Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Re: [Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image
by fsbuild 16 Feb '22

16 Feb '22

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 16, 2022, at 10:02, Cristina Pereira Priego <cristinapereira_31(a)hotmail.com> wrote:        External Email - Use Caution        Hi,My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. I'm waiting for your answer,Best regards,Cristina _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Virtualbox: developer's password
by fsbuild 16 Feb '22

16 Feb '22

External Email - Use Caution Hello Pål Please let us know how much memory your machine has and what OS is running.  I would also check you have 20-30G of free disk space on your boot drive, e.g., the C: drive on Windows. - R. On Feb 16, 2022, at 12:47, Pål Gunnar Larsson <pall@ous-hf..no> wrote:        External Email - Use Caution        Hello I have now look more into fsbuild (Virtualbox Win10/Win11). I find a major problem: The image lays out 4Gb. However, recon-all needs 8Gb. I’ve tried to increase the RAM to 8 (and 16) Gbin VB, but that destroys the virtual machine.Are there ways around, or will there be another image? BestPål  Pål G. Larsson M.D., PhD.Senior Medical OfficerDepartment of NeurosurgeryDivision of Surgery and Clinical Neuroscience Oslo University HospitalPo.box 4950 Nydalen0424 OsloNorwayTel:  (+47) 23074407Mobile: (+47) 93429791E-mail: pall@ous-hf.no Ikke sensitiv Fra: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> På vegne av fsbuildSendt: 15. februar 2022 03:11Til: freesurfer@nmr.mgh.harvard.eduKopi: francois.leroy2@gmail.comEmne: Re: [Freesurfer] Virtualbox: developer's password         External Email - Use Caution        Sending the info to your email shortly. -  R.On Feb 13, 2022, at 04:56, Francois Leroy <francois.leroy2(a)gmail.com> wrote:         External Email - Use Caution         Hi,I am trying to set-up Freesurfer (fs_ubuntu_18_04_06) from Oracle VM Virtualbox. Could you send me the developer's password useful for login?Thanks for your helpRegardsFrancois_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Virtualbox: developer's password
by fsbuild 16 Feb '22

16 Feb '22

External Email - Use Caution Sending the info to your email shortly. -  R. On Feb 13, 2022, at 04:56, Francois Leroy <francois.leroy2(a)gmail.com> wrote:        External Email - Use Caution        Hi,I am trying to set-up Freesurfer (fs_ubuntu_18_04_06) from Oracle VM Virtualbox. Could you send me the developer's password useful for login?Thanks for your helpRegardsFrancois_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mass-univariate LME - contrast for one group
by Franziska Haase 16 Feb '22

16 Feb '22

External Email - Use Caution Dear FreeSurfer experts, I am trying to use the spatiotemporal mass-univariate LME approach for my data but am struggling with choosing the right contrast. I have one group with 14 subjects, two timepoints for each subject and age. My goal is to test whether the subjects experienced any kind of change in cortical thickness from pre- to post-measurement, controlling for age. I followed the tutorial up to the point where I figured out that only one random effect is needed as most vertices did not survive multiple comparisons correction. If I am correct the next step is to test, whether a quadratic or a linear model is needed. Therefore, I tested the contrast CM1.C = [0 1 0 0] on my design matrix X with subjects, time in years, (time in years)², age: 1.0000 0 0 20.0000 1.0000 1.4800 2.1904 20.0000 1.0000 0 0 19.0000 1.0000 1.4800 2.1904 19.0000 ... Multiple comparisons correction revealed an empty vector (as in the tutorial), so that the quadratic term of time was removed and a linear model with one random effect is tested with the new design matrix 1.0000 0 20.0000 1.0000 1.4800 20.0000 1.0000 0 19.0000 1.0000 1.4800 19.0000 ... Next, I applied the contrast CM2.C=[0 1 0] to test for change over time. My question is if this is actually the right way to achieve my goal or whether I am doing something completely wrong. And if it is correct, I would go on by correcting for multiple comparisons, right? How would I visualize the results & additionally get information about significant clusters? Unfortunately, it seems like I am not understanding the last part of the tutorial. Any help would be much appreciated! Best, Franziska _____________________________ Franziska K. Haase, M.A. Sportmedizinisches Institut Department Sport und Gesundheit Fakultät für Naturwissenschaften Universität Paderborn Warburger Str. 100 33098 Paderborn Golfakademie 20b

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PetSurfer: CORTICAL volume-based analysis
by Jennifer Bramen 16 Feb '22

16 Feb '22

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see instructions for how to do a cortical surface-based group analysis. I also see how to do a subcortical ROI-based analysis. However, I cannot find detailed instructions for performing a cortical ROI-based analysis. This is how I think I should adapt the instructions from your subcortical ROI-based analysis instructions for cortical gray matter: mri_vol2vol --mov $PET_DIR/$ID/gtmpvc.output/mgx.gm.nii.gz --reg $PET_DIR/$ID/gtmpvc.output/aux/bbpet2anat.lta --tal --talres 2 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz mri_fwhm --smooth-only --i $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz --fwhm 5 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm05.nii.gz --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz Can someone confirm or correct these commands? I am especially concerned that I have selected the wrong mask. Thanks you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center

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white matter measurements for labels/annotations
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 16 Feb '22

16 Feb '22

External Email - Use Caution Hi, is it possible to extract white matter volume estimations for labels/annotations? I am specifically wondering about the brodmann atlas and the stanford atlas that is already included in latest FS. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image
by Cristina Pereira Priego 16 Feb '22

16 Feb '22

External Email - Use Caution Hi, My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. I'm waiting for your answer, Best regards, Cristina

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Postdoctoral fellow in multimodal neuroimaging
by Corinna Bauer 16 Feb '22

16 Feb '22

External Email - Use Caution We are seeking a full-time postdoctoral fellow with a strong background in resting state fMRI data analysis to join our team. We aim to better understand the neural correlates of visual perceptual dysfunctions observed in survivors of brain injury. We are actively working on an R01-funded project investigating the potential link between thalamocortical networks and severity of visual impairments. The multimodal project includes structural, diffusion, relaxometry, and functional MRI, in addition to behavioral correlates. We are seeking a candidate with the following qualifications: • Doctoral degree in computer science, neuroscience, or related field • Advanced skills in the processing and analysis of fMRI (resting state and task), particularly focusing on network-based approaches • Strong coding skills in python, MATLAB, bash, etc. • Experience with multimodal neuroimaging datasets is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, and their C.V. to Corinna Bauer (Corinna_Bauer(a)meei.harvard.edu) Additional details can be found at: https://secure-web.cisco.com/1ly1VCBmruOLMT0T7zR9O1yCBITb75_g6M5rEL4v_nj-QP…

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How to measure correlation using FreeSurfer
by Koustav Chatterjee 16 Feb '22

16 Feb '22

External Email - Use Caution Dear FreeSurfer experts, I am trying to find the correlation between the regional cortical thickness and volume with different clinical measures of a neurodegenerative condition. I am using DK atlas to get the cortical measures and establish the correlation using SPSS, a statistical software. But, I would like to get FreeSurfer developed images. I would like to learn how to get the areas through images (the FreeSurfer pipeline generated images showing brain regions associated with clinical measures I am interested in). Looking for your kind help. Regards, KC

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using T2 for recon-all
by Eszter Boros 15 Feb '22

15 Feb '22

External Email - Use Caution Dear FreeSurfer Team, We have collected T1 and T2 images in our study and running recon-all with T2 gives us much better results (it was really good to see it). Our aim is to compare these structural data (in Group A) to another patient group (Group B). The problem is that the data of Group B was collected 10 years ago and we did not have a T2 in that study. I am wondering what would be the best approach? Maybe we should not use T2 in Group A because we do not have a T2 in Group B? Or if we do the manual corrections correctly in Group B, this should not be a problem? I am using Freesufer 7.1.1 Thank you for your answer! I greatly appreciate it. All the best, Eszter Boros

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