Re: [Freesurfer] Zero angle for retinotopy

Does this mean that the zero angle is the one where the wedge starts rotating in the experiment? Does this apply to eccentricity experiment also (In my lab's protocol it doesn't start from zero)? On Sat, Feb 6, 2016 at 2:20 AM, dgw wrote: > Hi, > > I know Doug is away, so

Re: [Freesurfer] Planum temporale measurement

Hi Adam, sorry for the delay in my answer The aparc.a2009s is based on the anatomical rules we published in Neuroimage in 2010: - There are 2 separate labels : one is sulcal, for the posterior part of the lateral fissure (Lat_Fis-post), the other one is gyral, for the planum temporale

[Freesurfer] To use a ROI.label as seed in FS-FAST

Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.How can I do it?Should I use mri_label2vol? Thanks. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

Re: [Freesurfer] Paired analysis FSFAST

When you run isxconcat-sess add -paired-diff. This will compute 1-2 for each subject. You can then run mri_glmfit. With that FSGD file, your contrast should be 1 not 1 0 doug On 2/6/16 11:17 AM, Thục Trinh wrote: Hello, I'm working on group analysis in fMRI activation using FSFAST. I tend

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM,

Re: [Freesurfer] spot checking results

Even on the same operating system they will be different because there is stuff in the header that will change. Use mri_diff (volumes, segmentations, and surface overlays) or mris_diff for surfaces to check whether they are different. On 2/5/16 11:55 PM, dgw wrote: > Don, > > Running

Re: [Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

On 2/5/16 12:49 PM, Ilaria Sani wrote: Dear All, I have a functional and a T1 registered, but they are not in anatomical coordinates. Do you mean neither are in the "conformed" 256^3, 1mm^3 FreeSurfer coordinates? I put the anatomical in the desired position by using tkregister2. Was the

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Try multiplying the covariate by 100 (after subtracting the mean). On 2/5/16 8:28 AM, Nabin Koirala wrote: I did that but it still does not work, it is almost the same error except the condno is now 15521.8 before it was 27492.1, though I am not sure if that tells something about the error.

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

Can you send me the Xtmp.mat file? On 2/2/16 6:40 PM, Mcnorgan, Christopher wrote: > Hi, > I'm attempting an inaugural run through the FS pipeline on some event-related > data collected over 6 runs. I'm not sure if this makes any difference, but > the experiment is self-paced, and the events

Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

On 2/7/16 1:34 PM, Silas wrote: Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

Re: [Freesurfer] Fw: Gray matter intensity

Load them as an overlay in freeview or tksurfer. There should be examples on the wiki. On 2/4/16 10:04 PM, Sabrina Yu wrote: > Hi Doug, > > Thank you for taking the time to answer, I really appreciate it! I have > completed this step for all subjects, and created the lh.wm.mgh and rh.wm.mgh >

Re: [Freesurfer] Volume analysis in native space vs. mni305 space

Right. FSFAST uses "three spaces": lh (surface), rh (surface), and subcortical (volume). To prevent voxels from being counted twice, we mask cortical voxels out of the volume-based analysis. On 2/5/16 11:29 AM, Rodriguez-Thompson, Anais wrote: Hi FreeSurfer experts, I'm writing to follow

Re: [Freesurfer] generate .mgz file from DICOM

It looks like there is a lot of information missing from the dicom file. Did it come directly from the scanner? Or was it transformed in some way? Anonymized? On 2/4/16 5:06 PM, Kan Ding wrote: Hi, I am having trouble to generate .mgz file from DICOM. However, I was able to run the same

Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values

There is not a single command to do this, but there is a bit of a hack that will work assuming the value you don't want to include is 0. You will have to run mri_vol2surf multiple times using a different projection fraction, creating a different file for each. Then use mri_concat to