[Freesurfer] Warping an ROI from one subject to another

2016-09-21 Thread Joel Bruss
I have two subjects, subA and subB. subA has a binary ROI mask, native space, that I'd like to place in subB's native space. Both subjects have been run through all stages of recon, edited, etc. Is there a better or easier way to achieve this than what I've run?: #Resample the native space binar

[Freesurfer] Output uncorrected p-values using mri_surfcluster

2016-09-21 Thread Corinna Bauer
Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-

[Freesurfer] optseq2 question

2016-09-21 Thread Yoed Kenett
hello i am trying to use optseq2 to design a study. I have a new mac book pro with El Capitan installed. I have tried downloading all different optseq2 versions but each time when i try to run it through the terminal i get the same exact error: -bash: optseq2: command not found what am i doing wr

[Freesurfer] combining epi dewarping and motion correction w/ mri_vol2vol

2016-09-21 Thread Nathan Tardiff
Hello, I am attempting to combine my motion correction and b0 unwarping steps. I have .lta files produced by registering every volume of a BOLD run to the first volume using mri_robust_register and a vsmap for dewarping produced by epidewarp.fsl. Is it sufficient to input them both into mri_vol2vo

Re: [Freesurfer] Failure in testing newly installed FreeSurfer

2016-09-21 Thread Douglas N Greve
Note that you should not use the development version for final analysis. It should be treated as an alpha version. Any data you analyze will need to be reanalyzed with a fully released version On 09/21/2016 12:36 PM, Z K wrote: > Hello Saeed, > > The MNI tools shipped with freesurfer 5.3 are no

Re: [Freesurfer] Failure in testing newly installed FreeSurfer

2016-09-21 Thread Z K
Hello Saeed, The MNI tools shipped with freesurfer 5.3 are not compatible with the newer versions of perl being shipped on all the newer linux distros. This has been fixed in our development version and in the upcoming freesurfer 6 release. So to get around this issue you will need to download

Re: [Freesurfer] Failure in testing newly installed FreeSurfer

2016-09-21 Thread Saeed Bakhshmand
Hello Douglas, Any chance to look into this issue? On Tue, Sep 6, 2016 at 6:26 PM, Saeed Bakhshmand wrote: > Sure: > > /usr/local/freesurfer/subjects/bert/mri > /usr/local/freesurfer/bin/mri_nu_correct.mni > --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o > orig_nu.mgz > nI

[Freesurfer] Research Fellow or Research Associate Position

2016-09-21 Thread Lili He
Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier pediatric research institution. We are driven by our mission to improve child health and transform the delivery of care through fully integrated, globally recognized research, education and innovation. Post-doctoral research fellows

Re: [Freesurfer] Configuration question for unbuntu

2016-09-21 Thread Z K
On most (newer?) Ubuntu versions you can just type 'sudo apt-get install libjpeg62' and all the linking should be taken care of for you. On 09/21/2016 11:29 AM, Thomas Beaudry wrote: > Hi, > > > I installed freesurfer and followed all of the configuration steps. I > am now doing the sample te

Re: [Freesurfer] Configuration question for unbuntu

2016-09-21 Thread Thomas Beaudry
OK great that works. Thanks From: Z K Sent: Wednesday, September 21, 2016 11:37 AM To: freesurfer@nmr.mgh.harvard.edu; Thomas Beaudry Subject: Re: [Freesurfer] Configuration question for unbuntu On most (newer?) Ubuntu versions you can just type 'sudo apt

[Freesurfer] Configuration question for unbuntu

2016-09-21 Thread Thomas Beaudry
Hi, I installed freesurfer and followed all of the configuration steps. I am now doing the sample tests, and noticed that it can't find libjpeg.so.62. According to this resource: https://surfer.nmr.mgh.harvard.edu/fswiki/Download I should do the following: cd /usr/lib (/usr/lib/i386 or

Re: [Freesurfer] Recon hires 7T {Disarmed}

2016-09-21 Thread Falk Lüsebrink
Hi Theresa, first, if you use the -hires flag in version 5.3 the processing pipeline will not start to downsample your data at some point (if I remember correctly during the normalization stage). As you stated that you were expecting the automatic downsampling you should either omit the hires f

[Freesurfer] Recon hires 7T {Disarmed}

2016-09-21 Thread Köbe , Theresa
Dear FreeSurfer Developers, I am attempting to run recon-all on 7T MP2RAGE images (resolution 0.7x0.7x0.7mm³) with hippocampus subfield segmentation. I use the freesurfer version 5.3 so that I expect an automatic down-sampling to 1x1x1mm³. I used the data directly from the scanner (without reor

[Freesurfer] trac-all -path Segmentation fault

2016-09-21 Thread Lars M. Rimol
Hi, I ran trac-all -prep and bedpostx successfully and qc (in accordance with tutorial) was fine but trac-all -path failed, due to "Segmentation fault" on two subjects: Segmentation fault Linux compute-16-6.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64