Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

"deployed" (compiled) MATLAB scripts path manipulation
by slehar＠nmr.mgh.harvard.edu 09 Oct '14

09 Oct '14

I have been following the directions on this site to "deploy" (compile) my MATLAB script so as to be able to run it on launchpad without worrying about MATLAB licenses. https://nmr.mgh.harvard.edu/martinos/itgroup/deploytool.html They say that the deployed script cannot do path manipulations such as addpath() or path(path,xxx), so the script should use isdeployed to make sure that such path commands are only executed if isdeployed == 0. % Only add path if not deployed if isdeployed==0; addpath ~nummenma/matlab/work/connectome/HCP_preproc_tools; end but then I need to add the path back in again so it can access the functions on that path. In the deploytool GUI I click Settings (the little gear icon), and in the upper window "Additional Parameters passed to MCC:" I inserted ======[ Additional Parameters passed to MCC: ]====== -I ~nummenma/matlab/work/connectome/HCP_preproc_tools mris_gradient_nonlin__unwarp_volume__batchmode_HCPS.m ==================================================== (A web site I found said you need a path to the m-file itself, not just to the directory that contains it, and you separate the path and file) Then I found I had to circumvent more path(path,xxx) commands in my startup.m file too ======[ startup.m ]====== % If script is not deployed add paths if isdeployed==0; %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% end ========================= Now at least it compiles without error. But when I run it I get this: Set up FreeSurfer environment -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /space/ficus/4/users/SNEF_subjects MNI_DIR /usr/local/freesurfer/stable5_3_0/mni FSL_DIR /usr/pubsw/packages/fsl/current ./run_unwarpone.sh /cluster/matlab/8.2 /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/aahscout/001/001.mgz /space/ficus/4/users/SLOTS_sessions_unwarp/SLOTS010/aahscout/001/001.mgz /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/unwarpscout001.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cluster/matlab/8.2/runtime/glnxa64:/cluster/matlab/8.2/bin/glnxa64:/cluster/matlab/8.2/sys/os/glnxa64 The file '/usr/local/freesurfer/stable5_3_0/matlab/load_nifti.m' is not in the application's expanded CTF archive at '/homes/6/slehar/.mcrCache8.2/unwarp2'. This is typically caused by calls to ADDPATH in your startup.m or matlabrc.m files. Please see the compiler documentation and use the ISDEPLOYED function to ensure ADDPATH commands are not executed by deployed applications. An error occurred while trying to determine whether "load_nifti" is a function name. MATLAB:err_while_looking_up_function Error:An error occurred while trying to determine whether "load_nifti" is a function name. Error:Error in mclFreeStackTrace. Any idea what the problem is now? load_nifti is presumably a FreeSurfer function -- do I now have a problem with my paths to FreeSurfer? I searched my script code and found no explicit call to "load_nifti", I presume that is called deep inside some other function. Should I add the FreeSurfer paths also through the deploytool GUI and not call "nmrenv"? (from my .cshrc file... alias nmrenv 'source /usr/local/freesurfer/nmr-stable53-env' )

1 0

mri_thickness & mri_make_surfaces
by Seung-Goo KIM 09 Oct '14

09 Oct '14

Hi all, I’m trying to compute cortical thickness using mris_thickness (stable 5), but getting slightly different results from the recon-all 5.1.0-amd64-2.13 (mri_make_surfaces, stable 5). Hinted from an old thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05994.html, I set the switch “-N 20", but it returns different values: 50% of vertices have identical values with the cross-correlation of about 0.98 and RMS of 0.08 mm, which is of course very high, but a bit odd while I was expecting nearly identical results. When I checked the scatter plots, the mris_thickness returns a bit smaller values for many vertices than the standard result. Is this somewhat expected difference between mri_make_surfaces and mris_thickness? Also I found that mri_thickness reads “?h.gray”, not “?h.pial”. As I assumed that it reads “?h.pial” and “?h.white” to compute thickness, so I just linked “?h.pial” to “?h.gray”. Is this assumed input for mris_thickness? Best regards, -- Seung-Goo KIM

1 0

functional correlation
by Brian Donley 08 Oct '14

08 Oct '14

Hello Freesurfers A bit new to the program, so I hope the following makes sense. We would like to do a bottom-up vertex-by-vertex analysis to see where functional activation correlates with thickness. We've done our functional analyses through SPM and can get those maps into tksurfer. Most of the tutorials and information I see has to do with, for example, defining a ROI based on functional data and extracting the thickness measures "under" that ROI. But this would be a little different Does this make sense, and is this doable in freesurfer? If so, could someone point me to the relevant tutorial or commands? I appreciate your help

1 0

Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
by Reza Rajimehr 08 Oct '14

08 Oct '14

One more question: I tried to run: rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg iter05.sphere.reg -fwhm 2 -per-session And I got this: ERROR: experts key needed (-expkey) Not sure what this flag is. Reza

2 1

Mismatched dimensions with T1 and Flair inputs
by Vilde 08 Oct '14

08 Oct '14

Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards,Vilde

2 4

Re: [Freesurfer] Surface Viewer Issue.
by Gregory Kirk 08 Oct '14

08 Oct '14

i saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL greg On 10/08/14, Jamie Hanson wrote: > Hi Freesurfer List, > > > I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v. freeview. > > > I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png). > > > I believe the orientation of the images is correct (judging by the freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw) > > > Any thoughts are greatly appreciated! Thanks much! > > > Best, > Jamie. > > > > -- > Jamie L. Hanson > Postdoctoral Fellow, Carolina Consortium on Human Development > Duke University > 417 Chapel Drive > Duke West Campus > Sociology-Psychology Building, Room 07A > Durham, NC 27710 > Email: jamielarshanson(a)gmail.com > Website: http://jamiehanson.org/

1 0

Surface Viewer Issue.
by Jamie Hanson 08 Oct '14

08 Oct '14

Hi Freesurfer List, I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v. freeview. I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png). I believe the orientation of the images is correct (judging by the freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw) Any thoughts are greatly appreciated! Thanks much! Best, Jamie. -- Jamie L. Hanson Postdoctoral Fellow, Carolina Consortium on Human Development Duke University 417 Chapel Drive Duke West Campus Sociology-Psychology Building, Room 07A Durham, NC 27710 Email: jamielarshanson(a)gmail.com Website: http://jamiehanson.org/

1 0

Running GCA atlas, problem with talairach
by N/A N/A 08 Oct '14

08 Oct '14

Hi Freesurfers, I am trying to make an atlas using the GCA algorithm and the error message I just got is asking for the talairach.xfm file. The scans I am using were originally run through freesurfer 3.1 and talairach processing was not done. What do you suggest I do to use these scans in my new atlas? Kind regards, Alexarae

1 0

Re: [Freesurfer] sequence advice for GE 750 & 8-channel coil
by Antonio Algaze Beato 08 Oct '14

08 Oct '14

Hello Lee - thanks so much for your response. I looked into the document you referred me to and found a section on GE protocols here (page 3): http://martinos.org/~andre/FreeSurfer_recommended_morphometry_protocols.pdf I would appreciate your input on a few details. First, the document indicates "min (9150ms) for the TR value. However, the minimum TR is about 8 ms when I prescribe a similar IR-FSPGR sequence. I may be missing something obvious, but: a) Would that be 9.15 ms instead? (actually, the TR is not selectable when prescribing this 3D sequence). Also, we are mostly interested in getting good whole-brain segmentation and, from what I gather, the document mentions that multiecho FLASH is the way to go for this. b) Would the GE IR-FSPGR sequence specified in the protocol document still be OK for getting reliable whole-brain segmentation? c) I take it then that there is no "GE-version" for the multiecho FLASH, correct? Thanks again, Antonio

1 0

cortical and subcortical masks in txt
by stdp82＠virgilio.it 08 Oct '14

08 Oct '14

Hi list, I need to extract the cortical and subcortical masks created by using recon-all as .txt. I would work on the txt to import FS masks in Brain Voyager Qx which does not accept .nii.gz but only .par/.rec format. Thanks Best regards, Stefano

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer