Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

?Sequence for Hippo_subfields
by Kev 17 Jul '14

17 Jul '14

Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev

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Re: [Freesurfer] trac-all -prep error field map error
by Eileen Moore 17 Jul '14

17 Jul '14

Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1407141119560.23459(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Eileen - That step is run with the program epidewarp.fsl, which you can > run on the command line to see the available options. The input phase map > volume is expected to have either 2 frames (2 separate phase maps) or 1 > frame (the difference phase map). This error from trac-all means that it > found that your input phase map has something other than 1 or 2 frames, so > it doesn't know how to handle it. > > Hope this helps, > a.y > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring > to > > run tracula on some? images acquired from a GE scanner. I am running into > > problems when I try to perform the registration-based B0-inhomogeneity > > compensation, getting an error in the terminal output: "ERROR: > Unrecognized > > format of phase map". However, trac-all -prep runs fine when I skip the > > B0-inhomogeneity compensation step. Is there something else I need to do > to > > use field map correction? > > > > I've attached the trac-all.log and a copy of the terminal output. > > > > Thanks, > > Eileen. > > > > > > > > >

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Error in pre-processing
by 渡辺杏里 16 Jul '14

16 Jul '14

Dear TRACULA experts I am writing to ask about an error in pre-processing in TRACULA. After making FSL radiological header of dwi_orig_flip.nii.gz, an error occurs. When the name of file is changed from dwi_orig_flip.mghdti.bvals to bvals, I can't find the file dwi_orig_flip.mghdti.bvecs. So an error is mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory caused. The content of bvals is not overwritten. I attached my configuration file, the error log and bvals. -error log- fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory Many thanks for your help. Best Wishes, Anri WATANABE ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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Polar angle wedge default position
by Jackie Lam 16 Jul '14

16 Jul '14

Hello all, In Freesurfer’s analysis of retinotopy data, what is the phase assigned by freesurfer to the very beginning of the stimulation paradigm? I would assume that it should be 0, but it would be good to verify. Then, how do the phases proceed after the beginning? To negative values or positive values? In general, which phase values are assigned to a full cycle of the stimulation paradigm (start, 1/4cycle, 1/2 cycle and 3/4 cycle)? Thanks

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Watershed
by SOURAV RANJAN KOLE 16 Jul '14

16 Jul '14

Hello everyone, This is the FreeSurfer version that I am using: freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0 1. I am using watershed to perform more aggressive skull stripping but it seems to be not working for me. Below, I have provided every command I am running to identify the problem: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh cd to correct directory setenv SUBJECTS_DIR ${PWD} Before Watershed: tkmedit 1203/1203 brainmask.mgz -aux T1.mgz –surfs See attachment- Before_Watershed.png After Watershed: recon-all -subjid 1203 -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -no-isrunning tkmedit 1203 brainmask.mgz -aux T1.mgz -surfs See attachment- After_Watershed.png After watershed, skull stripping seems almost worse and it is not respecting the manual edits that I have done either. You can see the manual edits in the Before_Watershed.png file if you zoom in. 2. Which version of FreeSurfer do I need to have to use gcut as it is giving me the following error- recon-all -skullstrip -clean-bm -gcut -subjid 10 ERROR: Flag -gcut unrecognized.

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mri_glmfit-sim question
by Govindarajan, Koushik Athreya 16 Jul '14

16 Jul '14

Dear FS experts, I am trying to do a paired analysis between 2 time points obtained from the longitudinal pipeline and had some trouble interpreting the results. I have 2 different treatment groups I and II. I ran the paired analysis at p = 0.05, p = 0.01 and p = 0.001 vertex-wise thresholds. For p = 0.05, group I shows greater differences between the 2 time points whereas at p = 0.01 and p = 0.001, group II shows greater differences between the 2 time points. Is there any reason that might explain this discrepancy? If not, which result do I trust? The sample size in both groups is comparable (approximately 120 subjects in each group). Thanks Koushik

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mri_surfcluster --centroid
by Jockwitz, Christiane 16 Jul '14

16 Jul '14

Dear experts, in one of the earlier posts there was a discussion about mri_surfcluster and the -centroid option. I'am using Freesurfer 5.1 (Linux) so I don't have the --centroid option implemented. Is there a possibility to use it anyway (via a script)??? Thank you advance. Best. Christiane ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Position available at Hospital San Raffaele
by Zonca Lucia 16 Jul '14

16 Jul '14

The Neuroimaging Research Unit, Division of Neuroscience at Hospital San Raffaele is looking for a highly motivated junior researcher or postdoctoral fellow with previous experience in analysis of structural and functional MR scans in multiple sclerosis and other white matter conditions. He/she will work on projects aimed at improving the understanding of the mechanisms leading to the accumulation of irreversible physical disability and cognitive impairment in adult and pediatric patients with multiple sclerosis and other white matter diseases, including vasculitides, neuromyelitis optica, migraine and trauma. The Neuroimaging Research Unit (NRU) is an international research centre, part of the Institute of Experimental Neurology, operating since 15 years. NRU mission is to foster state-of-the-art neuroimaging research directed at understanding the structural and functional correlates of central nervous system (CNS) changes in healthy subjects and damage in diseased individuals. The NRU currently comprises a multidisciplinary team including physicians, post-Docs, bioengineers, PhD students, residents in neurology, technicians and data-managers (http://www.hsr.it/research/organization/divisions-centers/division-of-neuro…) The ideal candidate should have expertise in the acquisition and analysis of advanced MRI techniques (volumetric, diffusion tensor MRI and functional MRI). Expertise in voxel-based morphometry, tract-based spatial statistics, resting state and active fMRI analyses would be an advantage. The job requires the analysis and acquisition of MRI data sets and implementation of novel analytic tools, contributing to the design and programming of MRI experiments, assisting in analyzing the results, and participating in the writing up of the results. Good social skills are important as the candidate is expected to actively collaborate with other members of the laboratory. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Starting date: October 2014 for up to 3 years. Salary will vary based on previous experience. CVs, including name of two references, should be sent to: Prof. Massimo Filippi at filippi.massimo(a)hsr.it<mailto:filippi.massimo@hsr.it>. Thank you. Please feel free to advertize it to whoever you think might be interested. [cid:5x100osr201472d5.jpg] <http://www.5xmille.org/> Disclaimer added by CodeTwo Exchange Rules 2007 www.codetwo.com<http://www.codetwo.com>

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watershed error
by Janosch Linkersdörfer 16 Jul '14

16 Jul '14

Hi all, recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log) The image quality does not seem to be different... The error has been discussed on the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.…) but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. Thanks for your help, Janosch

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recon-all exits after mri_nu_correct
by ISAAC PEDISICH 15 Jul '14

15 Jul '14

Hi All, I'm trying to reconstruct surfaces using recon-all. Though many of the subjects have succeeded, a few are failing at the mri_nu_correct stage. The error file (posted below) provides little detail as to why the error is occurring. Even if it is not fixable, it would be nice to know what caused this error. I can provide data if requested. Thank you for your help, Isaac The following is the contents of the reocn-all.error file: ------------------------------ SUBJECT UP044 DATE Thu Jun 26 11:19:36 EDT 2014 USER analy HOST rhino.psych.upenn.edu PROCESSOR x86_64 OS Linux Linux rhino.psych.upenn.edu 2.6.18-371.4.1.el5 #1 SMP Thu Jan 30 06:08:24 EST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/global/freesurfer/bin/recon-all PWD /data3/eeg/freesurfer/subjects/UP044/mri CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

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Freesurfer