can I simply run -parcstats to extract the relevant stats from the newly created surfaces, or are there additional processing steps that are necessary? Thank you for the help! Example steps: *Step 1*: Run recon-all recon-all -subject ${SUBJECT} -i {$T1RMS} -sd ${OUTPUT} -mprage -3T -T2 ${T2} -T2pial -hires -threads 16 -all *Step 2*: Dura correction mris_make_surfaces -dura memprage_echo%d.mgz 4 -sdir ${OUTPUT} ${SUBJECT} ${HEMI} *Step 3*: Extract values from new surfaces?? recon-all -subject ${SUBJECT} -parcstats Sincerely, Keith Jones ------------ Keith G. Jones, Ph.D. Postdoctoral Researcher Laboratory of Dr. Robert C. Welsh Department of Psychiatry and Biobehavioral Sciences University of California, Los Angeles

1 0

Re: [Freesurfer] freeview runtime error...
by fsbuild 09 Feb '25

09 Feb '25

External Email - Use Caution  It would help if you provide some context as to:- which Ubuntu .deb installer you used, e.g., the 8.0.0 beta or 7.4.1 Ubuntu 22 installer- whether or not you are running Ubuntu in some kind of virtual machine (VM), WSL or alternately using a real linux box - R. On Feb 9, 2025, at 20:05, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi: I got the following error running freeview in Ubuntu: "freeviewThis 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, webgl, xcb."   How can I fix that?   Sincerely, Gonzalo M. Rojas-CostaAdjunct Assistant Professor School of Medicine Finis Terrae University MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qh5cU84qoB_gZ-A_E6QV8SKqTG0YBmW_ttbRN… MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1bH1OdvT7NGumjiKIXIMIVEMEByCvR1_DVhWEm… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1SqMs5q0s2tZZ_rfcieb1QF4xAGAsJ4KhrsrPi… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/162y-anbvb4bZDRn3EN9ooNJoSlv3SSGK6wOTkYfwYauxx…

1 0

Inquiry About Longitudinal Analysis Using recon-all-clinical.sh
by Taghizadeh Mortezaei, Nima 09 Feb '25

09 Feb '25

Dear FreeSurfer Community, I want to work on a longitudinal analysis with two time points (pre-treatment and post-treatment) and would like to follow the recommended longitudinal pipeline. However, I want to use recon-all-clinical.sh and I want to ask whether the commands and steps for recon-all-clinical.sh are the same as the standard recon-all longitudinal pipeline? Are there any modifications or additional considerations required when using this script for longitudinal processing? I appreciate any guidance or documentation references that could help with this analysis. Thank you for your time and support! Nima

1 0

freeview runtime error...
by Gonzalo Rojas Costa 09 Feb '25

09 Feb '25

External Email - Use Caution Hi: I got the following error running freeview in Ubuntu: "freeview 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, webgl, xcb." How can I fix that? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University https://secure-web.cisco.com/1jHtItZBI1_HqfTKY7dN3uKrfyZjRLbaS_jJP7o5sfFCRR… https://secure-web.cisco.com/1FWvFn1CGl1hRcv6f7o8rQ0IpiXo6UzMUs7uJLxAMMKv2Q… https://secure-web.cisco.com/19lYxQTvtqat9nHu19Y-dKiqfv2mFPEZxcWlxC8hqPlrKU…

1 0

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. 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.

2 1

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.

1 0

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

1 0

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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer