Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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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Regarding a problem in spatiotemporal linear mixed effects model analysis
by yildirim adalioglu 06 Nov '23

06 Nov '23

External Email - Use Caution To whom it may concern, Hello! We are currently trying to do a ST-LME (Spatiotemporal-LME) analysis based on bipolar disorder brain MRI images. We are having 2 problems: 1)In the lme_mass_fit_EMinit step, we get a warning that says matrix is singular, close to singular or badly scaled. 2)In the lme_mass_RgGrow step, it says "computing seeds" indefinitely and it never ends. We looked for people having similar problems, however we could not find a solution. Currently, we suspect that this may be due to the zeros in the columns of fs_read_Y('lh.thickness_sm10.mgh'). Do you happen to know the reasons of these problems? Thank you for your time. Sincerely,Yıldırım Adalıoğlu

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Longitudinal multimodal processing
by gabriel robert 04 Nov '23

04 Nov '23

External Email - Use Caution Dear experts in longitudinal neuroimaging We carefully read the papers about possible biases introduced by treating timepoints images differently (Reuter and Fischl NI 2011, for example) to estimate unbiased anatomical and functional changes of brain development in healthy individuals. We took good note that treating each time point independently would remove asymmetry biases at the cost of reduced power. In our project, we would like to analyze about 800 scans both 3DT1, diffusion (FA preprocessed with fsl TBSS) and functional task BOLD at 3 time points (14 years-old, 19 years-old and 23 years-old). Each time point scans are preprocessed individually and normalized to a specific group-based template at the corresponding time point (not a within-subject midpoint symmetric space) and to the standard MNI space. Our question: We'd like to use a home-made study-specific multimodal atlas to resample ROI BOLD mean contrasts and fractional anisotropy at each time point but this atlas is *based on the last time point only (23 years-old).* Does this situation fall into the 'asymmetry-induced bias in longitudinal processing' ? Our feeling is most probably yes but given the sample size this is likely to be marginal compared to the effect size and results would still be interpretable... ? Many thanks for time, interest and insight, Best wishes Gabriel

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Problem with mri_robust_register when using segmentThalamicNuclei.sh
by Xingyu Liu 02 Nov '23

02 Nov '23

External Email - Use Caution Dear freesurfer experts, I was trying to segment thalamic nuclei using segmentThalamicNuclei.sh after a preprocessing using fMRIPrep 23.1.4 with fs recon-all. But it turned out with an error regarding mri_robust_register. Log shown below. ------------------------------ PROCESSID 41966 PROCESSOR x86_64 OS Darwin ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin liu-imac 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:42:42 PDT 2023; root:xnu-10002.1.13~1/RELEASE_X86_64 x86_64 ------------------------------ freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 setenv SUBJECTS_DIR /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer cd /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer /Applications/freesurfer/7.4.1/bin/segmentThalamicNuclei.sh sub-01 /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer #-------------------------------------------- #@# Thalamic Nuclei processing Wed Oct 11 13:29:13 EDT 2023 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.4.1/MCRv97//runtime/maci64:/Applications/freesurfer/7.4.1/MCRv97//bin/maci64:/Applications/freesurfer/7.4.1/MCRv97//sys/os/maci64:/Applications/freesurfer/7.4.1/lib/gcc/lib: Registering imageDump.mgz to mask from ASEG /Applications/freesurfer/7.4.1/bin//fs_run_from_mcr /Applications/freesurfer/7.4.1/bin///mri_convert /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer/sub-01/tmp/THnuclei_v13_useTwoComponents_1_T1//THDEbinaryMask.mgz aux.mgz -odt float -vs 1 1 1 -rt nearest >/dev/null: Signal 127 mv: aux.mgz: No such file or directory /Applications/freesurfer/7.4.1/bin//fs_run_from_mcr /Applications/freesurfer/7.4.1/bin///mri_robust_register --mov imageDump.mgz --dst /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer/sub-01/tmp/THnuclei_v13_useTwoComponents_1_T1//THDEbinaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50 >/dev/null: Signal 127 Error using SegmentThalamicNuclei (line 249) Problem with mri_robust_register Darwin liu-imac 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:42:42 PDT 2023; root:xnu-10002.1.13~1/RELEASE_X86_64 x86_64 Thalamic nuclei exited with ERRORS at Wed Oct 11 13:29:23 EDT 2023 ------------------------------ Thank you very much for your help! Best, Xingyu

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FSPGR Recon All Error
by Massimo Valerio 02 Nov '23

02 Nov '23

External Email - Use Caution Il giorno dom 8 ott 2023 alle ore 16:58 Massimo Valerio < massimo.valerio(a)unito.it> ha scritto: > Hello FreeSurfer Developers, > > I'm attempting to compute the recon-all of my patient FSPGR (fast > spoiled gradient-echo) of three-dimensional MRI data > ERROR: mri_cc: no WM voxels found with norm > 40 -- check skull stripping > > > I've searched the list and no same 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-darwin-macOS-7.3.2-20220804-6354275 > 2) Platform: MacOs Ventura 13.6 > 3) uname -a: Darwin MacBook-Pro-di-Neuroland.fritz.box 22.6.0 Darwin > Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; > root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64 > 4) recon-all.log: see attached > > > Dott. Massimo VALERIO > > Neuropsichiatra Infantile > SSD Neurologia Pediatrica > Dipartimento di Patologia e Cura del Bambino Regina Margherita > A.O.U Citta della Salute e della Scienza della Citta di Torino > Presidio Ospedale Infantile Regina Margherita > Email: massimo.valerio(a)unito.it > > > <https://secure-web.cisco.com/1hGQ2Ktox86EwpKDERFOjsru_gSyhek2B23t1VWBMgvO6S…> Privo > di virus.http://secure-web.cisco.com/1OmCce9Gor4-SmaxBnuSXzDcrgpxIAHB9uE5V6KmR… > <https://secure-web.cisco.com/1hGQ2Ktox86EwpKDERFOjsru_gSyhek2B23t1VWBMgvO6S…> > <#m_-561044188468629674_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >

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