Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

External Email - Use Caution Hello, I have a tone of FS people who have been run through Recon-all and I am happy with the output but I would like to expand the existing labels to include the Buckner 7 tight labels. Is this still the best way to update my subject labels to include

[Freesurfer] Mean FA values for major tracts all greater than 1

External Email - Use Caution Hello Freesurfer Support group, I have run tracula on hundreds of subjects for a study and their primary tracts are all showing that MFA is greater than 1. Typically, I expected that MFA should be in the .3 to 1 range. Should I be suspicious that these

[Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

Hello Everyone, I would like to use the FreeSurfer labels for fMRI and DTI in graph theory analyses. I am attempting to use UMPC to generate the graphs, which requires that the diffusion tensor imaging be in .dtk form. However, I have been struggling to get the F

[Freesurfer] Extracting lgi cluster values over label

Hello Everyone! I have run LGI analyses according to the JoVE article: https://www.jove.com/video/3417/how-to-measure-cortical-folding-from-mr-images-step-step-tutorial-to I created labels from the significant clusters and would like to extract the lgi values from these labels and found that past

[Freesurfer] local gyrification index (lGI) Error in Design

Hello FreeSurfer Group I would like to make a two group comparison controlling for both gender and medication status. The only way that I have sorted out doing this is to make eight groups (ClinicalGroup x Sex x Meds) but I get an error that my design is poorly scaled: --

Re: [Freesurfer] Extracting significant clusters after qdec analyses

--i y.mgh), spec the > output with --avgwf to get a matrix of nsubjects by nclusters (make sure > to also include --exludeid 0) > > > On 01/23/2017 08:00 PM, Katherine Damme wrote: > >> Thank you so much! >> >> This got me to the stage of having separate labels

Re: [Freesurfer] Extracting significant clusters after qdec analyses

sure to use the --mask option passing it the > mask.mgh from the qdec output > > > On 01/22/2017 07:56 PM, Katherine Damme wrote: > > Hello Everyone, > > > > Is there a way to extract the significant clusters as masks from > > significant group comparison

[Freesurfer] Extracting significant clusters after qdec analyses

Hello Everyone, Is there a way to extract the significant clusters as masks from significant group comparisons using qdec? All I can seem to find is mri_glmfit-sim which doesn't quite replicate the QDEC FDR 0.05 output and doesn't seem to make anything that I could extract as a label, or hand dr

Re: [Freesurfer] Tracula Set: No Match

can. > > Best, > a.y > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ > katherine.da...@gmail.com] > *Sent:* Sunday, January 01, 2017 5:16 PM > > *To:* Fre

Re: [Freesurfer] Tracula Set: No Match

Sorry the phase map. How do I generate an appropriately formatted phase map? On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme wrote: > How do I generate a field map? > > On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > >>

Re: [Freesurfer] Tracula Set: No Match

nner, the small b is the b-value (diffusion weighting). > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ > katherine.da...@gmail.com] > *Sent:* Monday, December 19, 2

Re: [Freesurfer] Tracula Set: No Match

Is this meant to be calculated from the B0 dicoms? On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > No, it's a separate scan that you provide. > > -- > *From:* Katherine Damme [katherine.da...@gmai

Re: [Freesurfer] Tracula Set: No Match

ps) or 1 frame (a phase difference > map). > > ------ > *From:* Katherine Damme [katherine.da...@gmail.com] > *Sent:* Friday, December 16, 2016 5:18 PM > *To:* Freesurfer support list; Anastasia Yendiki > *Subject:* Re: [Freesurfer] Tracula Set: No Match >

Re: [Freesurfer] Tracula Set: No Match

emple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt" What is the next step in the code where it is failing? On Wed, Dec 14, 2016 at 9:19 PM, Kathe

Re: [Freesurfer] Tracula Set: No Match

- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ > katherine.da...@gmail.com] > *Sent:* Tuesday, December 13, 2016 9:21 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Tracula Set:

Re: [Freesurfer] Tracula Set: No Match

error? > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ > katherine.da...@gmail.com] > *Sent:* Wednesday, December 07, 2016 12:41 PM > *To:* Freesurfer support list > *Subject:* Re: [Fre

Re: [Freesurfer] Tracula Set: No Match

e? Thanks! > > a.y > ------ > *From:* Katherine Damme [katherine.da...@gmail.com] > *Sent:* Saturday, December 03, 2016 3:42 PM > *To:* Freesurfer support list; Anastasia Yendiki > *Subject:* Tracula Set: No Match > > Hello! > > I have been getting a "set: No match."

Re: [Freesurfer] Tracula Set: No Match

On Sat, Dec 3, 2016 at 2:42 PM, Katherine Damme wrote: > Hello! > > I have been getting a "set: No match." error. I haven't been able to sort > out what is causing it. > > Attached you will find the configuration file, command, and log files > associated wi

[Freesurfer] qdec long parsing table to look in non-existant directory

Hello everyone, I am running qdec for longitudinal data for the first time and although I have a file that matches the guide on the wiki, the script is looking in a non-exsistant file location (see below). While there is a 1001 file and a 1001_MR1, I am not sure where it is getting the 1001_MR1.lo

[Freesurfer] Qdec Clusters Graph Extracted

Hello FreeSurfer Group I would like to make my own box plot out of a cluster that I identified as significant in Qdec. Is there any easy way to extract the information that appears in the graph window so that I can create a box plot? I've tried extracting it by drawing an roi and using mris_anato

Re: [Freesurfer] Tracula: cannot open file `1000' for reading Bedpost file error

end...@nmr.mgh.harvard.edu> wrote: > > Hi Katherine - Did you specify the gradient table and b-value table in > your configuration file? I suspect that the issue is that it can't find > them. > > a.y > > On Tue, 3 Mar 2015, Katherine Damme wrote: > > > Hell

[Freesurfer] Tracula: cannot open file `1000' for reading Bedpost file error

Hello Freesurfers, I recently updated my Freesurfer version and now I am getting an error in tracula. awk: cmd. line:1: fatal: cannot open file `1000' for reading (No such file or directory) Any help would be appreciated. trac-all.error Description: Binary data Mon Mar 2 18:24:56 CST 2015 /ho

[Freesurfer] Probabilistic Tractography

Hello Freesurfer World, I am trying to decide how to threshold my probabilistic tractography data. Does anyone have recommendation on best define a threshold? Thank you, Kate Damme ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] From bedpostX and recon-all to tracula

xt. Are these files > the same? > > On Mon, 5 Jan 2015, Katherine Damme wrote: > > Sorry I just copied that from remotely accessing my desktop and viewing >> the doc in the terminal. Attached is the complete log. >> >> On Sat, Jan 3, 2015 at 9:45 PM,

[Freesurfer] FS/Diffusion dwi-infodump.dat error

Hello Freesurfer Users, I have been attempting to use the DWI prep steps described under FS/Diffusion , but have gotten the following error. ERROR: cannot extract sWiPMemBlock.alFree[8] from /home/k/ksd770/Desktop/Subj/041/dtrecon/dwi

Re: [Freesurfer] From bedpostX and recon-all to tracula

line, I need to see the entire output of trac-all, which is saved in > trac-all.log. > > On Fri, 2 Jan 2015, Katherine Damme wrote: > > I still get the error: >> mv -f /home/k/ksd770/Desktop/Subj/042/dmri/dwi_orig_flip.mghdti.bvecs >> /home/k/ksd770/Desktop/Subj/042/

Re: [Freesurfer] From bedpostX and recon-all to tracula

hould be the CentOS 6 64-bit, based on this line that I got from your > trac-all.log: > > build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > a.y > > > On Wed, 17 Dec 2014, Katherine Damme wrote: > > Thanks! That was exactly it! It was a FAT

Re: [Freesurfer] From bedpostX and recon-all to tracula

If you specify a > directory as an input/output we will assume that it contains COR files, > which is probably what you are seeing. > > cheers > Bruce > > > > On Sun, 14 Dec 2014, Katherine Damme wrote: > > At what point is the COR-*.info file made? >> I got the follow

Re: [Freesurfer] From bedpostX and recon-all to tracula

e field maps used to correct for inhomogeneities in the main > magnetic field (which in MRI lingo is referred to as the B0 field, not to > be confused with the b=0 images). You can skip that correction (you have to > skip it if you don't have field maps). > > > On Thu, 11 Dec 2

Re: [Freesurfer] From bedpostX and recon-all to tracula

enshot looks more like a low-b image from a diffusion > scan than a field map. In case this helps, the phase map data will have > either 2 volumes (2 phase maps acquired at different echo times) or 1 > volume (the difference of 2 such phase maps). > > Best, > a.y > > > On

Re: [Freesurfer] From bedpostX and recon-all to tracula

he log file > (scripts/trac-all.log), we can try to troubleshoot. > > a.y > > On Wed, 3 Sep 2014, Katherine Damme wrote: > > > Hello Freesurfer Community! > > I have sucessfully completed diffusion preprocessing in FSL and the > > recon-all of the structural image

[Freesurfer] From bedpostX and recon-all to tracula

Hello Freesurfer Community! I have sucessfully completed diffusion preprocessing in FSL and the recon-all of the structural image and would like to use tracula for the tract reconstruction. I keep having trouble with my configuration file. Does anyone have a bedpostX tracula config file they coul