Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Samseg cortex parcellation
by Stepanov, Valentin 06 Mar '23

06 Mar '23

External Email - Use Caution Hello, I hope this email finds you well. I am using Samseg for the MS patients' data and am very impressed with its performance in terms of lesions segmentation along with posteriors and probability maps saving. Also, compared to freesurfer, it has a remarkably better quality of cortical gray matter segmentation, particularly in subjects with juxta/intracortical lesions. However, to my knowledge, it does not allow doing a cortex parcellation. I used it with the —recon option, but in that case, the output (aparc+aseg.mgz) is identical or very close to those freesurfer provides and commonly has some segmentation errors, whereas seg.mgz saved in samseg directory demonstrates significantly better segmentation. I wonder if there is any way to run cortex parcellation using exact samseg seg.mgz output? I have attached a couple of images demonstrating the difference of segmentation output for freesurfer and samseg. Thank you, Best regards Valentin Valentin Stepanov Postdoctoral Fellow Center for Biomedical imaging Department of Radiology NYU Grossman School of Medicine 660 1st Avenue, office 212 New York, NY 10016

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Re: [Freesurfer] -pctsurfcon --fsvol default
by Antonio #30 06 Mar '23

06 Mar '23

External Email - Use Caution Hello again, I would like to ask one last thing. How can the class averages computed from csdbase.y.ocn.dat not match the gamma.mgh values in the cluster? e.g. How can gamma show +29 in a vertex that is part of the significantly positive cluster in an A-B contrast, while the average of all values taken from csdbase.y.ocn.dat referring to class A in that same cluster is lower than that of class B (average of values of input y for class A = 20.367; average for class B = 20.401)? Are the values in csdbase.y.ocn.dat not corrected by the variables chosen as covariates? Thanks again! Antonio Bonifanti Il giorno mer 15 feb 2023 alle ore 18:36 Antonio #30 < toni.bonif2511(a)gmail.com> ha scritto: > Hi, > > 1. I was wondering why the --fsvol argument in -pctsurfcon takes > rawavg.mgz by default, when most literature on grey/white contrast tends to > compute it from nu.mgz. > Is the intensity-corrected volume to be preferred in all cases or was > there a reason for choosing rawavg as a default while writing the script? > > 2. I would also like to ask whether or not you believe the values of > smoothing kernels seen in literature for grey-white contrast (which often > are over 20mm) to be adequate for such a measure. > > 3. As a final note, would you say it is appropriate, from a statistical > standpoint, to compare the results of group analyses conducted on the two > hemispheres with different covariates? (e.g. with mean left cortical > thickness and mean right cortical thickness rather than mean whole cortical > thickness) > > Thank you for your time! > > Antonio Bonifanti >

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WMH in aparc+aseg
by Alberto Del Cerro Leon 06 Mar '23

06 Mar '23

External Email - Use Caution Hello FS team! I am using the volumetric data of WMH obtained during the recon-all in the apar+aseg.mgz file. Where I could find the description of the method throught it is segmented? I find the Automated Labeling of Neuroanatomical Structures in the Human Brain but the label WMH doesn't figure on that. Thanks in advance

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Re: [Freesurfer] Recon-all exited without errors
by Goeckner, Bryna 06 Mar '23

06 Mar '23

External Email - Use Caution Thanks for the response. I should have been more clear in my first email. I have used tkregister2 in the past to fix talairachs, but this one does not appear to be fixable with the in-plane shifting, scaling, and rotating that is available within the tkregister2 GUI. The moveable appears to be in a different plane than the target. I’m attaching a screenshot from tkregister2. Is there a different way to fix the talairach or another recon fix (especially considering the apparent brainmask issue) that should be pursued? Thanks again for your help! Bryna Goeckner (she/her) Graduate Student Meier Lab Medical College of Wisconsin Neuroscience Doctoral Program Date: Fri, 10 Feb 2023 20:48:26 +0000 From: "Huang, Yujing" <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited with errors To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB5982D0100E4EC48D6FD8A2949DDE9(a)MN2PR04MB5982.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Bryna, In this tutorial, it talks about how to fix bad output from the talairach registration: https://secure-web.cisco.com/1AsdowaGUQbpsRB4dUWGRiDD2RdKWB-n1kUwwmPwq1WQ9Y…<https://secure-web.cisco.com/1YTUJIwB-u_KNhoI17IHgKhkMu-K4cxIGnnOeSiooClREn…> Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Goeckner, Bryna Sent: Friday, February 10, 2023 3:35 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all exited with errors External Email - Use Caution Hi All, I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated. I then tried recon-all with the -notal-check flag, which exited "without errors" although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white). I'm including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks! The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all And for the second run, -notal-check was added after -all For tkregister2: tkregister2 --s subj# --fstal --surf orig Bryna Goeckner (she/her) Graduate Student Meier Lab Medical College of Wisconsin Neuroscience Doctoral Program

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Question on mri_nu_correct for 3 Tesla data
by Saemann, Philipp 06 Mar '23

06 Mar '23

External Email - Use Caution Hi FreeSurfer specialists, we have problems with a strong non-intensity in 3 Tesla data of GE (mainly temporal poles and occipital area). We managed to rescue the occipital errors by a pre-Bias-field correction using SPM, but would of course try to optimize this in recon-all itself. When I open the recon-all scrip tin FS v7.1.1 I can find no difference in the parameters depending on if the the flag "-3T" is set or not. In both cases the parameters forwarded are: --n 1 --proto-iters 1000 --distance 50 (in line 1536 and line 1540 of /bin/recon-all.) Could someone explain this? What could be done (manual corrections etc. are obsolete due to the large sample size...) to improve the WM detection in the temporolateral/polar area (subsequently cortex detection)? The brainmask looks okay; the ribbon.mgz shows the cut off lateral parts of the cortex. Thanks in advance for any hints, Philipp

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pass code to open the Ubuntu compressed image with Freesurfer
by Chloe Lin 06 Mar '23

06 Mar '23

External Email - Use Caution Hi, I do not have the pass code to open the Ubuntu compressed image with Freesurfer, can you provide me with that? Thank you very much. Best regards, Chloe

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To freesurfer
by Kanokwanwijit Wongsook 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer My name is nan from Thailand and I’m interest in Freesurfer software but I can’t learn from the begin by myself. I’m confused. so please, can you ad rise me in the begin point of this Freesurfer or some course to learn.Thankyou Sincerely yours,

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List of vertices in defined region
by Sarah Lavelle 05 Mar '23

05 Mar '23

External Email - Use Caution Hi there, I want to get a list of all vertex numbers within a defined region. For example, to see what vertices are in the superior frontal lobe using the DKAtlas. Would you have any suggestions? I am currently using Matlab to analyse the cortical surface mesh so it would be great to have this list in a Matlab environment. Thank you very much, Sarah Lavelle

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Re: [Freesurfer] Request for Consent to Use Derivative Work for Commercial Use
by Douglas N. Greve 03 Mar '23

03 Mar '23

Hi Zuha, I'm not the person who can give permission. I think the license allows you to use the software in the way that you are describing. I'm cc'ing Heonick Ha, one of the MGH licensing lawyers, who should be able to tell you definitively. best doug On 3/3/2023 3:30 AM, Zuha Junaidi wrote: > > External Email - Use Caution > > Dear Sir/Madam, > > I am Zuha Junaidi, writing to you on behalf of the legal team > atBrainSightAI, > <https://secure-web.cisco.com/1fenN2fK-sZMU_yj5Vozshm1nAWqMTjXfYE64fp8_qeSeG…>to > request your consent to use the Freesurfer license for commercial use. > At BrainSightAI, a connectome-based analysis startup based out of > India, we enable personalized brain mapping which has implications > across neurosurgery, neurology, and psychiatry. > > Our product involves robust pre-processing of structural MRI > modalities, and we have found that Freesurfer's mri_convert and > mri_normalize functions give us the best results. We would like to > incorporate intensity normalisation functionality as part of our > pre-processing pipeline. > > As we are conducting clinical studies to validate our product and > obtain FDA approval prior to commercialization, we need your > permission to use Freesurfer's license to access and utilize its > mri_convert and mri_normalize functions in our analysis pipeline. > > We want to clarify that we would only be using the mri_convert and > mri_normalize functions from Freesurfer's software package, and we > will comply with all the license terms and conditions while using it. > Whenever applicable, we will give proper attribution to the authors > and developers of the software in any publications or presentations > resulting from our work. > > We will strictly adhere to all the terms and conditions set forth in > the Software License. Our use of the Software will be limited to the > specific functions of mri_convert and mri_normalize. We will preserve > and maintain all applicable attributions, copyright notices and > licenses included in or applicable to the Software. Any modified > versions of the Software will be clearly identified and marked as > such, and we will not misrepresent them as being the original Software. > > We believe that incorporating Freesurfer's functions in our processing > pipeline will enhance the accuracy and efficiency of our analysis, and > we hope that you will grant us permission to use them. > > Please let us know the process to receive permission. > > Thank you for your time and consideration. We look forward to hearing > from you soon. > > Sincerely, > > Zuha Junaidi > > +91-9205209836 >

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more detailed instructions for cloning voxels & confirmation that the cloning worked
by Harriott, Emily M 03 Mar '23

03 Mar '23

External Email - Use Caution Dear FS experts, I hope this email finds you all doing well. I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me. 1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)? * I read through https://secure-web.cisco.com/1edlOGwMXoyYaTFLL7CtR8DWHAzxHsiS014OXifU0XBn5y… but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google. 2. How do you tell if it worked? I saw https://secure-web.cisco.com/1FkHM4e40vXk3f7s77S0LuFO0Duz3wB6sJb6MPMmOOUvmn… this previous post but it does not seem to have been answered. Any assistance would be greatly appreciated. Thank you so much! All the best, Emily Harriott PhD student, Vanderbilt University

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Freesurfer March 2023