Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

fixing/editing white matter surface
by Eszter Boros 12 Feb '25

12 Feb '25

External Email - Use Caution Dear FreeSurfer Team, We are editing some longitudinal data using FreeSurfer 7.4.1. I am not sure how to fix the following issue (see the attached pictures). The white surface (blue line) almost touches the pial surface because some of the voxels are "too bright" at the edge, so they were misidentified as white matter. [image: Screenshot 2025-01-21 at 1.21.23 PM.png] [image: Screenshot 2025-01-21 at 1.21.32 PM.png] Which volume should I edit to fix this? I was thinking about deleting these voxels from the brainmask but that might lead to excluding/deleting gray matter incorrectly. Or maybe I could delete these voxels from the white matter. I was also considering cloning some of the surrounding voxels somehow to make this area less bright. Thank you, Eszter

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Research assistant position in Saygin developmental cognitive neuroscience lab
by Saygin, Zeynep 12 Feb '25

12 Feb '25

External Email - Use Caution Dear all, I'm hiring a full-time research assistant. Please see below! The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab, to assist with neuroscience research on the functional and structural architecture of the human brain in adults and children. The Z-lab studies the functional and structural differentiation of the human brain across early development and adulthood, and the plasticity of the brain in response to disorders and injury (see zeynepsaygin.com<http://secure-web.cisco.com/1A2V5xdtHqXRu1gDDSeTV04TCxQd4vckqgNezvnXCa0sZPt…> for recent publications). Please apply here: https://secure-web.cisco.com/1vvbd5X9-X7GCmMuGs_iDiFVhsIfX4Mf46Xn-dbhGBLvBW… Review of applications will continue on a rolling basis until the position is filled. The target start date is July 2025 but this is negotiable. This is a 1-year position with the possibility for renewal contingent on performance and funding. The Project Coordinator will oversee and execute data collection for ongoing studies in the lab, hire and oversee undergraduate research assistants, manage administrative study materials, and help analyze study data. This position is an excellent opportunity for an enthusiastic individual looking to gain research experience on related topics (development, cognitive neuroscience, psychology, brain injury) before applying to graduate or medical school. Responsibilities will include: * Overseeing and executing recruitment and retention of infant, child, and adult participants, including for an ongoing NIH National Institute of Child Health and Development R01 * Overseeing and executing data collection (including neuroimaging & behavioral assessments & experiments) * Managing lab materials, including: preparing and managing IRB protocols, study protocols, training materials; conducting literature reviews; maintaining and supporting website and github pages (including updating with datasets and analysis scripts/software). * Working with lab members and collaborators to collect and analyze data; hiring and overseeing undergraduate research assistants; training new staff members on study protocols; organizing progress meetings; cultivating diverse, inclusive, and collaborative workplace. * Attending and presenting at research conferences and co-authoring manuscripts. REQUIRED QUALIFICATIONS: * Bachelor's degree (preferably in psychology, neuroscience, cognitive science or related field). * Exceptional interpersonal skills and cultural sensitivity for interacting with infants, children, and parents from diverse backgrounds. * Candidate must be able to travel for recruitment, meetings, and data collection. * Strong organizational and time management skills, motivation to learn new skills, and determination to achieve study enrollment targets. PREFERRED QUALIFICATIONS: * Previous experience interacting with infants or families from diverse backgrounds. * Previous research experience (working with human subjects data; behavioral or neuroimaging) and/or coding experience (e.g., MATLAB, Python, shell scripting). Interested individuals should contact saygin.3(a)osu.edu<mailto:saygin.3@osu.edu> with a CV and names of 2-3 references. -- Zeynep M. Saygin, Ph.D. (she/her) Associate Professor of Psychology & Neuroscience The Ohio State University 205 Psychology Bldg. 1835 Neil Ave Columbus, OH 43210 zlab<http://secure-web.cisco.com/1A2V5xdtHqXRu1gDDSeTV04TCxQd4vckqgNezvnXCa0sZPt…>

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Re: [Freesurfer] [EXTERNAL] Re: Recon-all error - release 8.0.0-beta
by fsbuild 11 Feb '25

11 Feb '25

External Email - Use Caution  OK, thanks for the quick feedback.  I did not see an attached log.  Maybe you could cut and paste the end or section with the error and forward it along so we can see the last few commands in the pipeline that ran. - R. On Feb 11, 2025, at 20:16, Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe(a)mayo.edu> wrote:        External Email - Use Caution        The recon-all was running for around an hour. But it fails again, but in different way (I think).Now the process advanced more. The error in the terminal is: Loading surf /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/sub-01/surf/lh.white.preaparcFound 0 label voxelsERROR: found no voxels matching id 1 ERROR:Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-MSEL02220 exited with ERRORS at Tue Feb 11 19:09:36 CST 2025 The error log is attached.   From: fsbuild <fsbuild(a)contbay.com> Date: Tuesday, February 11, 2025 at 17:44 To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-beta Hello Lupita, Although the 8.0.0 release has not yet been officially announced, you could try downloading it from the link listed below. I would first remove your existing beta install with, $ cd /Applications/freesurfer/8.0.0-beta$ sudo bash uninstall.sh… answer Y to uninstall ... Then download the package installer via this link and run it.https://secure-web.cisco.com/1bTPb6RNd1UFnPCoRK-ER5lb8yUI8XAd2gN-0eQQx3-… you should end up with /Applications/freesurfer/8.0.0 and use that for FREESURFER_HOME Please let us know if you run into any issues. - R On Feb 11, 2025, at 14:42, Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe(a)mayo.edu> wrote:         External Email - Use Caution         Good to know, I am waiting for the new release. Thank you, Lupita From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Date: Tuesday, February 11, 2025 at 13:38 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThe new version will be announced  in the next couple of days. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 2:31 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all error - release 8.0.0-beta         External Email - Use Caution        Hello Yujing, Thank you for your response. “There are no details of the error message in the log.” In the terminal the error message is:2 root error(s) found.  (0) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]                [[unet/unet_bn_down_0/FusedBatchNormV3/_16]]  (1) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]0 successful operations.0 derived errors ignored. [Op:__inference_predict_function_1146]ERROR:Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-01 exited with ERRORS at Tue Feb 11 13:12:04 CST 2025I can’t see any other information, Only the log that I attached in the las email and the info in the terminal.I attached the terminal text. Does your error look something like this?  (0) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]                [[unet/unet_merge_4/concat/_64]]  (1) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] Yes it is. If so, we fixed the error in the coming FS 8.0 release.Just I used this version, is there other release? How can I have the fixed release?<image001.png> Thank you, Lupita From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard..edu> Date: Tuesday, February 11, 2025 at 12:36 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThere are no details of the error message in the log. Does your error look something like this?  (0) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]                [[unet/unet_merge_4/concat/_64]]  (1) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] If so, we fixed the error in the coming FS 8.0 release. Yujing  From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 1:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error - release 8.0.0-beta         External Email - Use Caution        From: Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe(a)mayo.edu> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Recon-all error - release 8.0.0-betaHello FreeSurfer Developers, I'm attempting to run recon-all and recon-all-clinical, but it is the first time that I used this since I changed my MacBook. ERROR:Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81..4~3/RELEASE_ARM64_T6041 arm64recon-all -s sub-01 exited with ERRORS at Tue Feb 11 10:33:15 CST 2025 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: FreeSurfer version 8.0.0-beta MacOS X darwin_arm64 (64b) PKG installer 2) Platform: macOs Sequoia 15.3. Chip Apple M4 Max3) uname -a: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm644) recon-all.log: see attached Thank you so much, I really need to use recon-all to complete my project. Have a great day, Lupita_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1hSLlW0Tx4WU9rOAvjc2c5Hc9vZ2n6LY6Sxfx-6SykHA-_… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all error - release 8.0.0-beta
by fsbuild 11 Feb '25

11 Feb '25

External Email - Use Caution Hello Lupita, Although the 8.0.0 release has not yet been officially announced, you could try downloading it from the link listed below. I would first remove your existing beta install with, $ cd /Applications/freesurfer/8.0.0-beta$ sudo bash uninstall.sh… answer Y to uninstall ... Then download the package installer via this link and run it.https://secure-web.cisco.com/1gGVRcHPllNn9JWw3eUZMXCROYrPLvXC4ab7XhFI7Uw… you should end up with /Applications/freesurfer/8.0.0 and use that for FREESURFER_HOME Please let us know if you run into any issues. - R On Feb 11, 2025, at 14:42, Yanez-Ramos, Lupita <Yanez-Ramos..MariaGuadalupe(a)mayo.edu> wrote:        External Email - Use Caution        Good to know, I am waiting for the new release. Thank you, Lupita From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Date: Tuesday, February 11, 2025 at 13:38 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThe new version will be announced  in the next couple of days. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 2:31 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all error - release 8.0.0-beta         External Email - Use Caution        Hello Yujing, Thank you for your response. “There are no details of the error message in the log.” In the terminal the error message is:2 root error(s) found.  (0) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]                [[unet/unet_bn_down_0/FusedBatchNormV3/_16]]  (1) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]0 successful operations.0 derived errors ignored. [Op:__inference_predict_function_1146]ERROR:Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-01 exited with ERRORS at Tue Feb 11 13:12:04 CST 2025I can’t see any other information, Only the log that I attached in the las email and the info in the terminal.I attached the terminal text. Does your error look something like this?  (0) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]                [[unet/unet_merge_4/concat/_64]]  (1) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] Yes it is. If so, we fixed the error in the coming FS 8.0 release.Just I used this version, is there other release? How can I have the fixed release?<image001.png> Thank you, Lupita From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Date: Tuesday, February 11, 2025 at 12:36 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release 8.0.0-betaThere are no details of the error message in the log. Does your error look something like this?  (0) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]                [[unet/unet_merge_4/concat/_64]]  (1) INVALID_ARGUMENT:  input must be 4-dimensional[1,72,72,72,24]                [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] If so, we fixed the error in the coming FS 8.0 release. Yujing  From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yanez-Ramos, Lupita Sent: Tuesday, February 11, 2025 1:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error - release 8.0.0-beta         External Email - Use Caution        From: Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe(a)mayo.edu> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Recon-all error - release 8.0.0-betaHello FreeSurfer Developers, I'm attempting to run recon-all and recon-all-clinical, but it is the first time that I used this since I changed my MacBook. ERROR:Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64recon-all -s sub-01 exited with ERRORS at Tue Feb 11 10:33:15 CST 2025 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: FreeSurfer version 8.0.0-beta MacOS X darwin_arm64 (64b) PKG installer 2) Platform: macOs Sequoia 15..3. Chip Apple M4 Max3) uname -a: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm644) recon-all.log: see attached Thank you so much, I really need to use recon-all to complete my project. Have a great day, Lupita_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Recon-all error - release 8.0.0-beta
by Yanez-Ramos, Lupita 11 Feb '25

11 Feb '25

External Email - Use Caution From: Yanez-Ramos, Lupita <Yanez-Ramos.MariaGuadalupe(a)mayo.edu> Date: Tuesday, February 11, 2025 at 11:53 To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Recon-all error - release 8.0.0-beta Hello FreeSurfer Developers, I'm attempting to run recon-all and recon-all-clinical, but it is the first time that I used this since I changed my MacBook. ERROR: Darwin R5523400.local 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-01 exited with ERRORS at Tue Feb 11 10:33:15 CST 2025 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: FreeSurfer version 8.0.0-beta MacOS X darwin_arm64 (64b) PKG installer 2) Platform: macOs Sequoia 15.3. Chip Apple M4 Max 3) uname -a: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 4) recon-all.log: see attached Thank you so much, I really need to use recon-all to complete my project. Have a great day, Lupita

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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

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