[Freesurfer] Using .label file as mask in mri_fdr

Hello, I want to do a FDR correction using mri_fdr within a ROI mask (in .label format). I see the option of passing the sig.mgh volume through a mask, and I read that one can use the mask.mgh in the GLMFIT folder. What is this mask.mgh? I tried to visualize it in Freeview but it doesn’t look l

[Freesurfer] e-mail error {Disarmed}

Hi FS list, When I sent an e-mail to you, I always recieved a disarmed e-mail, as follows: What' wrong? Is there any way to resolve it? Sincerely, Zheng | | 13181786167 邮箱：13181786...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@n

[Freesurfer] Recon-all {Disarmed}

Hi experts, I am using FS 6.0 for LGI. My data is fetal images. I ran "recon-all" pipeline for cotical thickness and LGI. Is it suitable? Or are the results reliable, such as the LGI value of precental? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 郑凤莲 邮箱：zhengf

[Freesurfer] Potential ways to overlay perfusion ROIs onto cortical thickness maps

Dear experts, I am trying to figure out the best way to overlay areas of low CVR reactivity and correlate that with cortical thickness measurements in those given regions. I was able to overlay our CVR map onto an inflated cortical surface in 3D and modify the configuration to see areas of low

Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

Hi Douglas, thanks for the advice. I have one more question: I want to find correlations of the lGI and the respective psychometric measurement, regressing out the effect of gender, sequence and the other covariates. I just had a look at the examples of FSGDs containing two factors with two

[Freesurfer] Can't open tkmedit

Hi, I tried opening tkmedit but received the following error: libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: GLXBadContext Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 6 (X_GLXIsDi

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

Hi, the two rows in the contrast matrix cannot be identical - this is also not the case in the tutorial example, please take a look there. Actually, how does your current design matrix (X, not M) look like? A contrast vector (or matrix) needs to have as many entries (or columns) as there are colu

Re: [Freesurfer] Reg Mapping automatic segmentations to functional space

Did you check the registration? Is the fMRI whole brain? On 3/6/18 2:00 PM, Anita S wrote: Hello all, I have mapped a subject's fMRI Feat data onto the anatomical scan and then mapped the segmentations to the functional space using the following commands: reg-feat2anat --feat  feat_folder

Re: [Freesurfer] getting h/o atlas into individual surface (and then volume) space

Hi Dorit, I would probably run recon-all on the mni152, then map the atlas onto the surface of the mni (mri_vol2surf with --regheader), then create an annotation of the atlas using mris_seg2annot (run with --help for examples), then use mris_apply_reg to transfer the annot to your individual su

Re: [Freesurfer] -qcache error

It was deleted but then it was created as a link. Does the link exist? On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs

Re: [Freesurfer] ASEG and APARCSTATS2TABLE on longitudinal data

On 3/7/18 6:46 AM, Lisa Delalande wrote: Hi FreeSurfer experts, I would like to use the asegstats2table and the aparcstats2table commands on my longitudinal data, which have been processing following the longitudinal pipeline (recon-all -cross, - base and finally -long). And I have two ques

Re: [Freesurfer] mir_vol2surface registration file error

You create it with bbregister. See the multimodal integration tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview On 3/6/18 6:36 PM, srishti goel wrote: I am sorry but that is what I am unsure about it. I don't know how to obtain a registration matrix or which reg

Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

Hi Kai, please remember to post to the list. Your FSGD file is not quite right. Gender is a discrete variable and should be represented by two groups not as a covariate. If Sequence is discrete, then you need four groups (Gender by Sequence). doug On 3/9/18 3:20 AM, k.ohmst...@stud.uni-heidel

[Freesurfer] PhD position on electrophysiology and cognition in multiple sclerosis patients!

*Doctoral Student* *Neuroscientist with focus on electrophysiology and cognition in multiple sclerosis * The *medical faculty of the University of Mainz*, Germany, invites applications for a *PhD Student * for a functional translational neuroscience (FTN) scholarship three year position to wor

Re: [Freesurfer] mri_ca_normalize error: Abort (core dumped)

Hi Theresa can you open the inputs to mri_ca_normalize in freeview ok? The nu.mgz for example? Please send us the recon-all.log so we can examine it. If all the inputs look fine, then upload your subject and we will have a look. cheers Bruce On Fri, 9 Mar 2018, Marschall, T.M. wrote: De

Re: [Freesurfer] RECON-ALL {Disarmed}

Hi Zheng can you please include the full command you ran, the full screen output and the recon-all.log file? cheers Bruce On Fri, 9 Mar 2018, 郑凤莲 wrote: Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't know

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

Hi Chris this probably means that the triangles aren't constructed according to our conventions. The ordering in faces is important as the cross-product of the legs of each triangle have to point outwards. That's how we define the surface normal vector field. Sounds like whatever software you

Re: [Freesurfer] Mean Curvature

Hi Kasper a) Yes, the sign of H is defined by the convention you choose for the surface normals. We choose outwards pointing normals, which implies that H is negative in convex regions (think of the sign of the coefficient on the quadratic term with the surface normal as the z axis) b) more

[Freesurfer] mri_ca_normalize error: Abort (core dumped)

Dear all, I’m currently running the -reconall command on 40 subjects. One of them exited the mri_ca_normalize step with an error saying: Abort (core dumped) I tried rerunning it, however the error keeps occurring. So I have search the list, but could not find a solution to my problem. Does

[Freesurfer] RECON-ALL {Disarmed}

Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't know how to resolve this problem. Looking forward to your reply. Thanks very much. Sincerely, Zheng | | 13181786167 邮箱：13181786...@163.com | 签名由 网易邮箱大师 定制___