Freesurfer

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30086 discussions

Re: [Freesurfer] Using fieldmap to correct EPI distortions
by Reza Rajimehr 12 Sep '14

12 Sep '14

Hi Doug, So I am using a command like this: epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf ~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw ~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46 --esp 0.31 --sigma 2 --perev (note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because this command apparently does not have --o option) Before running the above command, I have registered the mag and phasediff volumes to the template volume and I have generated new volumes (fid_mag and fid_phasediff) that are already in register with the template. I have two steps remaining in preproc-sess, which are register-sess and rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two commands? I assume that when I use the above flag(s), my EPI fmc volumes will be dewarped first, and then they will get registered to the anatomical and the surface, right? So I hope that when I view/check the result of registration with tkregister2 (for possible manual interventions), I will see the dewarped template ...? Finally what is the effect of specifying -b0dc in mkanalysis-sess? Thanks, Reza > Hi, > > I have a basic question, but the answer can be useful for others as well. > > I am doing a customized preprocessing of monkey functional data in FS-FAST > v5.3. After motion correction and before functional-anatomical > registration, I want to use fieldmap data to correct spatial distortions > of EPI data. So: > > My fieldmap data: dicom files from a fieldmap scan (there are actually two > series of dicom files for that scan) > > My EPI data: fmc.nii.gz files in run folders > > Now I have three questions: > > 1) How can I unpack the fieldmap data? An example command ... I think you get two series out, one magnitude and one phase, just convert those to nifti > > 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an > example command would be very useful. something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located) > > 3) How will the undistorted volumes be used later on in the FS-FAST > analysis stream? When you run preproc-sess and mkanalysis-sess add -b0dc to the command line > > Your help would be very much appreciated. > > Thanks, > Reza

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Monte Carlo Sim output / sig.masked.mgh
by Eryilmaz, Huseyin Hamdi 12 Sep '14

12 Sep '14

Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction? Many thanks! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email: heryilmaz(a)partners.org<mailto:heryilmaz@partners.org>

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social media: Facebook, Twitter and now LinkedIn
by Martin Reuter 12 Sep '14

12 Sep '14

Hi, many of you are aware of (yes, even excited about) our social media presence at Facebook: http://facebook.com/FreeSurferMRI Twitter: http://www.twitter.com/FreeSurferMRI and so we have just added a group on LinkedIn: https://www.linkedin.com/groups/FreeSurfer-8173404 (it's hard to believe, but it's true!) While these are all social media, they each have their special focus. While facebook is more personal with pictures of courses, social events etc, Twitter focuses on sharing news, and LinkedIn is a professional network group which will allow you to connect with other professionals in your field, browse and post related job offers, and even start your own discussions (Wow - they're all great). So, head over to any or all of these and 'follow', 'like' or 'join' us ... Cheers, Martin (how I love social media, it works completely without eye-contact ;-) )

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Lost toolbar in freeview
by 김영국 12 Sep '14

12 Sep '14

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Post Doc Position
by Fabrice Crivello 12 Sep '14

12 Sep '14

The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research unit of the Bordeaux University (UMR 5296, dir. Bernard Mazoyer) and a core member of the TRAIL Laboratory of Excellence. The GIN is a multidisciplinary research unit gathering scientists with initial training in mathematics and instrumentation, cognitive neurosciences, signal processing and databasing. One objective of the current GIN research project is to develop new tools to characterize and describe the gray matter anatomical connectivity networks. Within this area we have a position for a 2 years Post Doc. Description of the position Recent work on brain connectivity modeling revealed that the topographic organization of this connectivity is not limited to large-scale anatomical pathways generally observable in diffusion MRI, thus reinforcing the interest of studies focusing on the characterization of cortical structural connectivity and its variability. Therefore, the estimation of relevant grey matter connectomes strongly relies on the choice of an ad'hoc cerebral parcellisation. We propose a post doc project to first implement a probabilistic cortical atlas derived from cortical parcellisations defined individually to optimally extract cortical thickness and volume of each individual. The second aim of the post doc project is to compute cortical structural connectivity to quantify the inter-individual variability of brain organization together with the effects of specific factors such as gender, manual preference, functional lateralization or cognitive skills. The strength of the present project is that it will benefits from the already acquired BIL&GIN database composed of 453 healthy volunteers balanced for gender and handedness. Hence, the first probabilistic cortical atlas will be operated over a large sample, the 453 participants having been previously pre-processed. Qualification and experience The qualified applicant should have a PhD in neuro-image analysis, cognitive neuroscience, computer science or related field and a background in neuroimage processing. Applicants should have experience with existing tools for analysis of neuroimaging data (SPM, FSL, Freesurfer.) and a relevant programming experience (MATLAB). For further information, please contact Dr. Fabrice Crivello (fabrice.crivello(a)u-bordeaux2.fr) Employment and payment are determined by Bordeaux University (2 400 € per month, net salary). Job location is in Bordeaux, France. Interested candidates should send their applications including CV with full publication list, the names and contact information and a summary of research interests to fabrice.crivello(a)u-bordeaux2.fr. Dr. Fabrice CRIVELLO Groupe d'Imagerie Neurofonctionnelle UMR 5296 - CNRS CEA Université Bordeaux Université de Bordeaux 146, rue Léo Saignat CS 61292 33076 Bordeaux Cedex Mob : +33 618 064 753 Tel : +33 547 304 402 Fax : +33 547 304 394 www.gin.cnrs.fr See my publications : https://www.researchgate.net/profile/Fabrice_Crivello

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from freesufer label to diffusion mask
by Xiang-zhen Kong 11 Sep '14

11 Sep '14

Hi, all. I want to convert a freesufer label to diffusion mask with the following approach. # tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_annotation2label --subject S0001 --hemi rh --outdir ./labels --annotation aparc.a2009s tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_label2vol --label ./labels/rh.entorhinal.label --temp S0001_FA.nii.gz --subject S0001 --hemi rh --o rh.entorhinal.nii.gz --proj frac 0 1 .1 --fillthresh 0.3 --reg register.dat I wonder whether this is correct? In particular, what I am not sure about is the generation about the register.mat in the first line cmd. Best, Xiang-zhen 【小孔成像】http://www.conxz.net

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Compiling Freesurfer from source ends with error regarding libtool version mismatch
by Arman Eshaghi 11 Sep '14

11 Sep '14

Hi, I'm trying to compile Freesurfer current dev version from read only cvs repo according to developers guide on my machine with Ubuntu 14.04, gcc 4.8.2, I proceed as follows in dev/ directory: 1- ./setup_configure: which finishes without error 2- ./configure with vxl and mni library directory flags, also finishes without errors 3- make: it finishes with errors, specifically it seems to be a problem regarding the libtools mismatch of version, here is an example error I get from mri_segment source: /bin/bash ../libtool --tag=CC --mode=link g++ -I../include -L/usr/lib64 -L/usr/X11R6/lib64 -L/opt/mni_library/lib -L/opt/vxl/build/lib -o mri_segment_ms mri_segment_ms.o ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib ../libtool: line 469: *CDPATH: command not found libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.7ubuntu1, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.7ubuntu1 libtool: and run autoconf again. make: *** [mri_segment] Error 63* Error message seems to be pretty obvious and what I have done so far (in vain) are: 1- autoreconf -ivf 2- deleting alocal.m4 from dev, reconfiguring 3- issuing the command `make maintainer-clean` and reconfiguring and recompiling with make 4- libtoolize --force 5- deleting config.status, configure, Makefile.in, autom4te.cache I would be much grateful if anyone could help me here. All the best, Arman

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mri_glmfit-sim montecarlo analysis with mask
by Jon Alan Wieser 11 Sep '14

11 Sep '14

HI freesurfer experts We were wondering if it is possible to restrict the Monte Carlo analysis run by mri_glmfit-sim to a specific region fo the surface , instead of the whole surface, by using a mask or label to specify the ROI? I didn't see a --mask or --label option in mri_glmfit-sim Thank Jon

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aparc+aseg.mgz to nifti conversion
by Gabor Perlaki 11 Sep '14

11 Sep '14

Dear all, I'd like to convert the aparc+aseg.mgz to nifti and use it in the space of the original MR image. The basic conversion from mgz to nifti works fine "mri_convert aparc+aseg.mgz aparc+aseg.nii". However if I reslice it in the space of the original MRI than something fails and even negative intensities are presented in the converted aparc+aseg2raw.nii file " mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz aseg+aparc2raw.nii". Any idea how to convert it? Best Regards, Gabor

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Re: [Freesurfer] about issues with "recon-all"
by Lei, Chia-Ming 11 Sep '14

11 Sep '14

Thank you again for the reply, Bruce! After I typed: which mri_convert It came up with: Desktop/freesurfer/bin/mri_convert Let me know if any other info you need please. Thank you! PS. I changed the subject of this email from the Digest to my original question-related one. Really sorry, but I'm still trying to figure out how to manage/operate with this mailing list. -Abel (Chia-Ming) ________________________________________ ------------------------------ Message: 6 Date: Sat, 6 Sep 2014 16:02:05 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] about issues with "recon-all" To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.03.1409061601220.23927(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" after you run the source command can you type: which mri_convert and let us know what it says? This is not a FreeSurfer issue - it's a problem with your path Bruce On Sat, 6 Sep 2014, Lei, Chia-Ming wrote: > Thank you for the reply, Bruce. (Really sorry but I just changed my email address, so I decided to reply again with the currently subscribed email...) > > I'm running on Linux 3.13.0-35-generic with Ubuntu 14.04. I couldn't set up the permanent shell switched to .tcsh, i.e. when I opened a new terminal, nothing happened. So I deleted the .tcsh file I created and manually input the following steps when I opened a terminal: > > 1. setenv FREESURFER_HOME Desktop/freesurfer 2. source $FREESURFER_HOME/SetupFreeSurfer.csh > *note: the following message shows up withe the source command, > "-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME Desktop/freesurfer > FSFAST_HOME Desktop/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR Desktop/freesurfer/subjects > MNI_DIR Desktop/freesurfer/mni" > > 3. setenv SUBJECTS_DIR $FREESURFER_HOME/subjects > *note: I also tried to set SUBJECTS_DIR to the specific folder where the .dcm files are. > 3.1 setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/Dickey-Pilot/003 > > 4. recon-all -i $SUBJECTS_DIR/Dickey-Pilot/003/003-0001-00003-0.dcm -s mike-dickey -all > *OR > 4.1 recon-all -i $SUBJECTS_DIR/003-0001-00003-0.dcm -s mike-dickey -all > > Then the long error message pasted in the first email (below attached) showed up. Please let me know if any other info you need to figure out the issue is. > Again, thank you so much for your help! > > -Abel > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Saturday, September 6, 2014 9:56 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] about issues with "recon-all" > > Hi Abel > > what OS are you running on? Did you source the file > > $FREESURFER_HOME/FreeSurferEnv.csh > > ? > > cheers > Bruce > > > On Sat, 6 Sep 2014, Abel Lei > wrote: > >> >> Hi FreeSurfers, >> >> ? >> >> I'm a very beginner to both the Linux OS and the FreeSurfer program. >> After finally setting up the FreeSurfer, I was trying to do recon-all >> for my trial subject. But when I ran the "recon-all" command, it >> returned with a long error message indicating many commands not found. >> The message is copied and pasted below. I also attached the >> recon-all.log and recon-all.error in this email, which (probably) contains two failed attempts of the same command. >> Please let me know if you need any other info from me. I appreciate >> your help and time greatly! Thank you so much! >> >> >> Chia-Ming (Abel) Lei >> >> PhD Student/Graduate Student Researcher >> >> Language and Brain Lab (LABlab) & Adult Language Lab >> >> Department of Communication Sciences and Disorders >> >> School of Health and Rehabilitation Science >> >> University of Pittsburgh >> >> >> -----below is the long~ error message------ chiaming-PORTEGE-R835:~> >> recon-all -all -s mike_dickeySubject Stamp: >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> INFO: SUBJECTS_DIR is >> /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot >> Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer >> -rw-rw-r-- 1 chia-ming chia-ming 2119 Sep? 6 >> 01:34/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dic >> key/script >> s/recon-all.log >> Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug >> 15 >> 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> mri_motion_correct.fsl: Command not found. >> talairach_avi: Command not found. >> tkregister2_cmdl: Command not found. >> nu_correct: Command not found. >> mri_make_uchar: Command not found. >> mri_normalize: Command not found. >> mri_watershed: Command not found. >> mri_gcut: Command not found. >> mri_segment: Command not found. >> mri_label2label: Command not found. >> mri_em_register: Command not found. >> mri_ca_normalize: Command not found. >> mri_ca_register: Command not found. >> mri_ca_label: Command not found. >> mri_pretess: Command not found. >> mri_fill: Command not found. >> mri_tessellate: Command not found. >> mri_concatenate_lta: Command not found. >> mri_normalize_tp2: Command not found. >> mris_smooth: Command not found. >> mris_inflate: Command not found. >> mris_curvature: Command not found. >> mris_sphere: Command not found. >> mris_fix_topology: Command not found. >> mris_topo_fixer: Command not found. >> mris_ca_label: Command not found. >> mris_euler_number: Command not found. >> mris_make_surfaces: Command not found. >> mris_register: Command not found. >> mris_volmask: Command not found. >> mris_anatomical_stats: Command not found. >> mrisp_paint: Command not found. >> mris_curvature_stats: Command not found. >> mris_calc: Command not found. >> mri_robust_register: Command not found. >> mri_robust_template: Command not found. >> mri_and: Command not found. >> mri_or: Command not found. >> mri_fuse_segmentations: Command not found. >> mri_segstats: Command not found. >> cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or >> directory >> #-------------------------------------------- >> #@# MotionCor Sat Sep? 6 01:40:13 EDT 2014 >> ERROR: no run data found in >> /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. >> Make sure to >> have a volume called 001.mgz in? >> /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/m >> ri/or >> ig. >> If you have a second run of data call it 002.mgz, etc. >> See also: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion >> Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug >> 15 >> 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s mike_dickey exited with ERRORS at Sat Sep? 6 01:40:13 EDT >> 2014 >> >> For more details, see the log >> file/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dick >> ey/script >> s/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> ? >> >> ? >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 127, Issue 8 ******************************************

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