Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

.lta vs .dat questions
by Corinna Bauer 08 Nov '23

08 Nov '23

External Email - Use Caution Hi all, Can someone please explain the difference between .lta and .dat and why the registration looks different using the two file types? If bbregister outputs were already checked and edited (if needed) using the .dat file, is there a way to convert it to .lta? Thanks Corinna

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TR: Issues at the "tailarach_avi" transformation step of recon-all
by Hensenne, Eva (Stud. FHML) 08 Nov '23

08 Nov '23

External Email - Use Caution ________________________________ De : Hensenne, Eva (Stud. FHML) <e.hensenne(a)student.maastrichtuniversity.nl> Envoyé : mercredi 18 octobre 2023 14:41 À : freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Objet : Issues at the "tailarach_avi" transformation step of recon-all Dear Freesurfer Developers, I am currently running recon-all on a UNI scan. This scan has already been partly preprocessed by a script called "presurfer". This presurfered scan should work with recon-all (and it indeed works for my colleagues). However, I have systematically an error when I try to run recon-all on those files. The error says: "talairach_avi log file is transforms/talairach_avi.log... Error:mpr2mni305 failed, see transforms/talairach_avi.log Command exited with non-zero status 1". I attached you the talairach_avi.log and the recon_all.log files. 1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Unbuntu 22.04 3. Recon-all.log: attached Best wishes, Eva Hensenne

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Atrophy Maps on Coronal Slices
by Daniel Gutstein 08 Nov '23

08 Nov '23

External Email - Use Caution Is there a methodology in FreeSurfer for creating atrophy maps and displaying them on individual coronal slices? Thank you. Daniel Gutstein Research Data Analyst Northwestern University | Mesulam Center for Cognitive Neurology & Alzheimer's Disease 300 E. Superior Street | Tarry 8-734 | Chicago, IL 60611 daniel.gutstein(a)northwestern.edu<mailto:daniel.gutstein@northwestern.edu> | (312) 503 - 8150

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Common space
by Alberto Del Cerro Leon 08 Nov '23

08 Nov '23

External Email - Use Caution Good morning, I would be interested in observing regional differences in cortical thickness without using predefined regions. However the results offered by FreeSurfer arrange the thickness results etc. in an individual space which is difficult to compare between subjects before labeling. Is there a possibility to transform the results to a common mesh (like a template) in order to perform an exploratory analysis?

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Re: [Freesurfer] Question about Freesurfer
by fsbuild 07 Nov '23

07 Nov '23

External Email - Use Caution  Hello Mahdi, If you have not already done so, you might want to look at the Freesurfer wiki notes about setting up an X-server on Windows so linux applications running in WSL can display graphics using X-windows, https://secure-web.cisco.com/1IeFJcAKROeUNyLVra8oNytGyzB-Wv…  The setup listed there is for Xming, and you may want to look at both https://secure-web.cisco.com/1yLpWBJBzFQsVnx0Ncp8u61K6nbDOQ5sj4Uh-OSMos9GTr… and https://secure-web.cisco.com/1STa8uko59yOcskM83ifwl-XKlLZOFpLQkufk… Some people have found Moba X-term, https://secure-web.cisco.com/1ZVDzOuRds29V2esWHXhtFh_3s3wsJpkW…, easier to setup and test with glxgears compared to using Xming. It’s a good idea to get glxgears to display the spinning gears in an X-Window before trying to run freeview.  Or the display of glxgears can work, but freeview may still display a black/empty screen.  That can be from the graphics card drivers on the Windows host not being up to date or not supporting more recent versions of OpenGL. There are also quite a few postings about WSL on the freesurfer list. - R. On Nov 6, 2023, at 13:48, Mahdi Babaei <mahdibabaii45(a)gmail.com> wrote:        External Email - Use Caution        Thanks for the reply.Yes, glxgears command shows a blank window. I thought about it but couldn't find any solution. I'm working on WSL2.Best,MahdiOn Mon, 6 Nov 2023 at 13:16, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:It sounds like an openGL rendering issue. If you run glxgears command, do you see a blank window or spinning 3D gears?RuopengOn Nov 6, 2023, at 12:37 PM, Mahdi Babaei <mahdibabaii45(a)gmail.com> wrote:        External Email - Use Caution        Hi Paul,Thank you for your response. There was an issue with my description. I meant to refer to volume data. Freeview is displaying a black view, even though it loads the images. Unfortunately, nothing is visible.Best,MahdiOn Mon, 6 Nov 2023 at 11:30, Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> wrote:Hi Mahdi,I'm afraid I don't know what you mean by "Freeview opens fine but when I load a column in it just shows a black view."  What is a column in this context?As for registration between PET and MR, have you seen this page?MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1b4i3XSSINjUpxeaKg1CHfqqMtsa2ceG8AjVCH… suggests using mri_coreg.-Paul________________________________________From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei <mahdibabaii45(a)gmail.com>Sent: Sunday, November 5, 2023 2:25 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Question about Freesurfer        External Email - Use CautionDear FreeSurfer Team,I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem?I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using "bbregister"?Best,Mahdi_______________________________________________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/1MCAKtn_s75TZkFBGhMXTat_hIXbOfBbmm_tXU… 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/1s-1yROthyASTYOEPOhUbdSsufwH8Q5W68Z1B2… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/18nCLLteOP_SSoW4LOIxK-u3wXW2qxGSVpBtQX…; ._______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1uiWS-E4J_tnwDtq54dNgKynd5kcqnIL8AMjMj… 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/1MCAKtn_s75TZkFBGhMXTat_hIXbOfBbmm_tXU… 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/12aHwOhQ0p9xeCDRZ-cjw3MgfDXIHbw_2ZKFhy… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/18nCLLteOP_SSoW4LOIxK-u3wXW2qxGSVpBtQX…; ._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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DPABI V8.0, DPABISurfSlurm and DPABI Harmonization module were released!
by YAN Chao-Gan 07 Nov '23

07 Nov '23

External Email - Use Caution Dear colleagues, We are pleased to announce the release of DPABI V8.0, DPABISurfSlurm and DPABI Harmonization module. New features of DPABI_V8.0_231111 (download at http://secure-web.cisco.com/1iu1Tns8hOQhPl_19d90nC0eQexs39Tq6UxLJzJ-WyJoYkl…, please also update the docker file by: docker pull cgyan/dpabi and docker pull cgyan/dpabifiber): 1. DPABI Harmonization module was released. This module could be used to harmonizing the brain images (.nii/.nii.gz/.gii/.mat) to remove site effects for big data in statistical analysis. Please read our latest Reference: Wang, Y.W., Chen, X., Yan, C.G. (2023). Comprehensive evaluation of harmonization on functional brain imaging for multisite data-fusion. Neuroimage, 274, 120089, doi:10.1016/j.neuroimage.2023.120089. 2. DPABISurf 3.0. 2.1. DPABISurfSlurm: High Performance Computing Version of DPABISurf was released. Please read here for how to use it: http://secure-web.cisco.com/1-s7rUQYmnIYW5KNs2c_2Ua6A5hfNaBoITZqssWTtvVB7Vl… 2.2. Back engine updated to fMRIPrep V23.1.4, thus using FreeSurfer 7.3.2. 2.3. Segment subregions (Thalamus, Hippocampus, Amygdala and Brainstem) with FreeSurfer 7.3.2 was set to the default option now. 2.4. Added freesurfer atlases: {DPABISurf}/SurfTemplates/fsaverage5_lh_aparc_a2009s_annot.label.gii and fsaverage5_lh_aparc_annot.label.gii. 2.5. Could make use of DPABI Harmonization module. 3. DPABIFiber 1.1. 3.1. Back engine updated to QSIPrep V0.19.1. 3.2. Could make use of DPABI Harmonization module. 4. DPABINet 1.3. 4.1. Could make use of DPABI Harmonization module. 5. Fixed a bug in handling surface correlation analysis in y_Correlation_Image.m. 6. Fixed a bug of "Brace indexing is not supported for variables of this type" in DPABI_TDA. Appendix: DPABISurfSlurm DPABISurfSlurm is a high performance computing version of DPABISurf! You can use it on High Performance Computing (HPC, or supercomputing) center. The only requirement is Singularity! 1. Download the DPABISurfSlurm scripts to ${DPABISurfSlurmDIR}: https://secure-web.cisco.com/1ZkUL0iquwMSl08IjP7ZjP5AJFpFNw60h7dS6F4Wh0mxJH… 2. Download the singularity files: singularity pull dpabisurfslurm.sif docker://cgyan/dpabisurfslurm:latest and singularity pull freesurfer.sif docker://cgyan/freesurfer:latest. Or download from here <https://secure-web.cisco.com/1pYMqkkakGcgkJdcGjMUIsEqDKg_pLi4R0SfGcrWlbO0E_…>. Place them in the directory under ${SingularityDIR}. 3. Prepare your data in BIDS format in the BIDS directory under ${DATADIR}. You should also have a subjects.txt under ${DATADIR}. E.g., BIDS subjects.txt sub-Sub001 sub-Sub002 sub-Sub003 4. In the *.slurm files under ${DPABISurfSlurmDIR}, you should revise this line: #SBATCH -p normal #指定分区名称 normal is the partition you will use by Slurm. Ask your HPC administrator for the partition name you can use, and then revise “normal” to that partition name. You may also need to revise this line to correctly load the singularity module, please confirm with your HPC administrator. module load singularity/3.8.0 5. Copy DPABISurf_runSlurm.sh and SetEnv.sh from ${DPABISurfSlurmDIR} to your ${DATADIR}. 6. In DPABISurf_runSlurm.sh, you should define: export DPABISurfSlurmDIR="/work1/yancg/Scripts/DPABISurfSlurm" # Should have the DPABISurfSlurm files export SetEnvScriptDir="/work1/yancg/Data/Test/Test" # Should have SetEnv.sh # You should also go into SetEnv.sh to define your parameters!!! export DATADIR="/work1/yancg/Data/Test/Test" # Should have BIDS and subjects.txt 7. In SetEnv.sh, you should define: export DATADIR="/work1/yancg/Data/Test/Test" # Should have BIDS and subjects.txt export SingularityDIR="/work1/yancg/Soft/Singularity" # Should have dpabisurfslurm.sif. You can get it by singularity pull dpabisurfslurm.sif docker://cgyan/dpabisurfslurm:latest # Should have freesurfer.sif. You can get it by singularity pull freesurfer.sif docker://cgyan/freesurfer:latest export FreeSurferLicenseDIR="/work1/yancg/Soft/FreeSurferLicense" # Should have license.txt from FreeSurfer export RemoveFirstTimePoints="5" # Set up Number of time points needs to be removed export FunctionalSessionNumber="1" # Set up Number of Functional Sessions 8. Make a directory to save the log files under ${DATADIR} and cd to that directory. 9. source ../DPABISurf_runSlurm.sh. Submit your tasks! You can use squeue to check the status of running. 10. You will have all you want at ${DATADIR}/ResultsOrganized.tar.gz. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://secure-web.cisco.com/17VG5K3SI6ILdFFVqh0kzYbEF2O8UWDst5GyZx7oHeZTsvJ…>DPABI <http://secure-web.cisco.com/1Eua9pEq7RjI9OcbYSvyH9LGrVr5gJ5z_MysSjEcFNcuCbH…> <http://secure-web.cisco.com/17VG5K3SI6ILdFFVqh0kzYbEF2O8UWDst5GyZx7oHeZTsvJ…>, DPABISurf, <http://secure-web.cisco.com/19banVnArMBqoyFesUK6AIRWsVtmEfSbUXNuMmpa87BuRYx…>DPARSF <http://secure-web.cisco.com/17VG5K3SI6ILdFFVqh0kzYbEF2O8UWDst5GyZx7oHeZTsvJ…>, and The R-fMRI Network <http://secure-web.cisco.com/1vrRUKqL9BL9BG9wLl3HS-Gjd9BOWUTvE7BI7cA29sIrtl6…> ( RFMRI.ORG <http://secure-web.cisco.com/1Nlq2jr8swQKyYnhHOKmH1gCgpuV0mmVcXDW7gtZWbbbk0t…>) http://secure-web.cisco.com/1oPEXjqNco3J38IwZjsV0t80beCkUZ3KPVkIZOA8H2QPrMV… http://secure-web.cisco.com/1TDEJuaEuUUcKnGFp1_wijv_lgb6goWKjdyufACF9aP5YuH…

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FIPS compliant license file
by Huang, Yujing 06 Nov '23

06 Nov '23

Hi, We recently changed the Freesurfer license key encryption algorithm in our dev version to be FIPS compliant. If you have FIPS enabled machines, we would like to ask you to help us testing it, 1. download/install latest the dev version (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/) 2. request a new license file in 5-line format (https://surfer.nmr.mgh.harvard.edu/registration.html) 3. set FREESURFER_HOME to the install directory 4. set FS_LICENSE to the new license file 5. run 'mri_info <some image> --voxel 0 0 0' Older license files (4-line format) continue to work. The new 5-line license file will also work with previous releases. Do not replace your existing Freesurfer installation with this development build; this build is for FIPS testing purposes and has not been tested like stable releases. The FIPS changes will be incorporated into the next Freesurfer release. Let us know of any questions. Best, Freesurfer Team.

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Please remove my email from the list
by Jagruti Patel 06 Nov '23

06 Nov '23

External Email - Use Caution Hello, Please remove my email from Freesurfer list: *jagruti90(a)gmail.com <jagruti90(a)gmail.com>* Regards, Jagruti

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Please remove my email from the list
by Hânieh Mohammadi 06 Nov '23

06 Nov '23

External Email - Use Caution Hello, Please remove my email from Freesurfer list: hanieh.bme(a)gmail.com Regards, Hanieh -------------------------------- Hânieh Mohammadi , Ph.D (she/her) Postdoctoral researcher in Biomedical Engineering EPIC Center of the Montreal Heart Institute 5055 Rue Saint-Zotique, Montreal, Quebec H1T 1N6

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Question about Freesurfer
by Mahdi Babaei 06 Nov '23

06 Nov '23

External Email - Use Caution Dear FreeSurfer Team, I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem? I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using " bbregister"? Best, Mahdi

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Freesurfer November 2023