Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

VM password
by Eyesha Younus 28 Nov '22

28 Nov '22

External Email - Use Caution Hello, I need a password to install the VM. Is this password tied to an email address or to a machine? The reason I ask this is because I need to install the VM on two computers; one personal and one work. Thanks

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New subscriber
by Eyesha Younas 28 Nov '22

28 Nov '22

External Email - Use Caution Sending my email to become able to post to the forum. Thanks Sent from my iPhone

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Calculating Distortion in mris_flatten()
by Sarah Lavelle 28 Nov '22

28 Nov '22

External Email - Use Caution Hi Bruce, Thank you very much for your response. I would like to calculate this distance error for specific regions on the flatmap after the transformation, so I can formulate cuts to minimize it for the region I am interested in. Do you have any suggestions on how I can do it? From reading your paper : *Fischl B, Sereno MI, Dale AM. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage. 1999 Feb;9(2):195-207. doi: 10.1006/nimg.1998.0396. PMID: 9931269, *I understand that distances are calculated using the corrected *Dijkstra **algorithm* as an estimator of geodesic distances. In your response, you said that the distance error is calculated with: *100 * (mean(abs(distance error)) / mean(original_distances))* Are the *original_distances = the geodesic distances (gd) calculated (using the Dijkstra algorithm) for each vertex on the inflated surface*? Is the *distance error = (gd on the flatmap) - (gd on the inflated surface)?* Do you know how I can do this in matlab for just *one region using the DKTaltas*? for example, the superior frontal? Any help would be greatly appreciated! Kind regards, Sarah On Wed, 9 Nov 2022 at 17:02, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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/139TUXRjgPFOTa0MZdiWthcoqzpoQBP-aVztjPSGSautEU… > 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. Calculating Distortion in mris_flatten() (Sarah Lavelle) > 2. Fwd: average lobar cortical thickness (James Brown) > 3. Re: Calculating Distortion in mris_flatten() > (Fischl, Bruce R.,PHD) > 4. Re: volumes/surfaces FS6.0 vs FS7.2/3.2 (Nolan, Jackson) > 5. Re: [External] Re: Mapping the labels onto the aparc atlas > (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) > 6. Question about a skullstripping error (dimitra kokkinou) > 7. Re: Fwd: Longitudinal FS pipeline consistently interrupts at > -Sphere for all participants (Huang, Yujing) > 8. cortical thickness in frontal lobe (James Brown) > 9. Re: [External] Re: Mapping the labels onto the aparc atlas > (Huang, Yujing) > 10. Re: Option -contrasurfreg in FreeSurfer 7.X (Douglas N. Greve) > 11. Re: FreeSurfer Hippocampus Segmentation Question > (Douglas N. Greve) > 12. Re: Question about freesurfer default settings. (Douglas N. Greve) > 13. Re: Help: Vertex Properties (Douglas N. Greve) > 14. Re: acompcor in fsfast (Douglas N. Greve) > 15. Re: Fwd: average lobar cortical thickness (Douglas N. Greve) > 16. Re: Question about a skullstripping error (Douglas N. Greve) > 17. Re: cortical thickness in frontal lobe (Douglas N. Greve) > 18. Re: Fwd: average lobar cortical thickness > (Fernanda Hansen P. de Moraes) > 19. Cerebellum segmentation pipeline (AJ) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Nov 2022 17:20:22 +0000 > From: Sarah Lavelle <lavells1(a)tcd.ie> > Subject: [Freesurfer] Calculating Distortion in mris_flatten() > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > < > CABRNrkfJFpcKP0jhBX4Fmv6OKr1KamrNr5Tap_5bM3H5v--eyQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi freesurfers, > > Does anyone know how to measure the distortion of your inflated surface -> > flatmap transformation (using mris_flatten)? > > When being run, the function outputs "final distance error ...%" in the > terminal. What exactly does this mean? and how is this calculated? > > I would like to research optimal cuts for flatmaps, depending on the region > of interest (ROI), so we can minimize the distortion of the ROI itself > on the 2D map. If anyone has any ideas on how this can be done or is > interested in working with me on this, please contact me via < > lavells1(a)tcd.ie> > > Kind regards, > Sarah >

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recon-all failing to generate wm surface
by Christopher Mcnorgan 28 Nov '22

28 Nov '22

External Email - Use Caution A student and I have independently been trying to reconstruct a dataset. We've tried it a couple different ways using either an additional FLAIR or a T2 image and always hit a point where the process halts because of a missing surface file: Loading lh.white surf error: No such file or directory error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file This has happened when running just the autorecon1 step or both autorecon1 and autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is running 7.3.2 on a Mac. In my most recent test, I ran recon-all -autorecon1 -autorecon2 -i <path to T1 file> -T2 <path to T2 file> -subjid <ID> and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but not the ?h.white surface. I'm unclear what's causing the recon-all script to look for the wm surface before it's been created.

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TRACULA: domainname: Command not found.
by Ward Deferm 28 Nov '22

28 Nov '22

External Email - Use Caution DearFreesurfer developers, when trying to run trac-all -prep I am running into this error gbw-d-m0128:DIFFUSION r0755008$ trac-all -prep -c /Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt domainname: Command not found. Too many ('s. ERROR: Syntax error in configuration file /Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt I checked the file but there seem to be no errors in the ('s. This error has previously been encountered https://secure-web.cisco.com/1sKX4EXSdl-lzzKBfb369ful1KJMpWkExgYjXUfdMyAgEi… but there is no solution proposed for the facts that the domainname command is missing from my mac in the /usr/bin folder. What can i do to solve this error. In the attachments you can find the tracula config file if this would be helpful. Thank you for the help. Kind regards, Ward Deferm

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Editing the coregistration
by Asa Borzabadi Farahani 27 Nov '22

27 Nov '22

External Email - Use Caution Hi, I hope this email finds you well. I am doing slab imaging and when I run preproc-sess command to do the functional preprocessing, the results of co-registration are not optimal, hence I need to do manual editing and save a new transformation file. After that, should I run the preproc-sess with option -regfile again? if not, what is the solution. Regards, Asa Farahani

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Confirming FSGD Format and Contrasts
by Olivier Brown 27 Nov '22

27 Nov '22

External Email - Use Caution Dear FreeSurfer experts, I would like to confirm my FSGD file format and mtx contrasts prior to continuing with my analyses. Here is some background information: I have two groups (treatment, control) and would like to determine whether our quantitative scale, CDRISC, is associated with thickness within each group. I would like to control for sex, handedness, and age. Seeing as sex and handedness are categorical, I entered them as Classes instead of variables (Controlleftmale was not included, as no participant fell in that group). GroupDescriptorFile 1 Title CDRISC Class Controlrightfemale Class Controlleftfemale Class Treatrightfemale Class Treatleftfemale Class Controlrightmale Class Treatrightmale Class Treatrightmale Variables CDRISC_TREATMENT CDRISC_CONTROL age Input sub-1 Controlrightfemale 0 19 10.66 Input sub-2 Controlleftfemale 0 26 14 Input sub-3 Treatrightmale 35 0 14.02 Input sub-4 Treatleftmale 35 0 10.16 [...] My contrasts (DOSS) are as follows: [Nregressors = Nclasses + Nvariables Nregressors = 7 + 3 Nregressors = 10] Treatment CDRISC slope = 0 0 0 0 0 0 0 1 0 0 Control CDRISC slope = 0 0 0 0 0 0 0 0 1 0 Are there any glaring issues with this model? The only extra step of consideration here is that I have yet to demean the data. Any guidance is appreciated. Warm regards, Olivier Brown

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R: SAMSEG Lesion images not written
by Cerri, Stefano 27 Nov '22

27 Nov '22

Great! You can use the command "samseg" with the flag "--recon" instead of "run_samseg". This will first run SAMSEG to obtain a whole-brain segmentation, then recon-all will use this segmentation to perform surface analysis and cortical parcellation -- instead of using ASEG segmentation. Look at the help function for more information. Stefano ________________________________ Da: Giulio Siracusano <giuliosiracusano(a)gmail.com> Inviato: domenica 27 novembre 2022 10:07 A: Cerri, Stefano <SCERRI(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written External Email - Use Caution Hi Stefano, I've got this thanks. I simply use freeview and ingest region-specific .mgz files. I just wanted to understand one thing. I realize that using SAMSEG or ASEG it is possible to obtain subcortical segmentation (44 parameters are visualized, representing different regions). I realized that fusiform gyrus, middle temporal and entorhinal cortex volumes cannot be derived using one of the above mentioned methods. I just wanted to know if is there any way to achieve cortical parcellation without using ASEG? Or, in alternative, is there a way to estimate fusiform gyrus, middle temporal and entorhinal cortex volumes from the variables obtained in samseg.stats? Hope to be clear Giulio Siracusano On Sun, 27 Nov 2022 at 14:22, Cerri, Stefano <SCERRI(a)mgh.harvard.edu<mailto:SCERRI@mgh.harvard.edu>> wrote: Hi Giulio, I'm not sure I understand what your goal is. Are you just trying to visualize specific brain structures over your input image? Are you interested in segmentation maps or binary segmentations? If you want to visualize segmentation maps, you can just use Freeview and load the specific structure file(s). Note that these segmentation maps are 1) not binary, i.e., they have values *between* 0 and 1, and 2) they are in the same space as your input image. If you want to visualize binary segmentation for specific structures you can do this in Freeview. You load your segmentation (seg.mgz) as a lookup table and select only the label values that you're interested in. Hope it helps, Stefano ________________________________ Da: Giulio Siracusano <giuliosiracusano(a)gmail.com<mailto:giuliosiracusano@gmail.com>> Inviato: domenica 27 novembre 2022 04:01 A: Cerri, Stefano <SCERRI(a)mgh.harvard.edu<mailto:SCERRI@mgh.harvard.edu>>; freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written External Email - Use Caution Hi Stefano, I'd like to ask you a question wrt SAMSEG. I'd like to extract segmentation maps using SAMSEG, and I know already that we have to use '--save-posteriors' option when running the command. They will be saved in the samseg output directory under the "posteriors" folder. How is it possible, starting from these binary segmentation maps, creating multiple images of the brain where a given (segmentated) region is highlighed? In order to do that, you have to multiply a given reference brain images -over- each segmentation map (which is a binary matrix with 0's and 1's). What is the reference brain image all these segmentation maps are related to? I hope to be clear enough Best regards Giulio Siracusano 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://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1maz9AvYDfMlSPw4n3XIzXHlH00MqWKYxfe-RJHrZ_up6-…> .

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R: SAMSEG Lesion images not written
by Cerri, Stefano 27 Nov '22

27 Nov '22

Hi Giulio, I'm not sure I understand what your goal is. Are you just trying to visualize specific brain structures over your input image? Are you interested in segmentation maps or binary segmentations? If you want to visualize segmentation maps, you can just use Freeview and load the specific structure file(s). Note that these segmentation maps are 1) not binary, i.e., they have values *between* 0 and 1, and 2) they are in the same space as your input image. If you want to visualize binary segmentation for specific structures you can do this in Freeview. You load your segmentation (seg.mgz) as a lookup table and select only the label values that you're interested in. Hope it helps, Stefano ________________________________ Da: Giulio Siracusano <giuliosiracusano(a)gmail.com> Inviato: domenica 27 novembre 2022 04:01 A: Cerri, Stefano <SCERRI(a)mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written External Email - Use Caution Hi Stefano, I'd like to ask you a question wrt SAMSEG. I'd like to extract segmentation maps using SAMSEG, and I know already that we have to use '--save-posteriors' option when running the command. They will be saved in the samseg output directory under the "posteriors" folder. How is it possible, starting from these binary segmentation maps, creating multiple images of the brain where a given (segmentated) region is highlighed? In order to do that, you have to multiply a given reference brain images -over- each segmentation map (which is a binary matrix with 0's and 1's). What is the reference brain image all these segmentation maps are related to? I hope to be clear enough Best regards Giulio Siracusano

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Ubuntu 7z Password Requst
by RW :D 25 Nov '22

25 Nov '22

External Email - Use Caution To Whom It May Concern: I am requesting the password for the FS_7_2_0_ubuntu_18_04_06.ova.7z file so that I can extract the .ova file. I would really appreciate it if you could send it to me! Thank you so much! Sincerely,Rebecca Wu -

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Freesurfer November 2022