[Freesurfer] QDEC - Controlling for gender

Hi Freesurfer experts, I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, gender is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in

[Freesurfer] 3d brush in freeview

Is there a 3d option for the editing brush in freeview ala tkmedit? Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E

Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

Uploaded: https://gate.nmr.mgh.harvard.edu/filedrop2/index.php?p=6cwuw1zwaag Also, I've included a dwi_TRfixed.nii.gz file with the TR in the header fixed. Curious to see if that one works! mri_convert --in_type nii --out_type nii --out_orientation RAS dwi.nii.gz -tr 1000 dwi_TRfixed.nii.gz On

[Freesurfer] Multiple --meas files in mri_glmfit

Hi list, is it possible to have multiple --meas files in mri_glmfit? For example, for a group of 40 subjects, to check in every vertex if there is a relation between CT and the t of a fMRI contrast. Thanks! Gari ___ Freesurfer mailing list

Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

Hi Derek - It looks like it fails, but I suspect that it may be something unrelated to the warning. Can you please upload a zip file with this subject's TRACULA directories (dmri, dmri.bedpostX, dlabel, dpath, scripts) for me here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y

Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

Hi Derek - It sounds like the programs that you used to convert from dicom to nifti and to resample from anisotropic nifti to isotropic nifti don't copy the TE and TR info in the header correctly. This information is not needed to run -paths, however. Does trac-all stop running after this

Re: [Freesurfer] ribbon volumes

Almost. This will include medial wall voxels that are not GM. It will also not include subcort GM. It is better to use aparc+aseg.mgz and merge the GM ROIs together. On 1/15/17 1:01 AM, Zhivago wrote: Hi, Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall? Can I used

Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

Hi Anastasia, Thanks for the quick response! The TE and the TR are both listed as 0.00 with mri_info. Of note, these dwi images have been resampled from anisotropic to isotropic voxels using an in-house python script. I noticed that this error comes up only for the resampled, but not the

Re: [Freesurfer] mri_vol2surf

Thanks Bruce! Appreciate all the help, On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl wrote: > 1) This is up to you. Jon Polimeni had a nice paper describing the > trade-off between accurately representing the local neural response (which > is best at the white

Re: [Freesurfer] mri_vol2surf

1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface). 2) This is also up to you.Read the help in mri_vol2surf.

Re: [Freesurfer] mri_vol2surf

Hey Bruce, Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these. 1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which

Re: [Freesurfer] ribbon volumes

yes, I believe so On Sun, 15 Jan 2017, Zhivago wrote: Hi, Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall?  Can I used these as GM voxels? Thanks, Zhivago... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_vol2surf

Hi Zhivago 1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1-->