Freesurfer December 2024

freesurfer@nmr.mgh.harvard.edu

45 participants
62 discussions

FreeSurfer Labels Question
by Barsotti, Ercole 13 Dec '24

13 Dec '24

External Email - Use Caution Hi all, Sorry if this is a stupid question. In the FreeSurferColorLUT.txt, there is a label for "Unknown" brain material. What would most commonly be labelled as Unknown in an image? Thanks, John

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synthmorph for functional registration?
by Josh 13 Dec '24

13 Dec '24

External Email - Use Caution bbregister is known to be really could at registering functionals to T1w image. I am curious as to whether synthmorph performs close to bbregister or not when registering epi to the structural.

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Spiky Brains
by Bos, M.G.N. (Marieke) 13 Dec '24

13 Dec '24

External Email - Use Caution Hello FreeSurfer Developers, We are completing quality control in FreeView of two longitudinal datasets (participants age: 9-25) and have noticed that in one dataset the brains look much more 'spiky' than in the other dataset. More than half of the brains have some 'spikes', < 10% has severe spikes; the most obvious ones correspond with both underestimations and overestimations in frontal regions of the brain (e.g., frontal pole, rostral middle frontal and superior frontal). The datasets are collected on two different scanners: Dataset with the spiky brains: * Structural MRI data were acquired using a Philips Achieva 3.0 Tesla MRI scanner with a standard whole-head coil. The following parameters were used: FOV = 224 mm x 178.5 mm x 168 mm; TR = 9.8 ms; TE = 4.6 ms; flip angle = 8 degrees; voxel size = 0.875 mm x 0.875 mm x 0.875 mm. The duration of the anatomical scan was 297.8 s. To reduce head motion, foam inserts were used and a film was projected on a screen. Dataset without spiky brains: * Structural MRI data were acquired using a Philips Achieva 3.0 TX MRI scanner with a standard whole-head coil. The following parameters were used: FOV = 250 mm × 196 mm × 170 mm; TR = 7.9 ms; TE = 3.5 ms, flip angle = 8 degrees, 228 × 177 × 155 slices; voxel size = 1.1 × 1.1 × 1.1 mm. The duration of the anatomical scan was 251 s. To reduce head motion, foam inserts were used. We are not too sure what to do about these. Manual skull stripping, adjusting the watershed threshold and using control points are not perfect solutions for various reasons. And we have noticed that the spikiness is reduced in some brains when the scans are processed in version 6.0 compared to version 7.3 - but otherwise version 7.3 seems like the better fit. We couldn't find anything in the archives, but we wonder - have you come across this before? Do you have another idea for us to try? Or is it possible that data from these regions would be (mostly) unimpacted by the appearance of small, infrequent spikes? If we want to use global brain measures, do you think Freesurfer gives a reliable estimation or would you advise us to exclude them from the analyses due to bad data quality. We have attached one picture of severe spikes so you know what we mean. We have started to rate the spikes from 1 (small/infrequent) to 4 (large/frequent). Thank you in advance for any ideas you can share with us. Best wishes, Manon Marieke

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recon-all on poor MRI quality
by Francesco Lomi 13 Dec '24

13 Dec '24

External Email - Use Caution Dear all, I am writing you because I would like to know why recon-all on this subject exited with an error (I have uploaded the log file so you can see). Is it due to the poor quality of the T1 image? How to overcome this issue? I've added the FLAIR sequence to improve the surface reconstruction but the recon-all process did not end correctly. If you had any suggestions, they would be highly appreciated Best, Francesco

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Freesurfer v8.0.0 error
by 潘晨盛 12 Dec '24

12 Dec '24

External Email - Use Caution Hello FreeSurfer Developers, I installed freesurfer 8.0.0 successfully but failed to run "recon-all -i *** -s *** -all -localGI -qcache" for any subjects. I tried this version 8.0.0beta on both macos latest version and ubuntu 22.04, the error was the same as follows: "Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph" "ERROR: cannot use ML routines" The command line did not even start anything, thus no log file was generated. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one?

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recon-all-clinical rh.BA_exvivio.annot error
by Melissa Marie Rundle 11 Dec '24

11 Dec '24

External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, Melissa ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/recon-all-clinical/3CAMC005746_125300857_20240220/mri/wm.mgz... reading input surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... reading input pial surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.pial... reading input white surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 183858 Total vertex volume 183685 (mask=0) error: No such file or directory error: could not read annot file ./rh.BA_exvivo.annot error: No such file or directory error: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.annot computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/recon-all-clinical/3CAMC005746_125300857_20240220/mri/wm.mgz... reading input surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... reading input pial surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.pial... reading input white surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 183858 Total vertex volume 183685 (mask=0) error: No such file or directory error: could not read annot file ./rh.BA_exvivo.thresh.annot error: No such file or directory error: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.thresh.annot All done! ________________________________ This electronic message is intended only for the use of the individual(s) and entity named as recipients in the message. If you are not an intended recipient of this message, please notify the sender immediately and delete the material from any computer. Do not deliver, distribute or copy this message, and do not disclose its contents or take any action in reliance on the information it contains. Thank you.

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Re: [Freesurfer] Fwd: LME matrix design
by Diers, Kersten /DZNE 11 Dec '24

11 Dec '24

External Email - Use Caution Hi Daniel, please find my responses below. Hope this helps, Kersten External Email - Use Caution Hello FreeSurfer experts, I am currently working through the linear mixed effects pipeline to assess longitudinal cortical thickness changes in non-contact/contact athletes and have some questions. My design matrix is as follows: X = [ones(size(M,1), 1), M(:,1), M(:,2), M(:,3), M(:,1).*M(:,3), M(:,4), M(:,1).*M(:,4), M(:,5), M(:,6), M(:,7), M(:,8), M(:,9)]; M(:,1) = group M(:,2) = scan time from baseline M(:,3) = age With the rest of the columns in X being other covariates from M or *time interaction, and the random intercept term being the only random effect. 1. I’m using the spatiotemporal approach, but would vertex-wise yield more powerful results? I know that a previous thread had a similar question, but I am wondering if one would be more favourable for looking at regional CT changes. Hard to say, but I would not necessarily expect so, since the original paper demonstrated power increases for the spatiotemporal model as compared to the vertex-wise approach. 1. As well, the two groups have different distributions in timepoints and size. The contact athlete group is about double the size (42 vs 21) and has significantly more athletes with multi-year participation (2- or 3-years), whereas the non-contact athlete group is almost entirely single-year participation (one set of pre- and post-season scans). Is this something that the LME can inherently account for? Yes, the LME model can handle for designs with unbalanced number of cases, and differences in the number and interval lengths of longitudinal observations. 1. My main goal is to test if there is a significant difference in the slopes of the two groups (using lme_mass_F). I currently have this setup for my contrast matrix: CM.C = [0 1 zeros(1,10)]. Since I only have two groups, is it logical to use a single row? Additionally, I am a bit unsure of how to assign beta weights. Yes, using a single-row contrast like you say is fine. What exactly do you mean by "assign beta weights?" 1. After running the F-test, I am correcting the multiple comparisons using FDR2. Are there any other corrections/tests I should utilize before plotting data in tksurfer? You might want to take into account correcting for the fact that you are (likely) doing the analysis in two hemispheres: the tutorial suggests to simply do a bonferroni correction. Thank you in advance, Daniel The 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 https://secure-web.cisco.com/1spOb5VWb5CUeuy6CxGiwDR0ePXHBn09ABVNzN5LzwT8UJ… . 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.

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Re: [Freesurfer] Petsurfer: PET -> MNI305 problem
by Shen, Qian 10 Dec '24

10 Dec '24

External Email - Use Caution Hi Dr. Greve and Experts, I encountered an issue while running the following command to resample meltzer.nii.gz (or mgx.subctxgm.nii.gz) into the 2mm MNI305 space, as instructed in the PetSurfer wiki<https://secure-web.cisco.com/1W31n5cbq1zvsFiHcecMWmqEEiH13OUvfTH7j9X72O1Gdv…>. The output image appeared misoriented (see the attached screenshot for reference): mri_vol2vol --mov meltzer.nii.gz--reg aux/bbpet2anat.lta --tal --talres 2 --o meltzer.mni305.2mm.sm00.nii.gz Upon investigating, I realized the issue arises when using the --no-reduce-fov option in the mri_gtmpvc step. Specifically: (1)If I do not use --no-reduce-fov in mri_gtmpvc, the output image from above mri_vol2vol command is correct. (2)Alternatively, if I do use --no-reduce-fov, but replace aux/bbpet2anat.lta with either template.reg.lta or aux/anat2bbpet.lta in mri_vol2vol command, the output image is also correct. Could you confirm if this behavior is expected or if additional adjustments are needed? By the way, the version of Freesurfer I'm using is v7.1.0. Thank you for your guidance in advance, Shen

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Re: [Freesurfer] Error in longitudinal hippocampal fields
by Mark Wagshul 10 Dec '24

10 Dec '24

External Email - Use Caution This is a single case, all of my other subjects ran through without a problem. Thanks! 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<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] 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. From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>> Subject: Re: [Freesurfer] Error in longitudinal hippocampal fields processing To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <PH0PR04MB83881AEB5CC0EDD5534404A2FD3C2(a)PH0PR04MB8388.namprd04.prod.outlook.com<mailto:PH0PR04MB83881AEB5CC0EDD5534404A2FD3C2@PH0PR04MB8388.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="utf-8" ?Thanks for your message, Mark! Is this for a single case, or a more general issues? Cheers, /Eugenio

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Questions about CVS registration
by Tanxin Dong 10 Dec '24

10 Dec '24

External Email - Use Caution To whom this may concern: Hi, I’ve been working on creating a template for a certain metric using the applyMorph command to project the calculated metrics onto the CVS template. However, I'm curious if there’s a way to reverse this process. Specifically, can I morph the template in the CVS35 space back to the individual space? I would appreciate any insights or guidance you could provide on this. Looking forward to your response! Best regards T.D.

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Freesurfer December 2024