Re: [Freesurfer] Qdec vertex-wise clustering question

Not sure I know what you mean. For creating the design matrix, it uses the info from the qdec table. BTW, qdec is deprecated. On 7/12/2021 5:27 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > Hello, > > I had a brief question regarding Qdec vertex-wise clustering. Does >

Re: [Freesurfer] Average intensity from functional image within a label along the surface

Try using --fill-ribbon when running mri_label2vol On 7/12/2021 12:26 PM, Erik Jahner wrote: External Email - Use Caution Thank you very much for your assistance. In retrospect, my first question was a bit silly. I do have a follow-up question. I have a label that was made from a m

Re: [Freesurfer] Tracula 7.1.1 - trac-all - stat

Hi Fanny - The meaning of the statistics is explained in this section of the TRACULA tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics#Anisotropyanddiffusivityaveragedatcross-sectionsalongapathway Please note that the instructions in the tutorial have now been updat

Re: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

Hi Jürgen - In the 7.2 beta version (which will also be the official version any day now), you should be able to set the variable "dTE" (the TE difference) directly in the config file, so you don't need to provide the fieldmap scan as a dicom. There are many more and (more exciting!) reasons th

[Freesurfer] Qdec vertex-wise clustering question

External Email - Use Caution Hello, I had a brief question regarding Qdec vertex-wise clustering. Does Qdec use the data in the raw imaging files or the qdec.tables.dat file to generate the vertex-wise clustering results for cortical thickness group comparisons? Many thanks for y

Re: [Freesurfer] Developer login

External Email - Use Caution Hello Zachary, Sending some info to your private email shortly. - R. On Jul 12, 2021, at 16:33, Zachary Wickliffe wrote:External Email - Use CautionHey there, setting up virtualbox to run freesurfer and it's a

[Freesurfer] RAM per CPU for running Freesurfer 7.1

External Email - Use Caution Hi Freesurfer Experts, I am designing some new hardware for a mini-cluster running Freesurfer and other neuroimaging toolboxes and wanted to better understand requirements from Freesurfer. 1) Is there a minimum amount of ram per core that is needed/

Re: [Freesurfer] Developer login

External Email - Use Caution Hey there, setting up virtualbox to run freesurfer and it's asking for a developer login. Can you help? Thank you, Zachary Wickliffe +1-727-871-1733 zswickli...@gmail.com On Mon, Jul 12, 2021, 4:28 PM Zachary Wickliffe wrote: > Hey there, setting u

Re: [Freesurfer] Average intensity from functional image within a label along the surface

External Email - Use Caution Thank you very much for your assistance. In retrospect, my first question was a bit silly. I do have a follow-up question. I have a label that was made from a modified parcelation of the Yeo atlas. When I attempt to project that label onto the voxel

Re: [Freesurfer] mri_glmfit DOSS

External Email - Use Caution Thank you for your reply! Using DOSS is precisely what I was trying to do, but mri_glmfit doesn't let me. I worked around by creating the design matrix in matlab and specify it to mri_glmfit directly, but I was wondering whether this might be bug in

[Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction

External Email - Use Caution Hi, Back in February I already had some issues with FIR analysis using a task regressor. In the meantime, I switched to other analysis. But now we would want to try that again. I attached the old mails below, but since the problem slightly changed,

Re: [Freesurfer] question about longitudinal data analyses

Yes, it will work on both. If you use a table, then pass the table with --table tablefile instead of --y On 7/12/2021 7:54 AM, Ritobrato Datta wrote: External Email - Use Caution Good morning, Thanks Doug for the answers. Quick naive question. The analyses I want to perform are on v

Re: [Freesurfer] question about longitudinal data analyses

External Email - Use Caution Good morning, Thanks Doug for the answers. Quick naive question. The analyses I want to perform are on volumetric data parcellated using aseg and not surface data. Does mri_glmfit work with the output of the asegstats2table or on voxelwise FA maps ?