Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

DOSS Question
by WON JONG CHWA 20 Jul '21

20 Jul '21

External Email - Use Caution Dear FreeSurfer Experts, I have been having trouble with performing DOSS analyses with mri_glmfit. One of the groups in my sample is too small to be performed with DODS, but when I try to call the DOSS option in mri_glmfit, it returns the same error, saying that DODS is not possible with this sample. I even tried defining the design matrix manually using --X, but it returns the same error. mri_glmfit --glmdir lh.rate.CI.paired-diff.thickness.DOSS --y mgh/rates/lh.thickness-rate.stack.fwhm10.mgh --fsgd FSGD/CI_baselines/paired-diff-demean-CI.fsgd doss --surf fsaverage lh --C Contrasts/BMICorrelationCI_DOSS.mtx gdfRead(): reading FSGD/CI_baselines/paired-diff-demean-CI.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 BMIatBaseline -1.49788e-08 3.57667 1 AgeAtFirstTP -5.62933e-08 3.40434 Class Size and Means of each Continuous Variable 1 MaleNormal 26 -0.5852 0.2393 2 MaleCI 2 0.8115 2.2778 3 FemaleNormal 38 0.2564 -0.2749 4 FemaleCI 6 0.6414 -0.0556 ERROR: Class MaleCI has 2 members. With 2 variables and using DODS, you need at least 3 members If anyone has any ideas on how to go about this, that would be greatly appreciated. Thank you. William

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Re: [Freesurfer] Developer password
by fsbuild 20 Jul '21

20 Jul '21

External Email - Use Caution I’ll send the info to your private email shortly. - R. On Jul 19, 2021, at 07:07, Clemens M <cmielach(a)mailbox.org> wrote:        External Email - Use Caution        Dear Freesurfer Team,I am currently setting up freesurfer using the Ubuntu VM but I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you!Best,Clemens_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tenure research position in fMRI at ultra-high field, Neurospin, France
by Evelyn Eger 20 Jul '21

20 Jul '21

External Email - Use Caution Dear list members, A tenured researcher position for an MR scientist with focus on ultra-high-field fMRI is available at Neurospin (France’s advanced brain imaging center, located in the greater Paris area). The candidate should mainly help developing the applications of the center’s new 11.7 Tesla imaging system. Please see the attached job description for details on the ideal candidate’s profile. In case of interest, feel free to directly contact Nicolas Boulant (nicolas.boulant(a)cea.fr) with more specific questions. Thank you for your help in circulating this ad. Best regards, Evelyn Eger

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Announcing the new version of TRACULA, included in FreeSurfer 7.2
by Yendiki, Anastasia 20 Jul '21

20 Jul '21

Hi all - After a year of lockdown coding, and a couple more years of tireless work by the tract annotation team, we are pleased to share the new version of TRACULA. For a summary of new features see: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Of note, new protocols were developed for the manual annotation of 42 tracts, which you can see here: https://dmri.mgh.harvard.edu/tract-atlas/ These tracts were manually annotated on the bmax=10000, 512-direction data from our Connectom scanner and we now use them as training data for TRACULA, allowing it to reconstruct the same tracts automatically in much lower quality (e.g., b=1000, 32- or 64-direction) data. More details in Chiara Maffei's preprint: https://www.biorxiv.org/content/10.1101/2021.06.28.450265<https://www.biorxiv.org/content/10.1101/2021.06.28.450265v2> The tutorials and documentation have been updated to reflect this new version: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula I highly recommend skimming through the tutorial, even if you've used TRACULA in the past. A lot has changed in the configuration options, and there are some additional outputs that you can take advantage of. What we are missing is a new tutorial dataset that is compatible with this new version. That will have to wait until after our summer vacations 🙂 There is also ongoing work on adding more tracts, and more features to come in the future! In addition to Chiara and the tract annotation team (https://dmri.mgh.harvard.edu/tract-atlas/#acqknowledge) special thanks to Doug for his help integrating along-tract stats with the FreeSurfer statistical analysis tools, Ruopeng for the new visualization features for these along-tract stats in freeview, and Andrew for his patience with last-minute commit disasters... I hope everyone is having a great summer! Anastasia. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://scholar.harvard.edu/a-y

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Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 20 Jul '21

20 Jul '21

External Email - Use Caution While it does not currently work to change the default install path, that default install path for the .deb (and .rpm) 7.2.0 installer files is /usr/local/freesurfer/7.2.0 (which reads like the path you want to use). If you already have different releases under /usr/local/freesurfer/<rev> that are not rev=7.2.0, e.g. from using the tar files (as this is the first .deb package), then the packaging tools won’t know anything about them and should not touch them when installing 7.2.0.  Or apt install and apt remove will only affect /usr/local/freesurfer/7.2.0 with the freesurfer_7.2.0_amd64.deb package. Still looking into nu_correct. - R. On Jul 20, 2021, at 06:21, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Hello R,Thank you for letting me know that the deb file is now available. It's so useful for Ubuntu users to install FreeSurfer using the deb file.Can I ask you one more question? Can I specify the install directory using the deb file?I manage different versions of FreeSurfer by installing under /usr/local/freesurfer/{6.0.1, 7.1.1, 7.1.2}.If I can specify the directory, then I would love to use the deb file.As for the missing mni directory, I'm concerned about nu_correct.In my understanding, recon-all still uses nu_correct as default unless we set DoAntsN3 or DoAntsN4.nu_correct is located under $FREESURFER_HOME/mni/bin, so I thought it might be missed for some reason.Best regards,KiyotakaOn Tue, Jul 20, 2021 at 3:32 PM fsbuild <fsbuild(a)contbay.com> wrote:Hello Kiyotaka,You may not need to be concerned about that warning.  You can suppress it by setting the following in your shell environment.$ export NO_MINC=1For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the installer file instead of using the tar file, i.e.,$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb- R.On Jul 19, 2021, at 21:08, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Dear Doug,Thank you for the announcement of 7.2.0 update.I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing.As a result, now the shell shows warning about MNI=====-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl=====Is it intended?Best regards,KiyotakaOn Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:We are  please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check outMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BlHjRo1wiRb2WvddH8GfD4hFYtxGnnXI7YbPO… 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/1z6kK1yL1k60FJGc27E2kn8x07SbszbMudIGBC… 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 http://secure-web.cisco.com/1O14LpmCbLrvsH2LqoMBFq1uWO82zk5EdVR0-If…;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.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. -- Kiyotaka Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of Tsukuba1-1-1Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner 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] Announcing FreeSurfer version 7.2
by fsbuild 20 Jul '21

20 Jul '21

External Email - Use Caution Hello Kiyotaka, You may not need to be concerned about that warning.  You can suppress it by setting the following in your shell environment. $ export NO_MINC=1 For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the installer file instead of using the tar file, i.e., $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb - R. On Jul 19, 2021, at 21:08, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Dear Doug,Thank you for the announcement of 7.2..0 update.I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing.As a result, now the shell shows warning about MNI=====-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl=====Is it intended?Best regards,KiyotakaOn Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:We are  please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check outMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1b5VnwKaEKBSNi_MClrmr5mhsgtZpYrCJb2i3C… 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/1oN1v-0nlD3KNrEKeGheMD9zX46y7ILMiD9UbG… 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 http://secure-web.cisco.com/1L2nd_LrPOTdd2iOpi_WzkxLoF2dsLhVQ2K1inK…;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.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. -- Kiyotaka Nemoto, M..D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of Tsukuba1-1-1Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MNI to RAS conversion
by Bronwyn Overs 20 Jul '21

20 Jul '21

External Email - Use Caution Dear Mailing List, I have a set of MNI coordinates (from SPM2) that I need to visualise relative to the Desikan-Killiany Atlas parcellation. However, I'm unsure how to convert these coordinates so that I can load up Freeview and visualise their location in RAS. I took at look at the 'Co-ordinate Systems' wiki ( [ https://secure-web.cisco.com/1sbzzg5doGPykSwEzV3LinGmIIvWDNkgsNwyHDKOFsZ45-… | https://secure-web.cisco.com/1sbzzg5doGPykSwEzV3LinGmIIvWDNkgsNwyHDKOFsZ45-… ] ), but was unable to determine how this could be done. The coordinates I need to convert are x = − 31, y = 25, z = − 7 and x = 41, y = 25, z = − 9 . Any assistance you can provide would be much appreciated. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://secure-web.cisco.com/1XfLgNltTMcAj2hlB2lDXpneNH0BEKa7I3JWAe0V_YjLyyl… | neura.edu.au ] [ https://secure-web.cisco.com/1-OSuRhzQFyIpveSl9n2IYWwim3153jvTfOp0oP1NoQ9i8… | Twitter ] | [ https://secure-web.cisco.com/1zhTUDQgzdpMvHMPZJABMqxDyMdkh6R-Adj3u1S_KK6RNO… | Facebook ] | [ http://secure-web.cisco.com/1eRxCu2OH0byg9xiwEv_GHTtEbivbUdVd52g3sB-lt6fa9S… | Subscribe ]

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Claustrum segmentation
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 19 Jul '21

19 Jul '21

External Email - Use Caution ?Hi all, I was wondering if any of you guys have had experience wanting to segment the claustrum in 3T scans. It is a label that is found in Freesurfer, but isn't reported in the stats. Is that something that Freesurfer hopes to develop. Or is there some sort of toolbox that works well that can also segment it? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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recon all parallel
by Amar Shukla 19 Jul '21

19 Jul '21

External Email - Use Caution Dear All, Actually I am trying to run multiple subjects using parallel commands . So I am trying to run multiple .nii files in the current directory. Subject folder has been created for each file I can sinstructions in ee in the back end. but when i see in the terminal there is no response and the cursor is blinking. i am running this command ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache 1) I want to know if it is running parallely , or if it shows any further instructions in the terminal. 2) So please tell me if I am doing it correctly. I am adding the screen shots -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016

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Regarding recon-all
by Amar Shukla 19 Jul '21

19 Jul '21

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