Freesurfer

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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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Re: [Freesurfer] mri_easyreg tool
by Iglesias Gonzalez, Juan E. 22 Feb '23

22 Feb '23

Sorry for the late response, I went on vacation the very same day you posted your question. The floating image is the one you want to deform, and the reference image is the one you use as target for the registration /deformation. In other words: the deformed floating image should overlap with the reference image. More information here: https://surfer.nmr.mgh.harvard.edu/fswiki/EasyReg Kind regards, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Peters, Johnny Y" <jonathan-peters(a)uiowa.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, February 10, 2023 at 11:40 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_easyreg tool External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use the mri_easyreg on the developmental version of freesurfer but I am confused about what .mgz or .nii(.gz) I am supposed to use for the reference image, floating image, and the others. I saw no previous threads on the mailing list addressing my question so I decided to email you. Would you be able to give an example command line using the subject bert in the freesurfer directory? Thank You

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Correlating and/or linear regressing surface overlays
by Finn, Quentin 22 Feb '23

22 Feb '23

External Email - Use Caution Freesurfer experts, I have some surface data that I'd like to correlate with some other data, although a linear regression would also be fine if I could get something like a t-stat out of it. This data came from two different PET tracers -- voxelwise data was resampled via vol2surf onto each subjects cortical surface: So I have, say, data like this: tracer1_subj1_lh.mgh tracer1_subj2_lh.mgh . . . . tracer1_subjn_lh.mgh And then I have another set: tracer2_subj1_lh.mgh tracer2_subj2_lh.mgh . . . . tracer2_subjn_lh.mgh I'd really like to just stack them all up with mris_preproc, something like this: mris_preproc --is tracer1_subj1_lh.mgh --is tracer1_subj2_lh.mgh [etc] --is tracer1_subjn_lh.mgh --out tracer1_lh.mgh --hemi lh --fsgd tracer1.fsgd mris_preproc --is tracer2_subj1_lh.mgh --is tracer2_subj2_lh.mgh [etc] --is tracer2_subjn_lh.mgh --out tracer2_lh.mgh --hemi lh --fsgd tracer1.fsgd The FSGD's are the same because the subjects are the same. and then run something like... mri_glmfit --glmdir tracer1_tracer2_left --y tracer1_lh.mgh --fsgd tracer1.fsgd --pvr tracer2.mgh --no-contrasts-ok --surface fsaverage lh This doesn't have an output that's really what I'm looking for as far as I can tell though, there's no fit statistics type overlay in the output folder, probably because I'm doing something wrong. Any help on this would be just wonderful! -quentin finn Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas for 11 years in a row. Houston Methodist is the No. 1 hospital in Texas and No. 15 in the nation. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Hole in the insula
by Aaron Tanenbaum 22 Feb '23

22 Feb '23

External Email - Use Caution I have this subject that has holes in the insula. Please see attached. I was wondering what should freesurfer have classified it as.

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Please unsubscribe me
by Manuela Dorado Novoa 22 Feb '23

22 Feb '23

External Email - Use Caution Hi, Please, unsubscribe me from your mailing list. Thank you, Manuela

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