Re: [Freesurfer] dcmunpack Error

2018-11-08 Thread Maryam Tayebi
External Email - Use Caution Dear Greve, Thank you so much. It s finally fixed and now is working properly. Regards On Fri, 9 Nov 2018 at 02:50, Greve, Douglas N.,Ph.D. wrote: > It actually looks like it completed and created the desired output file. > Did you check it? Tho

Re: [Freesurfer] Multivariable linear regression with binary variables

2018-11-08 Thread Greve, Douglas N.,Ph.D.
You'd have 512 groups total, which is probably way too many regardless of whether you do so manually or automatically. You need to think about how you want to model all those variables since modeling all possible interactions is not going to be possible. On 11/08/2018 12:45 PM, Worker, Amanda w

[Freesurfer] Multivariable linear regression with binary variables

2018-11-08 Thread Worker, Amanda
External Email - Use Caution Hi, I am trying to run a multivariable GLM with mri_glmfit and I am currently setting up my fsgd file. I have 9 binary variables and 1 continuous variable. My understanding is that in the fsgd file, my "class" would be every possible combination of

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

2018-11-08 Thread Greve, Douglas N.,Ph.D.
The problem is a combination of things in that mri_tessellate writes out a file that read_surf.m cannot read. I have fixed this in our tree. You can get around it by using mri_mc instead of mri_tessellate (same exact command line). mri_mc uses marching cubes. On 11/05/2018 01:07 PM, Bruss, Joe

Re: [Freesurfer] mris_apply_reg failing for area/volume

2018-11-08 Thread Greve, Douglas N.,Ph.D.
Not sure what is going on. Can you send me the input rh.area file as well as lh.40tvs8ref_sym_20.sphere.reg and 40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here https://gate.nmr.mgh.harvard.edu/filedrop2 When it asks you for an email, use gr...@nmr.mgh.harvard.edu and not my email

Re: [Freesurfer] dcmunpack Error

2018-11-08 Thread Greve, Douglas N.,Ph.D.
It actually looks like it completed and created the desired output file. Did you check it? Those errors are generated because it is trying to figure out whether the file is a diffusion scan. You can turn it off by setting setenv FS_LOAD_DWI 0 or for bash export FS_LOAD_DWI=0 On 11/07/2018 09:5

[Freesurfer] Coordinates' annotations question

2018-11-08 Thread 王子谦
External Email - Use Caution Hi developers, thank for your amazing program, it’s really helpful. After using it for a short time, I met a question in the middle of my research. I have thousands sets of coordinates in MNI space. And I wanna get the information about where these co

Re: [Freesurfer] mris_apply_reg failing for area/volume

2018-11-08 Thread James Michael Roe
External Email - Use Caution Hi Doug Here is the output file James Michael Roe PhD. Candidate Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo PB 1094 Blindern 0317 Oslo Mobile: 958 49 437 Fr