[Freesurfer] brainGraph (graph theory analysis in R) major release v3.0.0

me know if you have any issues, bug reports, feature requests, etc. Chris Watson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freeview update error

External Email - Use Caution Hi Kelly, you can try yum install qt5-qtbase-gui qt5-qtwebkit qt5-qtwebkit-devel And if it still doesn't work, you can try yum install harfbuzz On Mon, Apr 22, 2019 at 9:05 AM Kelly Vaughn wrote: > External Email - Use Caution > > Hello

Re: [Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

s to get started with your toolbox, > > Best wishes, > > Gabriel Robert, MD, PhD > Rennes, France > > 2018-02-07 2:14 GMT+01:00 Chris Watson <cwa...@alum.mit.edu>: > >> Dear Freesurfer users, >> >> I am pleased to announce the 2nd major release of my R

[Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

- Calculation of network *communicability* and vertex *communicability betweenness centrality* Please let me know if you have any issues, bug reports, feature requests, etc. Chris Watson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] Matlab 2016b and localGI

Hi, I took a look at this and saw that the error comes from the "getmatlab" script ($FREESURFER_HOME/fsfast/bin/getmatlab). It is a CSH script, which I thought might be the issue. Specifically, the script checks for the existence of matlab by (unsurprisingly) set MATLAB = `which matlab`; On Dr.

[Freesurfer] Longitudinal stats: target space

Hi Doug, Martin, et al., I am going to use the LME tools for a study in kids 8-15 y.o. (some with brain injury). RE the target space (mris_preproc and mri_surf2surf), the LME wiki page says "study_average". I

Re: [Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

I apologize but the link to the Github page is: https://github.com/cwatson/brainGraph Chris On Tue, Apr 11, 2017 at 7:37 PM, Chris Watson <cwa...@alum.mit.edu> wrote: > Dear Freesurfer users, (apologies for cross-post) > > I am pleased to announce the first major release

[Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

gelog. This remains a work-in-progress, so I am very happy to receive bug reports, feature requests, general questions asking for help with code, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-hel

Re: [Freesurfer] Running analysis on a Linux Partition

You should ask the sys admin to create a directory for you on the shared drive. If only root can write to it, that defeats the purpose of a shared drive... On 02/10/2015 08:21 AM, Kate Riggall wrote: Hello, I am trying to run a paired analysis (a two time-point longitudinal analysis) on

Re: [Freesurfer] standardized community affiliation vector

You would have to get a connectivity matrix (either from someone who has analyzed the data, or from analysis that you do yourself). Even still, there won't be a standard because: * there are different ways of measuring connectivity (probabilistic vs. deterministic tractography; resting-state

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

You may have to transpose the bvecs and bvals files. I think that's how Tracula expects them. You can use the attached script to do it. On 12/17/2014 09:18 PM, Katherine Damme wrote: Thanks! That was exactly it! It was a FAT server and so that resolved that issue. Tracula is claiming that

Re: [Freesurfer] Command '-qa' in TRACULA

No, she is saying that you should open a terminal, and type only trac-all. This should display the help for that program, including the program's flags. If you don't see -qa listed, then the trac-all you're using is an older version. You need to verify that you have downloaded the latest

Re: [Freesurfer] [Fwd: Re: Modeling cortical thickness question]

No, just include age^3, if the mean function is E(thickness | X) = B_0 + B_1 * age^3 It's similar to taking the logarithm of one of your predictors. Just remember that the units for the parameter estimate will be different than if you were just including age. On 12/10/2014 12:12 PM,

Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

Have you tried installing 'xauth' on the server and connecting via 'ssh -X'? That should show all graphical output on the local machine. On 11/05/2014 05:03 PM, Bruce Fischl wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work,

Re: [Freesurfer] quick quality assessment for MPRAGE images

Try out Freesurfer's QAtools. It still isn't automatic, but you can get a bunch of screenshots and view them all on an html page. On 09/18/2014 11:42 AM, Harms, Michael wrote: Hi Ezra, I'd love to hear otherwise if someone has established some robust signal processing approaches to do this

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

You can try just re-running trac-prep -prior and trac-paths for the L uncinate and no other tracts On 09/11/2014 02:58 PM, Michele Cavallari wrote: So, I re-ran the case with the set reinit option. It half worked!...in the sense that the new results show the left uncinate right, but the

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

If you sym link the already finished bedpostx directory to $SUBJECT/dmri.bedpostX, you should be able to run trac-all -prep and trac-all -path without any issues (adjusting the config that comes with tracula) On 09/03/2014 05:04 PM, Katherine Damme wrote: Hello Freesurfer Community! I have

Re: [Freesurfer] Cortical Thickness Correction Factor

In your FSGD you'll have to add a covariate for scanner On 08/08/2014 12:34 PM, David Tate wrote: FreeSurfer Gurus, I would like to pose this question again to the group if possible. We are working with data that comes from two different scanners. Our experimental group was collected on one

Re: [Freesurfer] Tracula trac-all -stat flag -stat unrecognized

Do you have the latest version of Tracula? There was an update posted after FS 5.3 came out. On 07/18/2014 04:48 PM, Cat Chong wrote: Hello Anastasia, I have just converted pathstas.overall.txt files to a table for group analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a

[Freesurfer] Tracula with multi-shell data

Dear Anastasia et al. I have data DTI that has multiple b-values. I worked around this by skipping '-tensor', and sym linking 'mean_fsumsamples.nii.gz' to 'dtifit_FA.nii.gz'. However, at the end of 'trac-path', there is an error thrown. Specifically when 'dmri_pathstats' is called, because it

Re: [Freesurfer] Anonymizing Siemens DICOM files

You could also do it the following way: (you need to download dcmtk) Assuming you have a bunch of files called MR.* for dicom in MR.* do dcmodify -m (0010,0010)=PatientsName ${dicom} dcmodify -m (0010,0030)=MMDD ${dicom} done This backs up all the dicoms (they become MR.*.bak),

Re: [Freesurfer] mri_convert .tar.gz files of dicoms?

FYI, you can also get the first file like this: first_file=$(tar ztf ${in_file} | head -1) It will be much faster than 'find'. On 03/20/2014 05:18 PM, Nate Vack wrote: Also, for what it's worth, here's a little script that wraps this up: https://gist.github.com/njvack/9674025 Best, -Nate

Re: [Freesurfer] bvals and bvecs for dt_recon

dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the

Re: [Freesurfer] Problems dipslaying annotations in freeview

I've seen this happen after making manual edits and then not finishing a re-run of recon-all. Chris On 12/10/2013 02:00 PM, Laura Taylor wrote: Hi, I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a subject. When I use the freeview gui and select lh.aparc.a2009s.annot

Re: [Freesurfer] Linux recon-all error

You need to type sudo yum update, not command. On 11/16/2013 01:29 PM, krista kelly wrote: Thanks Alan for your response! I've tried typing sudo yum update into the terminal window, however it does not work. It says yum:command not found. I've tried googling how to do this, but I can't find

Re: [Freesurfer] LGI path problem

Are you in the 'surf' directory? If not, then do -overlay $subject/surf/lh.pial_lgi On 11/05/2013 11:26 AM, Linn Mittlestein wrote: Hi, Thank you very much, it works. I now however have another problem (sorry!). I have run the command on test subject and want to display using tksurfer. The

Re: [Freesurfer] Power analysis for Qdec

Here is a paper discussing post-experiment power analyses and why they are wrong: http://amstat.tandfonline.com/doi/abs/10.1198/000313001300339897#.Um_aDtexGkc On 10/29/2013 10:51 AM, MCLAREN, Donald wrote: For anyone who wants G*Power, here is a link to the download page. It is free for all

Re: [Freesurfer] gradient table question for Tracula

I have GE data and never had to make any changes to the gradient table. On 08/22/2013 01:05 PM, Anastasia Yendiki wrote: Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in. To make

[Freesurfer] Group thickness analysis, 2x2x2

Dear Doug et al., I have 2 groups, 2 genders, and 2 scanners (A and B). (I also have Age as a covariate). In my FSGD they are listed in this order: ControlFemaleA ControlFemaleB ControlMaleA ControlMaleB CaseFemaleA CaseFemaleB CaseMaleA CaseMaleB I used the following contrast to test for a

Re: [Freesurfer] Correction multiple comparisons for parcelated areas

You can use FDR correction. On 08/14/2013 08:16 AM, Anita van Loenhoud wrote: Dear FreeSurfers, I’m comparing two groups (patients (N=45) and controls (N=93)) on cortical thickness using 34 parcelated areas in each hemisphere (i.e. 68 areas in total). When correcting for multiple comparisons

[Freesurfer] Using gcut multiple times

Hello, Is there any value in running recon-all with -gcut multiple times? e.g. in a case where skull/dura continues to be left on brainmask.mgz? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [tracula] error running trac-all -prep

You may have to transpose the bval and bvec files. On 07/29/2013 11:17 AM, Borsodi Florian wrote: Hello, I have been trying to run tracula on my data and i keep getting the same kind of error repeatedly. For my imput I am using dicoms from a Siemens scanner with a stadard diffusion protocol.

Re: [Freesurfer] using two vs one scan(s) for optimal surface reconstruction

I only have anecdotal evidence on this. (using version 5.1) I found that if both scans had a little motion, then using both improved reconstruction. If one scan was pretty bad, and the other was pretty good, then using the pretty good one on its own was better than using both. If both were

Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?

You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz.

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

Can you check that the UID and GID both match on the client and server sides? Is it the same user that is able to use other programs, yet unable to write via Freesurfer? Is your user an NIS account? Can you output # ls -l $SUBJECTS_DIR I assume that since you say other programs can write to

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

,rsize=32768,nfsvers=3,tcp,noacl 0 2 (this is in the old app server, which worked before the migration to the new file system) thanks again! Gari On Sat, May 11, 2013 at 12:07 AM, Chris Watson christopher.wat...@childrens.harvard.edu mailto:christopher.wat...@childrens.harvard.edu wrote

Re: [Freesurfer] Fwd: Problems calling Free Surfer...

Can you post the contents of your ~/.bash_profile On 01/25/2013 01:41 PM, Rosalia Dacosta Aguayo wrote: Dear Free Surfer experts, Sorry for posting this again...but I have been trying this all the day and nothing seems to change the situation. I am having problems with my FS installation.

[Freesurfer] Tracula: pathway #7

Hello, When I go through trac-prep, pathway #7 always takes much much longer than any of the others. And for that pathway it always displays this: INFO: Distances between consecutive points are 34 37 34 40 WARN: Could not find satisfactory control point fit - try 90 Has anyone else had this

Re: [Freesurfer] trac-all -path error

merged_th2samples.nii.gz xfms Thanks, Chris On 03/23/2012 01:25 PM, Anastasia Yendiki wrote: Yes. On Fri, 23 Mar 2012, Chris Watson wrote: Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25 On 03/23/2012 01:22 PM

Re: [Freesurfer] trac-all -path error

, Anastasia Yendiki wrote: Yes. On Fri, 23 Mar 2012, Chris Watson wrote: Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25 On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: Oh, ok. That's a known issue, it has

Re: [Freesurfer] Clarification on centos version/updates/patches

H i Nick, Will the centos5 build of v5.1 work with centos6? I'm getting a new workstation and want to know which version of centos is better to install. On 04/10/2012 10:08 AM, Nick Schmansky wrote: Wil, Hi, the contents of that 'misc' directory is just a filedrop of sorts to supply fixes to

[Freesurfer] trac-all -path error

Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file

Re: [Freesurfer] trac-all -path error

my guess would be that bedpostx didn't finish processing. On Fri, 23 Mar 2012, Chris Watson wrote: Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject

Re: [Freesurfer] trac-all -path error

updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz

[Freesurfer] trac-all -prep error

Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths

Re: [Freesurfer] trac-all -prep error

actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac

Re: [Freesurfer] trac-all -prep error

Yes, the same error. Chris Anastasia Yendiki wrote: When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15 Feb 2012, Chris Watson wrote: Here's output from mri_info: [freesurfer@occipital dmri]$ mri_info lowb.nii.gz Volume information

Re: [Freesurfer] trac-all -prep error

Actually, it now works when I re-source my .bash_profile and .bashrc files. Not sure why that would be. Chris Chris Watson wrote: Yes, the same error. Chris Anastasia Yendiki wrote: When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15

Re: [Freesurfer] tksurfer display problem

, Chris Watson wrote: Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system

Re: [Freesurfer] tksurfer display problem

the problem. not sure why this would just happen now for you. to update (must be root or use sudo): /sbin/init 3 /usr/bin/nvidia-installer --update n. On Fri, 2011-01-14 at 13:19 -0500, Chris Watson wrote: Hi, when trying to look at surfaces in tksurfer, all I see is a small part

[Freesurfer] tksurfer display problem

Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system info: (CentOS 5.5, 64-bit;

Re: [Freesurfer] recon-all error

Thanks, that did the trick. Chris Nick Schmansky wrote: you will need to get a fixed version of mri_ca_label from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc n. On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote: I was running a subject, and got this

Re: [Freesurfer] modifying dicom headers

dcmtk works pretty well and is easy to use: http://dicom.offis.de/dcmtk.php.en Jared Price wrote: Hi all, I am looking for a powerful, robust tool for modifying dicom headers that can be called from the command-line and scripted. For example, I may need to alter the subject ID with which a

[Freesurfer] mri_convert with old GE-LX data

Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$

Re: [Freesurfer] mri_convert with old GE-LX data

/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running

Re: [Freesurfer] mri_convert with old GE-LX data

for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image

Re: [Freesurfer] mri_convert with old GE-LX data

1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge

Re: [Freesurfer] mri_convert with old GE-LX data

differently? Douglas N Greve wrote: sorry, also add -ic 0 0 0 Chris Watson wrote: Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0

Re: [Freesurfer] wm edits

If you use mris_wm_volume, it will compute the volume enclosed by the $h.white surfaces. It's more accurate than using mris_anatomical_stats for white matter. I believe you don't need to edit wm.mgz, assuming the $h.white surfaces accurately follow the white matter in your images. Nasim

[Freesurfer] General editing questions

Hello, I've been looking through the archives and still have some questions about getting the best data for GM volume, WM volume, and the volumes of each sub-cortical structure. This is lengthy, but I'm trying to save a lot of future man-hours that I wasted on the first dataset I was doing.

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Hi, So if the volumes are estimated from the surfaces and not aseg.mgz, does this mean it is unnecessary to edit aseg.mgz? Or is it still necessary, but only for the subcortical structures? Is it best to make pial surface/wm.mgz edits and control points for grey and white matter, and aseg.mgz

[Freesurfer] White matter hypointensities?

What are white matter hypointensities supposed to represent? I'm seeing this segmentation group a lot around the lateral ventricles, caudate, etc. thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz

. What resolution is your data? We have some newer sequences and code that avoid the dura, but they are by no means standard (and we only have them for Siemens). cheers, Bruce On Tue, 6 Nov 2007, Chris Watson wrote: Hello all, I was wondering if there is a quick way to make edits to multiple

[Freesurfer] Manual edits to aseg.mgz/brainmask.mgz

Hello all, I was wondering if there is a quick way to make edits to multiple slices of the aseg.mgz (or the brainmask.mgz) volume. Specifically, I am working on my first subject, and it seems that on almost every slice, pieces of the dura/skull/arachnoid/what-have-you get segmented as cortex

[Freesurfer] COR-files

Hello, this is my first time using Freesurfer. I was making some edits to the brainmask.mgz and T1.mgz volumes, and saved them and left Friday evening. I would like to continue making edits today. How do I open these volumes so that they include the edits I made? When I saved, 256 COR-files

Re: [Freesurfer] COR-files

they were saved directly in mri and not in a subdir? That means that there is only one volume, not two (brainmask.mgz and T1.mgz), do you know which one it is? To convert from cor to .mgz do: mri_convert directory that has the COR files output volume.mgz cheers, Bruce On Mon, 5 Nov 2007, Chris