Re: [Freesurfer] Tracula output variability & reinit

It's been a while, but we are still working on computing our tracts in tracula! We are still struggling with variability of the output from 'trac-all -path'. Running with the default number of iterations, there was enough variability in the output from multiple runs, that I ran longer iterations

Re: [Freesurfer] Tracula output variability & reinit

surements substantially, while also improving sensitivity > to longitudinal changes (the paper is in review). > > Best, > a.y > > On Fri, 19 Jun 2015, Peggy Skelly wrote: > > It's been a while, but we are still working on computing our tracts in >> tracula! >>

Re: [Freesurfer] Tracula output variability & reinit

ectional (but much > less than 100K). We should look into this with the full longitudinal set of > images to see why it's converging so much slower for your data. > > On Mon, 22 Jun 2015, Peggy Skelly wrote: > > Thanks for looking at the data. >> >> 1- Since the dat

[Freesurfer] tracula reinit failure filled my hard drive

Hi, I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and the latest version of tracula (downloaded Sept 2014). I was running 'trac-all -prior -c mydmrircfile.txt' with reinit=1 on a few tracts that initially reconstructed to look like single voxels. The log file indicated there was difficulty co

[Freesurfer] Trac-all -stat

Hi, I'm using tracula with stroke subjects with a mixture which hemisphere is lesioned, so I'd like to compare all contra- or ipsilesional hemis together. trac-all -stat combines pathstats.byvoxel.txt for group analysis. Is there a way to combine some subjects' LH tract and other subjects' RH tr

Re: [Freesurfer] Trac-all -stat

bject: > ln -s subj1/blah...rh...blah/pathstats.byvoxel.txt \ > subj1-fake/blah...lh...blah/pathstats.byvoxel.txt > > Then you put all subjects, real and fake, into your subjlist and run > trac-all -stat. It's ugly but it might just work! > > a.y > >

Re: [Freesurfer] Tracula mean path

e one that came with the 5.3 release? > > a.y > > On Tue, 15 Sep 2015, Peggy Skelly wrote: > > HI, >> I'm looking at the mean path output from the tracula tutorial. I ran >> 'trac-all -stat' on the tutorial data and examined the output in >> fre

Re: [Freesurfer] Tracula mean path

11:15 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Peggy - Dec 19 2014 sounds like it was built after the 5.3 release. Can > you try with the 5.3 version of freeview? > > a.y > > On Tue, 15 Sep 2015, Peggy Skelly wrote: > > I think it&#x

[Freesurfer] Flipping left-right hemispheres

Hi All, Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and

Re: [Freesurfer] Flipping left-right hemispheres

s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi >> >> I think this should work >> >> doug >> >> >> On 03/14/2014 03:39 PM, Peggy Skelly wrote: >>> Hi All, >>> >>> Although the question of flipping hemispheres has co

Re: [Freesurfer] Flipping left-right hemispheres

run long_mris_slopes? Peggy On 3/14/14, 7:13 PM, Peggy Skelly wrote: > Thanks -- (I thought I might not have understood the processing > pipeline properly.) > > I'm running 5.3, I'll try the patch and let you know how it works. > > Peggy > > > On 3/14/14, 16:07 , Do

Re: [Freesurfer] Flipping left-right hemispheres

t try entering the subjectids in the qdec > table as subjectTP and subjectTP/xhemi and use subject as the base (TP > is just a shorthand for time point, use whatever you used) > doug > > On 03/17/2014 01:09 PM, Peggy Skelly wrote: > > The patch works! Thank you. > > > >

Re: [Freesurfer] Flipping left-right hemispheres

to compute? > > doug > > > On 03/21/2014 01:20 PM, Peggy Skelly wrote: > > I tried your suggestion (using subjTP/xhemi in place of subjTP) in the > > qdec table. I doesn't work because long_mris_slopes uses subjTP and > > subjBase to create "subjTP.long.subjB

Re: [Freesurfer] Flipping left-right hemispheres

the time difference. (i.e. in long.qdec.table tp1's time = 0, and tp2's time = 1 for all subjects.) On Fri, Mar 21, 2014 at 4:44 PM, Douglas N Greve wrote: > > Is the time between tp1 and tp2 the same for all subjects? If not, are > you using that information? > > On 03

[Freesurfer] Freeview, fsaverage_sym & aparc.annot

Hi Freesurfer experts, I'm trying to view aparc.annot on a fsaverage_sym surface. I can load aparc.a2009a.annot with freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.a2009s.annot but attempting freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot results in

[Freesurfer] move annotations across hemispheres

Hi, I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with: surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've trie

Re: [Freesurfer] move annotations across hemispheres

opy here > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg > > > Run with --help to get docs > doug > > On 12/17/2015 01:02 PM, Peggy Skelly wrote: > > Hi, > > > > I am attempting to move an annotation file from the right

Re: [Freesurfer] move annotations across hemispheres

e_sym --lhrh Peggy On Fri, Dec 18, 2015 at 11:17 AM, Douglas Greve wrote: > > Try this one > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.mac > > On 12/18/15 10:53 AM, Peggy Skelly wrote: > > I downloaded the file, but cannot get it to

[Freesurfer] output from mri_glmfit

Hello Freesurfer statistical experts, I need some assistance in explaining the output generated by mri_glmfit (then followed by correction for multiple comparisions, mri_glmfit-sim). We fit one model and got some statistically significant clusters. Then, we ran another model, the same plus an addi

[Freesurfer] Tracula Pathway reconstruction

Hi Tracula Experts, How do you determine if a pathway reconstructed well? I've been examining the merged pathways (/dpath/merged_avg33_mni_bbr.mgz) in freeview, and if the pathway looked too small when viewing with the default threshold, I would reinitialize those pathways. Most of the time, the n

[Freesurfer] Processing then xhemi registration to group healthy hemispheres

Hi, In our analysis of stroke patients, I've followed the recommendation to process images, then flip the final surfaces with xhemi for only the subjects with RH lesions to group all healthy hemispheres together for stati

[Freesurfer] Tracula - May update version

I have a few questions about the May 2014 update to Tracula: 1. Between the 2013-12-04 trac-all version 1.53 and 2014-05-26 trac-all version 1.56, the longitudinal stream now uses the aparc+aseg.mgz from the *.long.* directories, and all output is saved there, too. Are the .long./dlabel/anat and a

Re: [Freesurfer] Tracula reconstructed tracts quality

ing-fiber model like the ball-and-stick model, which may explain the > noisy output. > > a.y > > On Mon, 8 Sep 2014, Peggy Skelly wrote: > > > Hello Tracula experts, > > I was wondering if you could comment on the quality of the tracts > reconstructed with our &

[Freesurfer] tracula -prep fails at mri_convert

Hi, I'm processing 3T data with 60 direction vectors and 2 images with b-val = 0. Trac-all -prep has been failing at the command: > mri_convert --frame 0 31 /dmri/dwi.nii.gz /dmri/lowb.nii.gz > mri_convert: extra argument ("/dmri/lowb.nii.gz") > type mri_convert -u for usage Since --frame seems

[Freesurfer] Tracula output variability & reinit

I've been interested in these 2 questions, since I have similar issues: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38213.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39282.html What does it mean if I find a valid-appearing tract with reinit=0, but then los

Re: [Freesurfer] Tracula output variability & reinit

f an effect. The nkeep parameter means that 1 sample > path is saved for every nkeep sample paths that are drawn. Not keeping > every sample increases independence between samples. These are standard > aspects of an MCMC algorithm. > > a.y > > On Mon, 15 Dec 2014, Peggy Skel