Re: [Freesurfer] label2annot issue

that would mean that mris_label2annot is probably not reading any of your labels because it is expecting the label name to be, eg, lh.parcel_1.mgh-0001.label.label based on what you have told me. Try changing he label name in the folder to lh.parcel_1.mgh-001.label and change the ctab names to

Re: [Freesurfer] label2annot issue

In the Yeo_split_surf/ the label have exactly the same names as in the ctab. They are named like that : parcel_1.mgh-0001.label parcel_2.mgh-0001.label parcel_3.mgh-0001.label ... parcel_112.mgh-0001.label Yes we had to split the Yeo_split_surface because the goal was to do some analyzes in fMRI

Re: [Freesurfer] label2annot issue

It may have to do with the label names that get created from the ctab. What are the names of the labels in Yeo_split_surf/ ? I can't figure out what you are doing with that code. Looks like you have broken the yeo atlas into labels, then you're combining them together again? On 08/03/2017

Re: [Freesurfer] label2annot issue

Thank you ffor your quick answer, I have attached the --ctab Here is the link for the .mgh files. https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE So my command line to extract the coordinates from the .mgh files : *I)* for f in ${1}/*.mgh do mri_surfcluster --in ${f} --hemi

Re: [Freesurfer] ROI labeling?

what do you mean by an average of the mask? Such an average would not be binary. On 08/03/2017 04:30 PM, Sadie Marvel wrote: > And what if I wanted to compute just one ROI mask (for each region) that is > an average of all the subjects individual ROI masks? >

Re: [Freesurfer] label2annot issue

Please send your full command line, terminal output, and the ctabfile On 08/03/2017 04:30 PM, Redwan Maatoug wrote: > Hi all, > > So my issue is the following : > > I have 112 mgh files. (They come from the Yeo 17 Network atlas (we > split the atlas in smaller regions). I have extracted the

Re: [Freesurfer] ROI labeling?

And what if I wanted to compute just one ROI mask (for each region) that is an average of all the subjects individual ROI masks? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve

Re: [Freesurfer] ROI labeling?

If you are just going to use them as a mask for mri_glmfit, then you can just pass it as --mask or --label, no need to map it back to the individual (which you could do with mri_surf2surf) On 08/03/2017 04:08 PM, Sadie Marvel wrote: > Hi again Freesurfers, > > I am doing a surface based ROI

[Freesurfer] ROI labeling?

Hi again Freesurfers, I am doing a surface based ROI analysis where for each subject, isomorphic ROIs of 300 vertices (centered around peak functional activations) were found on the fsaverage surface space. I was wondering if I should register these masks that I have created back to each

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

hi kirstie, this makes python 2 a requirement for freesurfer as distributed. i've started a PR that should at least help broaden the requirement to support python 2 and 3. https://github.com/freesurfer/freesurfer/pull/112 cheers, satra On Thu, Aug 3, 2017 at 3:41 AM, Kirstie Whitaker

Re: [Freesurfer] Medial Surface Problem

Sure thing, just let me know the filename once it's uploaded. Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bronwyn Overs Sent: Wednesday, August 02, 2017 10:02 PM To:

Re: [Freesurfer] Univariate Linear Mixed Effects {Disarmed}

Hi Martin, Thank you that makes sense now. I don't seem to be able to read a file into matlab containing hippocampal subfield volumes instead of the standard aseg using fast_ldtable. I haven't changed anything other than substituting hippocampal volume for dentate gyrus volumes. So the file

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

Hi freesurfer team, I just ran into this error. I fixed it by switching from python 3.6 to python 2.7. Does this sound like the right fix? I wonder if it is documented somewhere on the wiki? Thank you for the great tool! Kx On 18 November 2016 at 21:14, Douglas N Greve

Re: [Freesurfer] Univariate Linear Mixed Effects

Hi Amanda, the C matrix below has 14 columns ( 3 + 5 + 6 ). To find out what hypothesis are tested, look at the corresponding columns. column 4 for example is the MCIs slope delta with respect to controls (so slope difference MCIs and CN) the next test is slope difference between MCIs and