Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

copy headers
by Aaron Tanenbaum 08 Jan '25

08 Jan '25

External Email - Use Caution Hello All, Is there a FreeSurfer tool that will copy header information from one image to the other with the same dimensions. I tried mri_copy_params but it did not change the whole header, notably fov, startz, and endz.

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Assistance with mri_vol2surf: Missing Surface Values in Output
by Pandey, Shraddha 08 Jan '25

08 Jan '25

External Email - Use Caution Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the mri_vol2surf tool. The process I am following is as follows: 1. I first create the registration file using bbregister with the following command: bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1 2. Here, the goal is to generate the .dat registration file. 3. Next, I use this .dat file in mri_vol2surf to generate the surface with the following command: mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface" The input MRI for the bbregister command is flash data, and the input volume for mri_vol2surf is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by mri_vol2surf contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards, Shraddha [cid:3033bc8c-0a28-47a6-aa01-2a43edc2a75b]

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Re: [Freesurfer] Compatibility with M4 processor?
by fsbuild 07 Jan '25

07 Jan '25

External Email - Use Caution  Please check it works to run the tensorflow package in the included freesurfer python distribution.  The steps to follow below are from using the 8.0.0 beta release installed on an M2 Mac with 32GB RAM running MacOS Sonoma (14.7.2). … run bash shell and setup the freesurfer environment ... % bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1eM-n7fMXyTM4YjRyi_nmd00sm5zT6-WOTucjerTe2ffqj… FREESURFER_HOME=/Applications/freesurfer/8.0.0-beta$ 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/8.0.0-beta/FSFAST_HOME       /Applications/freesurfer/8.0.0-beta//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/8.0.0-beta//subjectsMNI_DIR           /Applications/freesurfer/8.0.0-beta//mni … unless you installed something extra on the machine, there should only be a python3 installed on the system and it should not have a tensorflow package installed … $ which python$ which python2$ which python3/usr/bin/python3 … run the default python3 on the system interactively and check there is no tensorflow package there … $ python3Python 3.9.6 (default, May  7 2023, 23:32:44) [Clang 14.0.3 (clang-1403.0.22.14.1)] on darwinType "help", "copyright", "credits" or "license" for more information.>>> import tensorflowTraceback (most recent call last):  File "<stdin>", line 1, in <module>ModuleNotFoundError: No module named 'tensorflow'>>> ^D          <—— type Ctrl D to exit … check it works to import and run a test with tensorflow in the python provided with the freesurfer distribution - see attached test.py file to run on the command line … $ which fspython/Applications/freesurfer/8.0.0-beta//bin/fspython … run fspython interactively and check tensorflow is version 2..13.0 ... $ fspythonPython 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:05:16) [Clang 12.0.1 ] on darwinType "help", "copyright", "credits" or "license" for more information.>>> import sys, os>>> import tensorflow as tf>>> tf.__version__'2.13.0'>>> ^D          <—— type Ctrl D to exit … run the attached test.py script and check for output similar to what's listed below.  Your output may not be exactly the same but the important thing is for the script to exit with status=0 … $ fspython  test.py2025-01-07 21:45:14.349299: I metal_plugin/src/device/metal_device.cc:1154] Metal device set to: Apple M2 Pro2025-01-07 21:45:14.349321: I metal_plugin/src/device/metal_device.cc:296] systemMemory: 32.00 GB2025-01-07 21:45:14.349325: I metal_plugin/src/device/metal_device.cc:313] maxCacheSize: 10.67 GB2025-01-07 21:45:14.349366: I tensorflow/core/common_runtime/pluggable_device/pluggable_device_factory.cc:269] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 0 MB memory) -> physical PluggableDevice (device: 0, name: METAL, pci bus id: <undefined>)2025-01-07 21:45:14.383371: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:375] MLIR V1 optimization pass is not enabled2025-01-07 21:45:14.383950: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:114] Plugin optimizer for device_type GPU is enabled.30.0 …. check the returned status=0 … $ echo $?0 … If the above succeeded, then tensorflow should run and you should try your recon-all command again. But on MacOS for the 8.0.0 beta, you need to set the environment variable FS_ALLOW_DEEP in order for recon-all to work, $ export FS_ALLOW_DEEP=1… run your recon-all command again … - R. On Jan 7, 2025, at 18:29, Kayla Bohlke <Kayla.Bohlke(a)barrowneuro.org> wrote:        External Email - Use Caution        Yes, that is the version I used. From: fsbuild <fsbuild(a)contbay.com> Date: Tuesday, January 7, 2025 at 4:20 PM To: freesurfer@nmr.mgh.harvard..edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Compatibility with M4 processor? Did you try installing the arm64 package for Macs with M1-M4 processors from this download link ?https://secure-web.cisco.com/1OOjVZiPsB9ymKAm1p508oOzwSq06id_KmFFxJfnwRDtY7yETjt4qjMoo4la3FbCsg3Eiw3D8XwHzRDrgtlnToWusCsza8q79Xt29GHQQEAYNVGsd7HUJhWP08BwgZkFpQGbH2zMOWyYac5acakG9RkxDJcLefQ75OOXELtOC7eyzWy3CtZSAz3O8uj72xg-v_fI8Kogzo7Abbt1KGmT9UH2iO1PK4yV-H_O6SAeGzmfMHnhDIVOXuRxWb_qtLy5tDoVkkFsywHaC6juEvOcM-dHus0I9xR9_FWlMBidrhyOmpq9R2ahMP-xtSJM1BLEk7EZv3Bj5fW72QR6HifmNdA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0-beta%2Ffreesurfer-macOS-darwin_arm64-8.0.0-beta.pkgI would first uninstall what is already there with the provided script via the command, $ sudo bash $FREESURFER_HOME/uninstall.sh - R. On Jan 7, 2025, at 15:41, Kayla Bohlke <Kayla..Bohlke(a)barrowneuro.org> wrote:         External Email - Use Caution         Hello, I recently have been trying to use the 8.0.0-beta version on my mac which has an M4 processor. I have been trying to run recon-all but after a couple of minutes get the following error during the mri_synthseg function: “The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.” The TensorFlow package downloaded does not seem to be compatible the M4 processor, it seems to be only setup for Intel processors? Has anyone had this issue before and solved it? Would I be better off going back a version to the 7.4.1 release? Is FreeSurfer just not ready for M4? Thanks,Kayla_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Compatibility with M4 processor?
by fsbuild 07 Jan '25

07 Jan '25

External Email - Use Caution Did you try installing the arm64 package for Macs with M1-M4 processors from this download link ?https://secure-web.cisco.com/1X_XVMAbIa1yzB_jguZ1_dKOohNcA0wwvsGIH-tfCmHfXxmRA76ranongqarPBNSueDOO2DdEYaIzoFLmacl7xzC3-86hUcNikiXeLm2ISC2BsjDd6gj2Kkjvpct8Qpdm8I5QhyOFgr727zV6s23a8ig2tclH2IpR5r3jNgisXIYltT_gIaQfOtVMTeUrZ9jauZK6zgqllVaIROoWKatvBGLQ3NuirsiglYZ3Xu3Dga3yVpuNMlHbTnJ7dYyGj_USuI57gHkBSD_vk6SQhcptdXKCm348FRtf0JcfePtjd-RJLF4hRzbA5FDqYB85Oxcw1WAMOGYFsjzHCjW0WZVJVQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0-beta%2Ffreesurfer-macOS-darwin_arm64-8.0.0-beta.pkgI would first uninstall what is already there with the provided script via the command, $ sudo bash $FREESURFER_HOME/uninstall.sh - R. On Jan 7, 2025, at 15:41, Kayla Bohlke <Kayla.Bohlke(a)barrowneuro.org> wrote:        External Email - Use Caution        Hello, I recently have been trying to use the 8.0.0-beta version on my mac which has an M4 processor. I have been trying to run recon-all but after a couple of minutes get the following error during the mri_synthseg function: “The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.” The TensorFlow package downloaded does not seem to be compatible the M4 processor, it seems to be only setup for Intel processors? Has anyone had this issue before and solved it? Would I be better off going back a version to the 7.4.1 release? Is FreeSurfer just not ready for M4? Thanks,Kayla_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Compatibility with M4 processor?
by Kayla Bohlke 07 Jan '25

07 Jan '25

External Email - Use Caution Hello, I recently have been trying to use the 8.0.0-beta version on my mac which has an M4 processor. I have been trying to run recon-all but after a couple of minutes get the following error during the mri_synthseg function: “The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.” The TensorFlow package downloaded does not seem to be compatible the M4 processor, it seems to be only setup for Intel processors? Has anyone had this issue before and solved it? Would I be better off going back a version to the 7.4.1 release? Is FreeSurfer just not ready for M4? Thanks, Kayla

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Re: [Freesurfer] Fwd: LME pipeline for individual ROIs
by Diers, Kersten /DZNE 07 Jan '25

07 Jan '25

External Email - Use Caution Hello, I am not sure if there is a right or wrong here; personally, I'd do a single whole-brain analysis, and apply ROIs only as the very last step, correcting for multiple comparisons within each ROI and for the number of ROIs. I would not expect fundamental differences between this approach and your approach, though. FDR2 may be more sensitive than FDR, but not necessarily in all circumstances. Hope this helps, Kersten External Email - Use Caution Hello FreeSurfer experts, I am using a mass-univariate pipeline to assess cortical thickness changes longitudinally at a regional level (based on the D-K atlas), and have been following this thread: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1OH1IdmTmp1zegRFjxpfr0wXoZPd0LxA71jtB…<https://secure-web.cisco.com/1gfQ9eWAEqDZ3DGmI9NL7F2WPKbHBLsM60VyuP_LVR3dT1…>. My pipeline is set up so that lme_mass_fit, lme_mass_F, and lme_mass_FDR are all run independently in a for-loop for each individual ROI, rather than altogether. Is this correct? As well, would using FDR2 be more advantageous than FDR? Best, Daniel Bondi 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/1v1L_BCMivW3bCQUU9Uu8NHjxSCKVstRZIv84UcEfiz1t-… . 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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Neuroimaging Analyst Position at University of Seville
by PATRICIA POMBO SEGURA 07 Jan '25

07 Jan '25

External Email - Use Caution We’re hiring! 🚀 Are you passionate about neuroimaging, MRI, brain charts, or genetics? 📊🧠 * Join our research team at the Neuroimaging Lab, University of Seville, and work on "Resil-net: Resilience and vulnerability—from neural circuits to networks". 🌐✨ Resil-Net is a European project bringing together 6 research groups to explore how brain reorganization relates to vulnerability and resilience. Predoc and postdoc candidates will be considered! https://secure-web.cisco.com/1zve6DjfggQCRWhak2xSLQJiOa-i-Br7WUB4WQ-IGtvMoh… https://secure-web.cisco.com/12-gDglo7g1H8gccIBBRTxKETQjKjNfUl5FAq_nwB-DLW0… https://secure-web.cisco.com/1srEdi67CckI8YYhEok8zLTL4YWZyVb2kf3Iab3sQYMLUS… https://secure-web.cisco.com/1s2RdRBBD3pTutq7jv6nfU-ctalIdDqqcu2PO6O3utKciw…

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Re: [Freesurfer] Freesurfer Digest, Vol 251, Issue 6
by 黄月虹 06 Jan '25

06 Jan '25

External Email - Use Caution Thanks，please don't send emails！ > -----原始邮件----- > 发件人: freesurfer-request(a)nmr.mgh.harvard.edu > 发送时间:2025-01-06 22:12:15 (星期一) > 收件人: freesurfer(a)nmr.mgh.harvard.edu > 主题: Freesurfer Digest, Vol 251, Issue 6 > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_Bv… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: [ext] Re: Freeview crash (Tietze, Anna) > 2. How to Plot Surface with ROI Boundaries Using Harvard-Oxford > Brain Atlas? (Zeng, Xinglin) > 3. Re: [ext] Re: Freeview crash (Wang, Ruopeng) > 4. Re: [ext] Re: Freeview crash (Dicamillo, Robert) > 5. registration error (Ramesh Babu) > 6. Re: [External] Re: Assistance with mri_vol2surf: Missing > Surface Values in Output (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Jan 2025 20:58:14 +0000 > From: "Tietze, Anna" <anna.tietze(a)charite.de> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <89FA2C60-63FF-4959-8039-0724E56EF3CC(a)charite.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Ruopeng, > > It works with the app when I move the licence.txt! It doesn?t work from the terminal so far, but this helps a lot. Thank you very much! > > Best, Anna > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4(a)MGH.HARVARD.EDU> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Date: Friday, 3. January 2025 at 18:17 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > > I mean /Applications/freesurfer/license.txt. > > > On Jan 3, 2025, at 11:36 AM, Tietze, Anna <anna.tietze(a)charite.de<mailto:anna.tietze@charite.de>> wrote: > > > It?s there: > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) > Or do you mean /Applications/freesurfer/license.txt? > > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Im Auftrag von Wang, Ruopeng > Gesendet: Freitag, 3. Januar 2025 16:58 > An: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Betreff: Re: [Freesurfer] [ext] Re: Freeview crash > > To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data. > > On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze(a)charite.de<mailto:anna.tietze@charite.de>> wrote: > > External Email - Use Caution > Yes, I?ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent?sometimes I can load a file without any issues, but most of the time, it crashes in the same way. > I?ve this problem on two different Macs: > > * System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. > * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0. > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu<mailto:RWANG4@mgh.harvard.edu>> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 2. January 2025 at 19:04 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [ext] Re: [Freesurfer] Freeview crash > > Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze(a)charite.de<mailto:anna.tietze@charite.de>> wrote: > > > Hi, > > When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me? > > Operating system: Mac, Sonoma 14.7.1 > Fressurfer version 7.4.0 > XQuatz 2.8.5 > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) > environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh > > When I run the command freeview, the following message is given: > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Or trying to open a file: > freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Attached is a detailed error report. > > What did I overlook?? Thank you so much for help! > > Best, Anna > <problem report freeview.rtf> > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr…<https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34i…> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr…<https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQit…> > > <smime.p7s> External Email - Use Caution > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr… > 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/1C3Rm_EJQFroDFSeUXGwlWJGelS12bb9i0uJ0bBhV30bmw… <https://secure-web.cisco.com/1C3Rm_EJQFroDFSeUXGwlWJGelS12bb9i0uJ0bBhV30bmw… > EvnvCxt9TqD/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . > 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. > > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr… > > >

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registration error
by Ramesh Babu 06 Jan '25

06 Jan '25

External Email - Use Caution Hello, I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local subject space. For this, I want to generate a registration.dat file which will be used for registration with local subject image. But I am facing an issue which I pasted below. echo $SUBJECTS_DIR /usr/local/freesurfer/subjects bbregister --ss sample-001.mgz --mov /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz --reg registration_matrix.dat --init-fsl --dti ERROR: Flag --ss unrecognized. --ss sample-001.mgz --mov /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz --reg registration_matrix.dat --init-fsl --dti I tried with -s flag, but still the same error. Could you please provide me a solution? Regards Ramesh

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How to Plot Surface with ROI Boundaries Using Harvard-Oxford Brain Atlas?
by Zeng, Xinglin 06 Jan '25

06 Jan '25

External Email - Use Caution Dear Community, I am currently working on visualizing ROI boundaries on the brain surface using the Harvard-Oxford brain atlas. My goal is to generate a surface plot that overlays ROI boundaries from the atlas in a clear and accurate manner. I also tried visualizing in Freeview, connectome_workbench, and I could plot the surface but I was unable to plot the boundaries correctly. Specific challenges I’m facing: I don’t know how to combine the ROI boundaries with a functional surface overlay while keeping the boundaries visible. [image]<https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJF…> image800×330 95 KB<https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJF…> I would really appreciate any tips, example commands, or references to similar workflows. Thank you in advance for your help!

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