Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

Doug, This is a new problem. I figured out my earlier issue. This makes a 8V1+aseg.mgz file there are just no 4001 and 3001's in the file so when I binarize there is nothing there. So my question is why is it not identifying the wm next to my label? This is happening in multiple subjects on

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

I don't know, you'll have to look at how you computed the first frame. Maybe the 1st and 2nd time point for that subject are the same On 02/05/2018 04:27 PM, miracle ozzoude wrote: > Hello Doug, > > Thank you. How do i got about fixing? Do you think it's a good idea to > start afresh on this

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, Thank you. How do i got about fixing? Do you think it's a good idea to start afresh on this subject (i.e. recon-all and longitudinal pipeline)? Best, Paul On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve wrote: > The first frame in your input file is all

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

I have resolve the previous error (there was a typo in the fsdg file) but re-running I obtain this error: Normalized matrix condition is 1 Matrix condition is 1 mghRead(/Applications/freesurfer/subjects/rh.GROUP.thickness.10B.mgh, -1): could not open file fsgd file is:

[Freesurfer] Curvature Index and Folding Index

Dear FreeSurfer Expert, Could you explain me what does the curvature index and folding index mean in the Parcellation Stats File? In which way they are calculated? or you can give me some related documents. Thanks a lot. Ting ___ Freesurfer mailing

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Try running selxavg3-sess with -monly sxa3.m Then start matlab and run sxa3.m On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote: > Dr. Greve, > > I tried with root access and it still gave the same error. I am using a > virtual machine from our server that I connect with VCN, and it has >

Re: [Freesurfer] FSFAST

Only fmc.odd.sm5.nii.gz is in the same dimensions as the f.nii.gz. However, I found a flag in the selxavg3 (-no-con-ok)that I do not need to specify a contrast. If I am not mistaken, all is good now. Thank you for your response. On Sat, Feb 3, 2018 at 2:03 PM, Douglas Greve

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Dr. Greve, I tried with root access and it still gave the same error. I am using a virtual machine from our server that I connect with VCN, and it has freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

I obtain this error: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh Reading source surface

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

I don't know, it is all very weird. What platform are you using? On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote: > Dr. Greve, > > Yes I have tried making new files. (I also gave the previous files and > folders full permission with chmod which again didn't work) Mkanalysis-sess > did not have

Re: [Freesurfer] One Group (One Factor), Two Covariates

The 2nd contrast (slope) is the one you want. On 02/05/2018 01:21 PM, std...@virgilio.it wrote: > > Thanks. > > Only for I quick check of my understanding, if I'm using: > > > FSGD File (g1v1.fsgd) > > GroupDescriptorFile 1 > > Title OSGM > > Class Main > > Variables Age > > Input subject1 Main

Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

Sorry, is this related to the earlier question about how to remove non-wm labels or is this a new submission? If a new subj, can you describe the problem you are having? On 02/05/2018 01:23 PM, Sims, Sara A wrote: > > This is the whole process output from a rerun on a subject that didn’t >

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Dr. Greve, Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it

Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

This is the whole process output from a rerun on a subject that didn’t work the first time or with the rerun: Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab Number of ctab entries 2 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd

Re: [Freesurfer] One Group (One Factor), Two Covariates

Thanks. Only for I quick check of my understanding, if I'm using: FSGD File (g1v1.fsgd) GroupDescriptorFile 1 Title OSGM Class Main Variables Age Input subject1 Main 30 Input subject2 Main 40 . A) Contrast 1 (intercept.mtx) 1 0 B) Contrast 2 (slope.mtx) 0 1 Considering that my

Re: [Freesurfer] Removing labels after extending parcellation into white matter

You mean you want to remove everything but the WM labels? You can do it in two steps: 1. Create a mask of the wm labels: mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz 2. Mask the wmparc: mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz

Re: [Freesurfer] One Group (One Factor), Two Covariates

If you have one class and two variables, then [0 1 0] and [0 0 1] On 2/4/18 10:23 AM, std...@virgilio.it wrote: I would like to find where the functional connectivity is correlated to VARIABLE 1 regressing out the VARIABLE 2. How I should set my contrast.mtx? Thanks Stefano Il 3

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

On 2/4/18 10:06 AM, std...@virgilio.it wrote: I have run: 1) mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval

Re: [Freesurfer] Fwd: Re: One Group (One Factor), Two Covariates

I guess you could make the contrast [1 1 0], but I have no idea what the interpretation would be. I'll leave that up to you On 2/4/18 8:58 AM, std...@virgilio.it wrote: Thanks. what do I do if I would like to maintain the effect of "main" in the points 2 and 3. Best regards Stefano

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

The first frame in your input file is all 0s, so something is wrong with the fist subject On 2/3/18 3:03 PM, miracle ozzoude wrote: Hello Doug, I have uploaded the files you requested. Thank you for your help. Best, Paul On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails? On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote: > Hello Dr. Greve, > > The analysis.info file is below. I should also say that, when I am trying to

Re: [Freesurfer] How to compile FreeSurfer with CUDA?

Once upon a time I had many problems with OpenGL/GLU problems in my FreeSurfer build. Ultimately the problem was that the version of GLU installed with Mesa package was not really compatible with the compiler that I was using. After straightening this problem out using the configure option

[Freesurfer] How to compile FreeSurfer with CUDA?

Hello Freesurfer experts, I am trying to compile FreeSurfer to make use of its CUDA capabilities. The precompiled version does not run on my system. But when I try to compile FreeSurfer I get the following error: # ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages

Re: [Freesurfer] mpr2mni305 talaraich transformation error

Dear Emma, Thank you for your response! Since I got this message I added the -cw256 flag: The physical sizes are (512.00 mm, 512.00 mm, 110.00 mm), which cannot fit in 256^3 mm^3 volume. ERROR! FOV=512.000 > 256 Include the flag -cw256 with recon-all! However, when inspecting the orig.mgz