Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Postdoctoral Position at Boston/Children’s Hospital/Harvard Medical School
by Gaab, Nadine 09 May '13

09 May '13

Postdoctoral Position at Boston/Children’s Hospital/Harvard Medical School The Gaab Labhttp://childrenshospital.org/research/gaablab and (babymri.org)<http://www.babymri.org)>) at the Laboratories of Cognitive Neuroscience at Boston Children’s Hospital (Developmental Medicine Center) invites applications for a NIH funded post-doctoral associate in the area of developmental cognitive neuroscience/pediatric fMRI. Available resources include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis platforms based in MATLAB/UNIX. The candidate will be expected to oversee pediatric and infant (f)MRI experiments, analyze behavioral and fMRI data, prepare manuscripts for publication, and participate in conferences. The NIH and foundation funded projects will focus on language processing in autism, neural and behavioral pre-markers of developmental dyslexia in infants and pre-reading children as well as typical reading and language development throughout childhood. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, psychology, developmental psychology, medicine). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of functional brain-imaging experiments. Experience with one of the fMRI analyses programs (SPM, FSL, Freesurfer) a must. Programming skills (MATLAB, C++; Python) are desirable and experience with MVPA or connectivity analyses a plus. Experience with pediatric functional neuroimaging and language and reading research are useful. Approximate start date is Summer/Early Fall 2013 (the earlier the better). Successful applicants will be appointed at Children’s Hospital Boston and Harvard Medical School. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Nadine Gaab, PhD (nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>). The search will continue until the position is filled. -- "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Assistant Professor of Pediatrics Harvard Medical School Faculty Affiliate Program in Neuroscience, Harvard Medical School Member of the Faculty of Education Harvard Graduate School of Education Children's Hospital Boston Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience 1 Autumn Street (Office 643) Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: (857)-218-3021 Main Lab: 617-355-0400 fax: 617-730-0518 http://www.childrenshospital.org/research/gaablab www.babymri.org<http://www.babymri.org/>

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Re: [Freesurfer] Working with MEMPRAGE
by Bruce Fischl 09 May '13

09 May '13

it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the "4" which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: > I input: > > mris_make_surfaces -dura memprage_echo%d.mgz subjid lh > > it returns: > > detecting dura using 0 echos from memprage_echo%d.mgz > > > Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. > > > On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: > >> can you send me the full command line? It should say 4 echoes, not 0 >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> Thanks Bruce, >>> >>> should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? >>> >>> Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. >>> >>> jon >>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>> >>>> Hi Jon >>>> >>>> yes, the subject and hemi need to be defined (they are required parameters) >>>> Bruce >>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>> >>>>> Hi all, >>>>> combed through the mail archives to figure out how to work with multi echo >>>>> mprage, found what I need but I wanted to confirm which of these two >>>>> commands is the appropriate >>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>>>> jon >>>>> >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it is >>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>> contains patient information, please contact the Partners Compliance HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>>> but does not contain patient information, please contact the sender and properly >>>> dispose of the e-mail. >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > > >

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recon-all completes without all the info..
by Sudhin A. Shah 09 May '13

09 May '13

Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder..

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Freesurfer License issue/bug on Opensuse 12.3
by Nick Jones 09 May '13

09 May '13

Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurfer>echo $shell /bin/tcsh /usr/freesurfer>source SetUpFreeSurfer.csh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl /usr/freesurfer>tkmedit bert orig.mgz -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- /usr/freesurfer>cat .license hotmail(a)hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer> This license file has been obfuscated. /usr/freesurfer>ll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfer>cat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurfer>zypper targetos openSUSE-12.3-x86_64 /usr/freesurfer>uname -a Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux Name: tcl Version: 8.5.12-3.1.3 Name: tk Version: 8.5.12-3.1.1 Thanks to anyone who can provide some insight or workaround. I'm also curious if anyone knows the reasoning behind using this type of license mechanism, as opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer? Nick

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Re: [Freesurfer] Subcortical Choi 17 networks ROIs
by Douglas N Greve 09 May '13

09 May '13

Hi Mario, you cannot use the m3z for this since the atlas is in mni152 space. You can run mni152reg to register your subject to 152 space. Then use the resulting registration matrix and mri_label2vol to map the Choi atlas to the individual space. The registration will not be perfect since it is only 12dof. You could remove voxels that are not in the subject's striatum. You can then use fcseed-sess and specify this volume and an index in the volume. doug On 05/09/2013 10:42 AM, Mario Ortega wrote: > HI Doug. > So Im thinking of comparing the 7 striatal networks that are created > found here. > http://ftp.nmr.mgh.harvard.edu/fswiki/StriatumParcellation_Choi2012 > I want to transform the 7 netwrok striatal roi estimate to subject > space, then run fcseed-config and fcseed-sess. with an altered LUT and > segmentation. > Im assuming the talairach.m3z can be used to transform the 7-networks > to subject space in each mri/transforms. to do this. > Is this a feature that is coming into next version 5.3? Also, do I > have to go to subject space? > Thank you for your response. > -Mario -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Using FSL matrix for Talairach transform
by Johannes Klein 09 May '13

09 May '13

Hi Doug, Thanks! I've tried that now, but it didn't help. Looking at the output, I get the impression that some of the axes might be swapped over. I've done a manual registration now to process my subject. Maybe it's worth following this up for future use of FSL-supplied matrices - however, the problem only applies to XFM-style output, and e.g. mri_vol2vol works fine, so I guess there aren't many other users affected. If you like, I can send you a few volumes and the associated registration matrix. Thanks for your help! Cheers, Johannes Douglas N Greve Wed, 08 May 2013 12:16:36 -0700 Hi Johannes, as a quick fix can you try inverting the matrix? doug On 05/08/2013 01:31 PM, Johannes Klein wrote: > Hi Doug, > Thanks for your reply! I'm getting closer to a solution now, with > tkregister2's display showing a correctly transformed mni305 file, > but I still cannot get a valid talairach.xfm file out of this. > > Here's what I tried: > tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz > --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg > works fine. > > Next, to obtain a suitable .xfm file, I ran > tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz > --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg --xfmout > testtal.xfm --noedit > and copied the output (testtal.xfm) into mri/transforms/talairach.xfm > > Now, when I view the result with > tkregister2 --s test --fstal --mgz > the transform is way off again. Apparently, tkregister2 reads and > interprets the FSL matrix correctly, but the output transform that I > get is not in the right format for transforms/talairach.xfm. > I wonder if I'm using the wrong output switch now - but looking at > tkregister2's documentation, it seems to be the one to use? > Thanks, > Johannes > > > > Date: Tue, 07 May 2013 14:11:27 -0400 > From: Douglas N Greve <gr...(a)nmr.mgh.harvard.edu > < mailto:gr...@nmr.mgh.harvard.edu >> > Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform > To: freesurfer(a)nmr.mgh.harvard.edu < mailto:freesurfer@nmr.mgh.harvard.edu > > Message-ID: <518943cf.7050...(a)nmr.mgh.harvard.edu > < mailto:518943cf.7050...@nmr.mgh.harvard.edu >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure > what regdat2xfm is doing. > doug > > On 05/07/2013 12:42 PM, Johannes Klein wrote: >> Dear all, >> I have some tricky subjects that I cannot get to register properly >> with the standard Talairach process, or even the use-mritotal option. >> However, with some fiddling, I've produced a reasonable registration >> matrix with FSL's FLIRT. >> >> I'm now looking to convert my FSL registration matrix, and use it as >> Freesurfer's Talairach transform. From the documentation, I gathered >> that I need to get it into Freesurfer's xfm format, and I suppose >> this is a two step process. >> >> I converted the FLIRT-provided matrix cor2raw.xfm like so: >> tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz >> --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat >> >> I then converted register.dat to the xfm data format: >> regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz >> register.dat tal.xfm >> >> and finally replaced talairach.xfm in the transforms directory with >> the output of the last command. Unfortunately, this doesn't work, and >> the transform is very much off target when I view it in tkregister2. >> Obviously, I've made a mistake when converting between the different >> transforms - could anybody point me in the right direction? >> Thanks all, >> Johannes >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu < mailto:Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu < mailto:gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > < http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Working with MEMPRAGE
by Jonathan Holt 09 May '13

09 May '13

Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon

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Labels and parcellations
by Tudor Popescu 09 May '13

09 May '13

Hello all, I have some more burning questions, for which I thank you in advance!! 1) I expected that "mri_annotation2label --subject 01 --hemi lh --outdir $SUBJECTS_DIR/myLabels" would give me labels corresponding to structures of the standard FreeSurfer atlas (Destrieux), instead it produced labels with completely different names, e.g. "lh.postcentral.label" instead of the Destrieux name "lh_S_postcentral". Exactly how different are they, and which ones should be used in mri_glmfit for ROI analyses? 2) Does it make sense to use mri_glmfit with volumetric masks, or should it only be used with labels? 3) Say I want to do a ROI analysis for a particular brain structure; how much is there to gain by manually (visually) creating a label/mask for that structure in each subject (i.e. taking into account individual anatomy), as opposed to just using an atlas to create a single label/mask for use with all subjects? 4) I used the command "tkmedit 01 aparc+aseg.mgz" (I also tried adding " -aux brainmask.mgz -surfs –aseg"), thinking that it would display an image like this<http://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pia…>, i.e. with all the main cortical structures displayed in different colours. Does aparc+aseg.mgz not contain all the necessary information to produce such an image? 5) Which mask file corresponds to the brain extraction procedure of recon-all? I see that a subject's /mri/brainmask.mgz is not a binary map, as expectd, but instead a BETted (skull-stripped) version of that subject's structural. Thank you so much for your help! Tudor

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Qdec error and design problem
by Sinead Kelly 09 May '13

09 May '13

Dear all, I am trying to run statistical analysis on cortical thickness data using Qdec. I have one group of control subjects that are split into three genotype groups. I want to investigate if cortical thickness significantly between the three genotype groups. Is it possible to look at differences between three groups using Qdec? I am getting the following error when I try to analyse - ERROR: QdecGlmDesign::Create: zero factors! I would really appreciate if anyone could shed some light on this for me as this is the first time I have used Qdec and I don't know what is causing this error. Thank you for your help. Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Why does smoothing make non-zero intensity to zero in many vertices?
by Glen Lee 08 May '13

08 May '13

Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2surf (with fwhm ==4) and examined the values in the output map. As it turns out, values become 0 in a number of vertices after smoothing while those in many other vertices look normal (i.e., more or less similar to the values in the vertex of unsmoothed map). I'm not sure why this happened as smoothing average values locally within the kernel (4mm). Any helpful answers would be greatly appreciated. Glen p.s) fyi, the original EPI is a slap data covering only the temporal & occipital cortex.

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