[Freesurfer] complete list of structures for SubCortGray

Hi, >From https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats "SubCortGray - includes thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there). This is a simple voxel count of structures identified as subcortical GM." Could you please let me know if

Re: [Freesurfer] make_average_subject monkey data

See if the talairach.lta is any better, eg cd subject/mri/transforms tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta If so, you can try running make_average_subject with --xform talairach.lta I've never done this, but it might work :) On 03/15/2018 01:02 PM, Francesca Strappini

[Freesurfer] Postdoctoral Fellow Position at the University of Pittsburgh

Hello fellow neuroimagers! The Laboratory for Child Brain Development at the University of Pittsburgh is looking for a postdoctoral fellow starting this summer or fall. The LCBD employs multimodal neuroimaging to study child affective development from infancy to middle childhood. Please see the

Re: [Freesurfer] make_average_subject monkey data

Thank you, Doug! One monkey has a pretty decent registration while the other one does not even appear in the window when I try to manually check the registration with this command line: tkregister --mgz --s MonkeyCelia --fstal --surf orig It looks like if there is no brain. 2018-03-15 16:57

[Freesurfer] Skull stripping error dataset

I uploaded the datasets to the ftp site, does anyone have further advice regarding this issue? Both datasets are for the same subject for a longitudinal concussion study and fail for different reasons. matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails with "CORRECTING

Re: [Freesurfer] LME univariate data

Dear Kersten, Thanks a lot, it's really help. I have another question, after I got results that two group have significant, then how could I get direction? Thanks, Lanbo On Tue, Mar 13, 2018 at 5:40 PM, Diers, Kersten /DZNE wrote: > Hello, > > On Di, 2018-03-13 at

Re: [Freesurfer] Using .label file as mask in mri_fdr

It sounds like you want to convert your label into a binary mask to use with mri_fdr. Use mri_label2label, something like mri_label2label --srclabel your.label --s subject --hemi lh --outmask your.label.nii.gz Run with --help to get more info On 03/14/2018 10:41 PM, Chen Jen-I. wrote: > This

Re: [Freesurfer] make_average_subject monkey data

Check the talairach.xfm registration. It is probably way off. It does not have to be perfect (esp since they are different species), but the two subjects should have a similar registration On 03/14/2018 07:27 PM, Francesca Strappini wrote: > Both average hemispheres look very bad, they don't

Re: [Freesurfer] Registering functional data between scan sessions

Register day 1 to one of the anatomicals with bbregister, call output day1.lta Register day 1 to the same anatomical with bbregister, call output day2.lta mri_concatenate_lta -invert1 day1.ltaday2.lta day2-to-day1.lta Check: tkregisterfv --mov day2.nii --targ day1.nii --reg day2-to-day1.lta

Re: [Freesurfer] resting state motion censoring

Hi Freesurfer team & Doug, Just thought I'd check back in as you had asked! Any thoughts on censoring resting state volumes for fcseedcorr? Thanks, Adam On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve wrote: > Currently there is no way to do this. But it might

Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0

The command below appears to have run successfully but I get a note that the 'volumesAmygdla.txt' file could not be moved. See message below at the end of the freesurfer run. I am using 6.0 (Jan. 18, 2017 release). Is this expected? Jim

Re: [Freesurfer] Installation problem

Hi Neda, That’s unusual - can you send the output of sourcing the file in a debug shell: sh -x export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh You’ll probably have to ctrl-c to stop this as well. After running it, can you also send the ouput of: env |