Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

Thanks Doug, This does seem like it will do the right thing, but it’s failing because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have an ico subject in my subjects_dir Should this normally be in the subjects_dir? I don’t recall ever seeing this made when I’ve run recon-all in th

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

> On Sep 29, 2016, at 12:00 AM, Douglas Greve wrote: > > you can actually skip the ico thing and just use --trgsubject fsaverage6 > > On 9/28/16 7:06 PM, Jared P Zimmerman wrote: >> Thanks Doug, >> >> This does seem like it will do the right thing, but it’s fai

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

> Bruce > On Thu, 29 Sep 2016, Jared P Zimmerman wrote: > >> I want to project to the native subject surfaces though, not fsaverage. If >> I use —trgsubject subjID would that work with the —icoorder flag? >> Alternatively I guess I could project to fsaverage and th

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

ys went to fsaverage space. Do you want to decimate the > native space surfaces? > > > On 09/29/2016 10:15 AM, Jared P Zimmerman wrote: >> I want to project to the native subject surfaces though, not >> fsaverage. If I use —trgsubject subjID would that work with the >&

[Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Hi FS Experts, I’m having trouble getting anatomical stats from a parcellation I made out of scanner-space volume ROIs. I have taken the following steps to do this. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o myROI_orig.nii.gz --interp nearest mris_sample_parc Subj111 lh myR

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Any chance I could get some help on this? still having this problem > On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman > wrote: > > Hi FS Experts, > > I’m having trouble getting anatomical stats from a parcellation I made out of > scanner-space volume ROIs. I have take

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

; Hi Jared > > can you send us the full command line and screen output? > > cheers > Bruce > On Wed, 26 Apr 2017, Jared P Zimmerman wrote: > >> Any chance I could get some help on this? still having this problem >> >> On Apr 20, 2017, at 6:26 PM,

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Hey Bruce et al, any update on this? Thanks, Jared > On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman > wrote: > > Here’s the script that I’m running and the merged stderr stdout. I’ve also > tried various permutations of mris_sample_parc using the -t flag and using > d

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

ments changed >>>>> pass 2: 0 segments changed >>>>> writing annotation to s111_bla_8mm_orig2_annot.annot… Thanks, Jared > On May 4, 2017, at 11:36 AM, Bruce Fischl wrote: > > can you try it with -ct > > and send us the output if that doesn't wor

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

fwiw, this problem persists in FS6.0 -jared > On May 4, 2017, at 12:11 PM, Jared P Zimmerman > wrote: > > That’s what I did below, see the script and log.txt attached to a previous > email. This is the output from the mris_sample_parc step > >>>>>&

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

the mris_sample_parc command line. Can you just send it > and the entire screen output? > On Thu, 4 May 2017, Jared P Zimmerman wrote: > >> That’s what I did below, see the script and log.txt attached to a previous >> email. This is the output from the mris_sample_parc step

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

ork > > cheers > Bruce > On Thu, 4 May 2017, Jared P Zimmerman wrote: > >> mris_sample_parc ${sub} \ >> lh ${targ}.nii.gz \ >> ${targ}_fs6_annot.annot \ >> -ct ${SUBJECTS_DIR}/${sub}/bla_test_table.txt >> >> >> T