Freesurfer February 2023

freesurfer@nmr.mgh.harvard.edu

85 participants
122 discussions

Failing to execute QDEC
by vittal korann 24 Feb '23

24 Feb '23

External Email - Use Caution Hi Freesurfer experts, I am trying to run Qdec on schizophrenia pre and post intervention scans. I created .dat and .levels files within the qdec folders and loaded the .dat file into qdec gui. It is suddenly crashing when I select my design and hit the Analyze button. And the same error message copied below from the terminal. Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/15DaQ_a1o5YqT7dopqDTQDqaw-6K4jw9WyiYPYFheSvTtpu… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. Even though I renewed my license file, the issue still persists. FYI I did use qdec in the past and am quite comfortable with it. Also, I attached my license file if anything is missing. Any help would be appreciated! With regards Vittal

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Re: [Freesurfer] FreeSurfer installation in a Code Ocean Capsule
by fsbuild 24 Feb '23

24 Feb '23

External Email - Use Caution Hello Chiara, It reads like Code Ocean wants to be a solution for someone to host all their research files for published articles, scripts, applications and binaries to run - in 1 place.  But it’s not clear to me applications/scripts/binaries can be run from there in real-time.  It looks more like another form of source control, e.g., GitHub, to enable sharing and managing of files (including disaster recovery).  The text at the bottom of this page, https://secure-web.cisco.com/1aH9sOdWmoRBiry1WokL4RYzdttBbVqc-sC…, indicates they use Amazon AWS servers.  So maybe a code capsule would connect with and run software via an AWS server image with the needed software installed.  That server would in turn need to run a flavor of linux that would allow installing one of the freesurfer distribution packages from https://secure-web.cisco.com/17phn5CctlPx0-cSxitH_2EOSCGyEjytacc8… For scientific clusters, you usually file a ticket to request installation of a software package not already available to run on the cluster.  I would ask Code Ocean tech support how a code capsule currently runs python scripts and/or linux binaries in real-time from a users account.  If that already works to run python scripts or some programs installed on linux servers, then you could ask tech support how 3rd party software packages (like freesurfer) could be managed and installed to run from a users account. - R. On Feb 24, 2023, at 03:50, Chiara Marzi - UniFI <chiara.marzi(a)unifi.it> wrote:        External Email - Use Caution        Dear Freesurfer, I am trying to use some FreeSurfer tools inside a Code Ocean capsule (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-WWfxxHb5KgsxJyNmbX2M5iZmuUeIU8z2QsbW… cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover, and run code published in academic journals and conferences. Specifically, I set up my capsule environment including a Python package (freely available at Github: XXX) that requires FreeSurfer for full functionality. Is it possible to install FreeSurfer on such a platform? Do you have any suggestions?Thanks!Have a nice day,Chiara_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer installation in a Code Ocean Capsule
by Chiara Marzi - UniFI 24 Feb '23

24 Feb '23

External Email - Use Caution Dear Freesurfer, I am trying to use some FreeSurfer tools inside a Code Ocean capsule (https://secure-web.cisco.com/1F1n6n0E7KQZBogoJ-y7cciJe_z3d-WxxhEPHp2zwkasIm…) a cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover, and run code published in academic journals and conferences. Specifically, I set up my capsule environment including a Python package (freely available at Github: XXX) that requires FreeSurfer for full functionality. Is it possible to install FreeSurfer on such a platform? Do you have any suggestions? Thanks! Have a nice day, Chiara

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[FreeSurfer] recon-all exited with error
by Krystal Xiwing Yau 23 Feb '23

23 Feb '23

External Email - Use Caution Dear FreeSurfer experts, I ran the command "recon-all -s Sub-139 -i 139.nii -all -qcache -parallel -openmp 6" successfully in the first few hours, and exited with error before generating all the output files. It happened to other subjects, too. The attached file contains the whole processing steps and ended with error. I have set SUBJECTS_DIR to the shared folder, which was mounted in FreeSurfer beforehand. Then, the data for analysis was copied to the Desktop. I typed in the command and it exited with error in the end, though. Would somebody kindly advise how to fix it, please? Your help would be highly appreciated! OS: Windows 11 VM: ubuntu 18 Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Tracula 6.0 - : Command not found. set: Variable name must begin with a letter. does not exist.DIR
by Thorn, Kathryn 23 Feb '23

23 Feb '23

External Email - Use Caution Hi Freesurfer Experts, I’m attempting to run Tracula and receiving the same error for both Tracula 6.0. Note: I have also tried updating to Freesurfer 7.2 and running recon-all (which runs without issue) and then Tracula (which returns the same error as 6.0), so I don’t think version is my issue. I have gotten Tracula 6.0 to run in the past on the machine I’m using now and I have not made any major modifications or updates since then. Here is the set of commands I am passing to Tracula: export FREESURFER_HOME=/Applications/freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export TUTORIAL_DATA=/Users/kayti/Desktop/Projects/MIND/Freesurfer6 export SUBJECTS_DIR=$TUTORIAL_DATA/02_Data/01_recon_all cd $SUBJECTS_DIR trac-all -prep -c $TUTORIAL_DATA/01_Protocols/dmrirc.mind95 And here is the full text of my config file: setenv SUBJECTS_DIR $SUBJECTS_DIR set subjlist = (A201) set dcmlist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.nii) set bveclist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bvec) set bvallist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bval) set dob0 = 0 set doeddy = 0 set intrareg = 2 set interreg = 2 And here is the full text of the error message: domainname: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all I have ensured that the directory above DOES exist. I have seen other posts in these forums with this issue and I have tried all of the fixes I’ve found: removing trailing/extraneous spaces, correcting my paths, etc. Does anyone have any ideas why this is happening? Thank you! Ryn Thorn (she/her) Lab Manager Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425

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Re: [Freesurfer] Freesurfer Digest, Vol 228, Issue 26
by Juan Rivas 23 Feb '23

23 Feb '23

External Email - Use Caution Hi, I have 2 samples with schizophrenic patients. The first one was analyzed with FreeSurfer version 6, and the second one with version 7. Is it possible to compare results using two different versions? Juan Carlos Rivas, MD, PhD El jue, 23 feb 2023 a las 9:16, <freesurfer-request(a)nmr.mgh.harvard.edu> escribió: > 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/1cNeKOSCv3wTRW7YJdo3QUKmDB2ind2BwutfXTr5lU1Bn-… > 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. Visualizing transparent surface with non transparent > annotations (Leonardo Tozzi) > 2. Failing to execute QDEC (vittal korann) > 3. Re: different clusters in mri_surfcluster output versus > viewing in Freeview (Huang, Yujing) > 4. Re: segmenThalamicNuclei.sh exited with ERRORS (beh?et ayy?ld?z) > 5. Re: Extracting brain volume seperately (Douglas N. Greve) > 6. Re: Nuisance regressors (Douglas N. Greve) > 7. Please unsubscribe me (Manuela Dorado Novoa) > 8. Re: Hole in the insula (Douglas N. Greve) > 9. Re: Correlating and/or linear regressing surface overlays > (Douglas N. Greve) > 10. Re: different clusters in mri_surfcluster output versus > viewing in Freeview (Smith, Christine) > 11. Re: mri_easyreg tool (Iglesias Gonzalez, Juan E.) > 12. MGH35 template (Maffei, Chiara,PHD) > 13. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation > (Kumar, Avnish) > 14. Re: mri_robust_register --minsize (Reuter, Martin,Ph.D.) > 15. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation > (Aaron Tanenbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Feb 2023 19:34:40 +0000 > From: Leonardo Tozzi <ltozzi(a)stanford.edu> > Subject: [Freesurfer] Visualizing transparent surface with non > transparent annotations > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > BYAPR02MB5352E6F3CF76C8B3FC793BD0A9AA9(a)BYAPR02MB5352.namprd02.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Dear Experts, > > I would like to use Freeview to achieve the following. > > I would like to visualize a transparent brain surface, with only some > annotations visible. In other words, I would like the surface to be > transparent, but the annotations I choose to visualize to not be > transparent. > > Is there a way to achieve this? > > Thank you, > > Leonardo Tozzi, MD, PhD > Director of Computational Neuroscience & Neuroimaging Program > Stanford Center for Precision Mental Health and Wellness > Stanford University > ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 > > Connect with us! > [signature_1075933358]< > https://secure-web.cisco.com/10OmKEEhtSQzpfvnfJVDeLBEHHi9OqaBVJ9LAvZsQvsNWt…> > [signature_1282923475] < > http://secure-web.cisco.com/1I3hXNj6irLn6oQYZFgxz73In-4_EGzX-NMOPCnUJP3yv02…> > [signature_911042299] < > https://secure-web.cisco.com/10-8-bEWGWgfQnDhesaI2ZU2QywWqHHyTXTPc8TI7RfrgI… > > PJNke0vXiDMTDtTzHDVcY1_nAXyUu39dY-RgRIy2-1NQRoN-HECK_k-kfkXj7byQRegabkSC2x2Rpk1EnMy5oNG4aKglnBXwSdEu9mMGHy4sv651W2PDESfROkyPk5dUJYgH6pftVhm7jKLjIdK3cZX_UCOVIMk6GPAjZZwWsHpvulKamZgcFMdAerPif2k-2pu2GWnu2Sh0ixq2_80N-H5f/https%3A%2F% > 2Fwww.youtube.com%2Fchannel%2FUCN8g9b2eCpSRMs6AyY15U3g> >

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Re: [Freesurfer] Infant Freesurfer - manual edits
by Kang, Jee Won 23 Feb '23

23 Feb '23

External Email - Use Caution Dear all, Could anyone provide an update as to whether there is a way to incorporate manual edits into the infant Freesurfer pipeline? Thank you, Jee Won -----Original Message----- ------------------------------ Date: Thu, 16 Feb 2023 13:38:44 +0000 From: "Kang, Jee Won" <JeeWon.Kang(a)childrens.harvard.edu> Subject: Re: [Freesurfer] Infant Freesurfer - manual edits To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DM8PR16MB452084E15CF083820BE8E5F2A5A09(a)DM8PR16MB4520.namprd16.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Dear Freesurfer experts, Hello, I have started experimenting with Infant Freesurfer (version 4a14499), and we have run into a problem with very poor segmentation of the thalamus in one of our subjects. Is there a way to incorporate manual edits, as in adult Freesurfer, to improve the segmentation? From this post: https://secure-web.cisco.com/17dOvwIxNLzp7uy4sPSZtQcx10XecPwg7CgGSbSZM5j-Yw… it looks like the option to make manual edits was a feature in the works, but I am not sure if that is still the case. I am guessing it would be inadvisable to re-run the infant data after making edits (to wm or aseg.presurf) in adult Freesurfer? Thank you for your advice on this! Sincerely, Jee Won

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Re: [Freesurfer] T2pial: Numerical argument out of domain
by AmirHussein Abdolalizadeh 23 Feb '23

23 Feb '23

External Email - Use Caution Hi Yujing, Trying with 7.3.0 also results in the same error. Of note, running recon-all 7.3.2 without -T2/FLAIR and -T2/FLAIRpial flags works without any issues. However, I couldn't try recon-all in the 7.2.0 version (I can give it a try if you think it is necessary). As I said before, running recon-all using the flags above with 7.1.0 works fine, however, I noticed that pial surfaces estimated using T1s alone align far better than surfaces estimated with the addition of T2/FLAIRs. Amir

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Re: [Freesurfer] Freesurfer Digest, Vol 228, Issue 26
by Mark Wagshul 23 Feb '23

23 Feb '23

External Email - Use Caution Thanks, that's perfect. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thursday, February 23, 2023 9:13 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 228, Issue 26 CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the "Phish Alert" button on the top right of the Outlook dashboard to report any suspicious emails. 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/1qMGKEeYiMzwHNefB-sAdkW4AyzGXAF_zakMU_eWB3ayIT… 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. Visualizing transparent surface with non transparent annotations (Leonardo Tozzi) 2. Failing to execute QDEC (vittal korann) 3. Re: different clusters in mri_surfcluster output versus viewing in Freeview (Huang, Yujing) 4. Re: segmenThalamicNuclei.sh exited with ERRORS (beh?et ayy?ld?z) 5. Re: Extracting brain volume seperately (Douglas N. Greve) 6. Re: Nuisance regressors (Douglas N. Greve) 7. Please unsubscribe me (Manuela Dorado Novoa) 8. Re: Hole in the insula (Douglas N. Greve) 9. Re: Correlating and/or linear regressing surface overlays (Douglas N. Greve) 10. Re: different clusters in mri_surfcluster output versus viewing in Freeview (Smith, Christine) 11. Re: mri_easyreg tool (Iglesias Gonzalez, Juan E.) 12. MGH35 template (Maffei, Chiara,PHD) 13. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation (Kumar, Avnish) 14. Re: mri_robust_register --minsize (Reuter, Martin,Ph.D.) 15. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation (Aaron Tanenbaum) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Feb 2023 19:34:40 +0000 From: Leonardo Tozzi <ltozzi(a)stanford.edu> Subject: [Freesurfer] Visualizing transparent surface with non transparent annotations To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BYAPR02MB5352E6F3CF76C8B3FC793BD0A9AA9(a)BYAPR02MB5352.namprd02.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear Experts, I would like to use Freeview to achieve the following. I would like to visualize a transparent brain surface, with only some annotations visible. In other words, I would like the surface to be transparent, but the annotations I choose to visualize to not be transparent. Is there a way to achieve this? Thank you, Leonardo Tozzi, MD, PhD Director of Computational Neuroscience & Neuroimaging Program Stanford Center for Precision Mental Health and Wellness Stanford University ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/1MmfwoA7hTbD59QWB10QQcD9GUKsHKYR9ZBI5ttOdayR8d…> [signature_1282923475] <https://secure-web.cisco.com/12UUdk9X1J-4aODIHV6cxTjcYOtE4-VfZIF9Z1hWpLGFno…> [signature_911042299] <https://secure-web.cisco.com/1rdJHznNOPhIImE3a79IodDAbmJDVYxy6GoR6Em21O6K1M… PJNke0vXiDMTDtTzHDVcY1_nAXyUu39dY-RgRIy2-1NQRoN-HECK_k-kfkXj7byQRegabkSC2x2Rpk1EnMy5oNG4aKglnBXwSdEu9mMGHy4sv651W2PDESfROkyPk5dUJYgH6pftVhm7jKLjIdK3cZX_UCOVIMk6GPAjZZwWsHpvulKamZgcFMdAerPif2k-2pu2GWnu2Sh0ixq2_80N-H5f/https%3A%2F%2Fwww.youtube.com%2Fchannel%2FUCN8g9b2eCpSRMs6AyY15U3g>

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MGH35 template
by Maffei, Chiara,PHD 22 Feb '23

22 Feb '23

Hi Mark, Sorry for the late reply. The population template was built using the FA images only, so there is no corresponding T1 template image. You can use the transforms stored in dmri/xfms in your TRACULA directory to map the subject’s anatomical images to this template space, or you can set the interreg variable in your dmrirc configuration file to 1 or 2 to have your TRACULA common space be the MNI152 T1 1mm space instead. I hope this helps, Chiara Dear Freesurfer developers, Hi, this message may have slipped through the cracks, hope someone can help us out on this. We're looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_FA_template image which is used in TRACULA? Does such a template exist, and if so, would it be possible to share? Thanks so much! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.ed<mailto:mark.wagshul@einsteinmed.edu>

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Freesurfer February 2023