[Freesurfer] Help -Quality control of the splitting of midline structures?

Dear Freesurfers, I have a question about whether it is possible to check how well each participant in my study lines up with the Freesurfer template in order to check how midline structures were split. I am concerned about how well my ACC ROIs line up with the midline of the brain, and wo

Re: [Freesurfer] Help -Quality control of the splitting of midline structures?

Hi Sarah do you want to look at the surfaces? This can actually be done in freeview if you don't mind messing around with the command line a bit (you can specify offsets and rotations for the surfaces so that you can see the medial wall if you want). Perhaps Ruopeng can comment? cheers Bruce

Re: [Freesurfer] 3dvolreg Error for preproc-sess

I am able to run AFNI normally, it was just an issue with this particular command. I did however figure out a solution, which was just that I needed to use v5.3 instead of 5.2. I'm not sure if it's just our copy here that's outdated, but as soon as I loaded 5.3, I ran the same command I was trying

Re: [Freesurfer] free-surfer longitudinal Qdec table

Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command *mris_preproc* --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mg

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Thank you Paul that is very helpful, but I could use a little more specific help. A little more context: I ran a group vertexwise analysis with all my subjects mapped to the fsaverage and traced my group cluster in QDEC and saved the label. Now I would like to somehow get it into afni in the sa

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hello all, I believe Ziad Saad and friends have written AFNI/SUMA to make this easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will convert all the volume-space segmentation and parcellation files to be readable in AFNI. Takes only a couple of minutes. Run @SUMA_Make_Spec_FS

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Tara, You have to run the mri_annot2label command on the individual subject's aparc.annot files (R&L hemi). This will give you the medial wall labels you can then use to construct your own annotation. You have to include it in your ctab file, after "unknown." I think it may be the bankssts.label

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hello all, I believe Ziad Saad and friends have written AFNI/SUMA to make this easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will convert all the volume-space segmentation and parcellation files to be readable in AFNI. Takes only a couple of minutes. Run @SUMA_Make_Spec_FS

[Freesurfer] Using Gender as a Covariate in glm_fit

Hello, I am performing an mri_glmfit analysis between my control and my clinical group, and I'm including age and total intracranial volume in the model. However, I'd like to regress out the effects of gender, and I'm curious if the best approach to do this is to group my subjects by their gender

[Freesurfer] mri_segstats

Hi, I have two questions about mri_segstats. I want to measure the surface area of a functionally-defined ROI. I used the mri_segstats as below and I want to be sure that it is correct. Please note that ROIs were defined in the native space. mri_segstats --i $SUBJECTS_DIR/SBJ1/surf/rh.area -

Re: [Freesurfer] Seg fault (fwd)

Gillian, This tkmedit crash problem is a strange one. Something must have changed, and I’ll try to suggest some things to try. Was your .cshrc file changed? Anything added to it that might change LD_LIBRARY_PATH s? What is the output if you run: otool -L `which tkmedit.bin` it should be

Re: [Freesurfer] A question about mri_glmfit-sim --3spaces

Hi, doug: Thanks for your answers,I got it. Han At 2014-06-05 00:23:15, "Douglas N Greve" wrote: > >The first and third are the same. Don't use the 2nd >doug > >On 06/04/2014 06:12 AM, 王晗 wrote: >> Hi,all: >> I was using mri_glmfit-sim for multiple correction,but I'm wondering >>

Re: [Freesurfer] epidewarp.fsl

Hi again, I posted a question about the script "epidewarp.fsl" but didn't see the answer. Anybody know where I can find a version working under fsl-5.X? Thanks. On 6/7/2014 5:29 PM, XJ Kang wrote: > Hi, > The script "epidewarp.fsl" included in the FreeSurfer package for > field map correction

[Freesurfer] registering functional labels to another anatomical data

Dear experts, I have functional labels registered to Brain A. I also have another anatomical data (Brain B) of the SAME SUBJECT, scanned at a different time. I'd like to calculate cortical thickness of Brain B at those labels, using the functionally defined label that was created with Brain A.