Re: [Freesurfer] problem with contrast in 1st-level analysis

External Email - Use Caution Hi, Doug I find two mistakes which may affect the final output after going through FSFAST tutorial again. first, the onset time of each block is wrong. the *original *parameter file is 0 1 16 1 3D 17 0 16 1 FIXATION 33 2 16 1 ZERO-DISPARITY 49 0 16 1 FI

Re: [Freesurfer] Yeo labels

External Email - Use Caution Hi Duygu, I don't think that's the case at this moment. We usually use the following command: mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh --sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval $SUBJECTS_DIR/yoursubje

Re: [Freesurfer] problem with contrast in 1st-level analysis

did you look at the zero-disparity vs fixation contrast? Can you send your paradigm file? Can you send pictures? On 1/9/19 12:26 AM, xi star wrote: > > External Email - Use Caution > > Hi! FS Experts! > In the fMRI experiment, there are 2 conditions: > 1#  3D picture > 2#  zero disparity

Re: [Freesurfer] mris_apply_reg failing for area/volume

I have found and fixed the problem. You will need a new version of mris_apply_reg from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg Copy it to $FREESURFER_HOME/bin (after making a backup copy of the one that is there) On 1/7/19 2:10 PM, James Michael Roe wrote: > >  

[Freesurfer] Talairach Transform failure

External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri*

[Freesurfer] Fwd: problem with contrast in 1st-level analysis

External Email - Use Caution I also tried anther task-related fMRI, which has similar parameter, list as follow: 0 1 16 1 move 17 0 16 1 blank 33 2 16 1 static 49 0 16 1 blank 65 1 16 1 81 0 16 1 97 2 16 1 113 0 16 1 129 1 16 1 145

Re: [Freesurfer] Questions About Effect Sizes in Vertexwise GLM Anlaysis

External Email - Use Caution Hi, I just wanted to follow up and see if there was anyone who could answer my questions: 1. What is the unit of effect size for the gamma.mgh file created by vertexwise GLM Analysis using mri_glmfit? 2. Based on two previous posts ( https://www.mail

Re: [Freesurfer] Subcortical divide parcellation

Hi Huifang what is your goal? We do have tools that will generate sub-segmentations of some structures (thalamus, amygdala and hippocampus). These are along anatomical lines rather than purely geometric ones. cheers Bruce On Wed, 9 Jan 2019, WANG Huifang wrote: External Email - U

Re: [Freesurfer] Programs samples two surface parcellation into volumetric segmentation

Hi Yerong mri_aparc2aseg combines the aseg and the aparc to generate files like the aparc+aseg.mgz. You can look in the recon-all.log or recon-all.cmd file to see how it is run (or the help) cheers Bruce On Tue, 8 Jan 2019, Yerong Li wrote: >External Email - Use Caution > > Dear Free

Re: [Freesurfer] On relationship between aparc+aseg.mgz and ?h.aparc.annot

Hi Yerong the indices and names are all in the FreeSurferColorLUT.txt file. The indices in [1000,2000) are for lh and in [2000,3000) are rh. For example, 2008 is ctx-rh-inferiorparietal. cheers Bruce On Tue, 8 Jan 2019, Yerong Li wrote: >External Email - Use Caution > > Dear Bruce

Re: [Freesurfer] (no subject)

External Email - Use Caution Dear Ruopeng, I tried the UpdateFreeview procedure below, however I received the error message: >> This application failed to

[Freesurfer] Surface maps of cortical thickness

External Email - Use Caution Hello everyone, I have some problems with the computation of the SD of thickness maps (mgh file) of 10 subjects. First I computed the average thickness map (to fsaverage) with the command: mris_preproc --fsgd qdec/subject_list.fsgd --target fsaverage