Freesurfer July 2022

freesurfer@nmr.mgh.harvard.edu

90 participants
122 discussions

Passcode FreeSurfer 7.2.0
by Gomez,Julieth 12 Jul '22

12 Jul '22

External Email - Use Caution Hello Freesurfer family, Could you please share the passcode to unzip the folder for the following release: Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/19abC5jXMkA6x9Yd2W5e_hfVxltVss7cSjfS5uZCITfrgq…> ? I appreciate your help, >> Best regards, [cid:image001.png@01D89603.ED122FD0] Julieth Gómez Durán Ph.D. Student | Brain Mapping Lab J. Crayton Pruitt Family Department of Biomedical Engineering Herbert Wertheim College of Engineering University of Florida [Image result for phone icon](352) 226-6956

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I need pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Vinod 12 Jul '22

12 Jul '22

External Email - Use Caution When I try to open it asks for pass code. Can you please give me the pass code. Thanks

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Re: [Freesurfer] help troubleshooting lta_convert error
by fsbuild 12 Jul '22

12 Jul '22

External Email - Use Caution Hello Megan, The errors you list below usually result from running a version of Freesurfer that does not match the operating system you are using, i.e., it looks like you are trying to run the version built for Ubuntu linux, 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) … on a CentOS6 system, Description:    CentOS release 6.7 (Final) If you have admin privileges on your system, then I would try installing the Freesurfer 7.2.0 CentOS6 rpm file on your CentOS6 system, which you can download from, https://secure-web.cisco.com/1_TrIriXqcfLg6YdYhz-fK97TtRKLaLawhDUmlefqUI_U6… If you do not have admin privs to install the RPM, then you can download and expand the tar archive from,https://secure-web.cisco.com/1Fhw7EkvdlF04-nFWgMtF44HHWjdGMGEq_-VbJMp1… The Freesurfer 7.2.0 distributions available for each operating system are currently listed on this page, https://secure-web.cisco.com/1Sbf8V045U7e_z5ui8AhyYxoVSIwU0U2msh… - R. On Jul 1, 2022, at 13:32, Megan Schendel <mschendel(a)mrn.org> wrote:        External Email - Use Caution        Hi all,I had a working distribution on an old system a few weeks ago, but now I'm getting an error.  Can anyone offer any troubleshooting ideas?I am working on a shared server with a freesurfer distribution that I own.Here is some system info:[mschendel@earth scripts]$ lsb_release -aLSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarchDistributor ID: CentOSDescription:    CentOS release 6.7 (Final)Release:        6.7Codename:       FinalOn the command line, the error looks like this:lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by lta_convert)lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by lta_convert)lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by lta_convert)lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by lta_convert)The recon-all.log file contains the following:Fri Jul  1 11:08:24 MDT 2022cd /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all -all -i /export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm -s /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539 -openmp 8subjid M87124539setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysisFREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/Actual FREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurferbuild-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bLinux earth.mind.unm.edu 2.6.32-573.26.1.el6.x86_64 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linuxcputime      unlimitedfilesize     unlimiteddatasize     unlimitedstacksize    10240 kbytescoredumpsize 0 kbytesmemoryuse    unlimitedvmemoryuse   unlimiteddescriptors  1024memorylocked 64 kbytesmaxproc      unlimited########################################program versions used7.2.0 (freesurfer-linux-ubuntu18_x86_64-7..2.0-20210721-aa8f76b)ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?'MEG TechnicianPronouns: she/herThe Mind Research Network1101 Yale Blvd. NEAlbuquerque, New Mexico 87106_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Thalamus subnuclei ICC
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 11 Jul '22

11 Jul '22

External Email - Use Caution Hi, Can someone send me the full ICC for all of the thalamus subnuclei that are parcellated? Just want to have that ready if a reviewer asks. Thanks Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 10 Jul '22

10 Jul '22

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recon-all error: mri_cc
by cooperr1＠student.unimelb.edu.au 10 Jul '22

10 Jul '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all with the longitudinal stream, but one subject (out of >500) fails recon-all (I've re-started many times). The cross-sectional and base (i.e. steps 1 and 2 of the longitudinal processing) have completed successfully; it's this final step that has the error. It appears that the error lies in mri_cc. The final lines of the recon-all.log are below: #-------------------------------------- #@# CC Seg Wed Jun 29 14:56:47 AEST 2022 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta reading aseg from /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz error: No such file or directory error: mri_cc: volume /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz already has CC in it. Run with -force to reprocess (not recommended) @#@FSTIME 2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 21240 F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78 @#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78 Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022 Freesurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b (I have also attempted with version 7.1.0 with identical results) Platform: centos7_x86_64 Recon-all.log: attached. With thanks, Rebecca

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Cohen's D from selxavg3-sess output
by Caspar M. Schwiedrzik 10 Jul '22

10 Jul '22

External Email - Use Caution Hi! I would like to compute Cohen's D for individual subjects. I was wondering whether I can use the output from selxavg3-sess for this: ces./rstd Or does this only work with gamma and rstd after mri_glmfit? Thank you, Caspar

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Problem with sxconcat-sess
by Shapiro, Noah Lorenz 10 Jul '22

10 Jul '22

Hello, I am trying to concatenate my functional data with the following command (Ps: I am relatively new to FreeSurfer): sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right. I get an error that says the dof file cannot be found for my 26 scans in $SUBJECTS_DIR. However, running: find . -name "dof" The dof file was created for 12 scans. I used the same analysis pipeline for all the scans. I searched the mailing list, and haven't found anything that could help my problem. Any idea why the dof was not created for all scans? How can I create the dof for the remaining scans? Please let me know if you need further details. I am using Freesurfer version 6.0.0. Any help is very much appreciated. Please find the terminal output below. Best wishes, Noah actrumri[0]:RECONS$ echo $SUBJECTS_DIR /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right DMN_Right/PCC_Bold_R/log/isxconcat.log ERROR: cannot find /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof actrumri[0]:RECONS$ find . -name "dof" ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config -o DMN_Left DMN_Left/PCC_Bold_L/log/isxconcat.log ERROR: cannot find /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof actrumri[0]:RECONS$ find . -name "dof" ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof actrumri[0]:RECONS$

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Tksurfer Error
by Rachel Wagner 10 Jul '22

10 Jul '22

External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/pubsw/packages/tcltktixblt/current/lib/tix8.1 How can I fix this error? Thanks, Rachel

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mri_concat killed
by Benjamin Deck 10 Jul '22

10 Jul '22

External Email - Use Caution Hi there, I am attempting to concat a number of volume files that are filled cortical ribbons from a series of label files. My workflow is to take the following steps: *Convert overlay file to label file* mri_vol2label --i ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.mgh \ --id 1 \ --l ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label \ --surf ${sub} ${hemi} white \ --dilate 2 mri_label2label --srclabel ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label \ --s ${sub} \ --hemi ${hemi} \ --trglabel /${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \ --regmethod surface *Convert label to volume * mri_label2vol --label /${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \ --identity \ --fill-ribbon \ --subject ${sub} \ --hemi ${hemi} \ --o /${subDir}/${sub}/mri/li2019_vols/${hemi}.${netMaskName}_native.mgz *Finally concatenate the vols together* mri_concat --f rois.txt --o yeo2011_nat.mgz --sum ninputs = 104 Checking inputs nframestot = 104 Allocing output Done allocing Killed Not sure why this is being killed. OS: WSL2 Ubuntu FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Thanks for your help! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1YhK4K5F2roM94PXj8RhOckUkCKJ0E3EcVeEJ8IfNRgJUQ…> Virus-free. http://secure-web.cisco.com/1YLbrDWxmBkdEGq0tv_IFuOJQDM7x0wCDq8h35ylt8kjv2A… <https://secure-web.cisco.com/1MZHAAPhLAJ8ofUmsU3lV3kCeJvwetaDxZd4U6AuxDlSyz…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Freesurfer July 2022