[Freesurfer] Extract the ROI mapping

External Email - Use Caution Hello Freesurfer developers, After I recon-all my subjects, the label files are generated. Could you please kindly help me how can I extract the special brain region from these label files by matlab: But I don't know if it is the mean thickness for

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Hello，Bruce I attached my subjects. Please help me. Thank you. Abby 2851A_T1_w4.nii Bruce Fischl 于2019年4月18日周四 下午10:53写道： > Hi Abby > > it's hard to tell from the

Re: [Freesurfer] issue running trac-all longitudinal

External Email - Use Caution Sorry, the beginning of the email seems to have been cut off. I was trying to run trac-all on one of my subjects to troubleshoot running the following command. trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh I posted the errors and at

[Freesurfer] MRI RA position available at Ohio State Buckeye Brain Aging Lab

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position in the Buckeye Brain Aging Lab (B-BAL; https://u.osu.edu/bbal/)

[Freesurfer] issue running trac-all longitudinal

External Email - Use Caution Hello, trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the attached configuration file. I get the following error message INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.

Re: [Freesurfer] fixing errors with pial boundary

This often happens because the white surface is in accurate and fixing the white surface will fix the pial. Is the white surf ok? Sending pics would be helpful On 4/18/19 1:28 PM, Morgan Botdorf wrote: > > External Email - Use Caution > > Dear Freesurfer Experts, > > I asked about this a

[Freesurfer] fixing errors with pial boundary

External Email - Use Caution Dear Freesurfer Experts, I asked about this a few months ago, but didn't receive a reply so thought I would ask again! We have come across several subjects where the pial boundary line does not extend far enough outward and misses some gray matter. We

Re: [Freesurfer] convert aseg to functional space

External Email - Use Caution Thanks again Doug, that makes sense. I was aware that the matrix could be inverted but I thought we would need --inv for that. Does mri_label2vol also convert label-to-temp when --label is used, or is this specific to seg-to-temp conversion? I'm asking

Re: [Freesurfer] convert aseg to functional space

The registration actually goes from anat to func. mri_label2vol knows this. In any case, it is just a matrix that can easily be inverted. On 4/18/19 11:58 AM, Sam W. wrote: > > External Email - Use Caution > > Hi Doug, > Thanks! After registering with bbregister -mov example_func.nii (to

Re: [Freesurfer] convert aseg to functional space

External Email - Use Caution Hi Doug, Thanks! After registering with bbregister -mov example_func.nii (to get reg.dat), I tried mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o aseg-in-func.nii --temp example_func.nii the result looks good, but I'm wondering why

Re: [Freesurfer] CORRECTING DEFECT 1 problem

Hi Abby it's hard to tell from the image, but it looks like there is a big I/S bias field as well as large amounts of pathology. If you upload the subject to our ftp site we will take a look cheers Bruce On Thu, 18 Apr 2019, Abby tang wrote: External Email - Use Caution

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open fil

Re: [Freesurfer] Issue with longitudinal surfaces

Hi Maxime, also how do the surfaces look on their respective time point images from long? Do they look accurate there? Could be that there are differences across the time points that cause the surfaces to differ this much. Was the same hardware (scanner, coil) and same protocol used for both time

Re: [Freesurfer] Thalamic segmentation

External Email - Use Caution Dear Zheng One of the other developers can help you with Freeview. But, as a workaround, you can always use an earlier version of Freeview, and load the lookup table of the Dev version. Cheers Eugenio Sent from mobile, please excuse brevity and typos

[Freesurfer] Thalamic segmentation

External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by /opt/freesurfe