Freesurfer

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30132 discussions

regions in FreeSurferColorLUT.txt and the atlas
by Xinyang Liu 14 Oct '13

14 Oct '13

Dear all, In the "FreeSurferColorLUT.txt", what brain regions are represented by "right-vessel" and "left-vessel", respectively? Is there a file or document that explains the definition of regions listed in "FreeSurferColorLUT.txt"? Also, the atlas for subcortical segmentation is in $FREESURFER_HOME/average/RB_all_2008-03-26, which is a ".gca" file. What is this format? Is there a way that I can "see" this atlas in 3D? Can it be transferred to a ".nii" file? Thanks, Xinyang

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bvecs and bvals don't have the same number of entries
by Laura Christine Anderson 11 Oct '13

11 Oct '13

Hi Anastasia, Thanks so much for your help! Attached are bvec, bval and trac-all.log files. I have been stuck at one of the preprocessing steps (trac all) for some time and keep getting the error: bvecs and bvals don't have the same number of entries. I saw a couple blogs online about this, but did not see any resolution. I am wondering if it is because the B0 images are interspersed? (see attached bvec file). If you have any insight, I would love some feedback whenever you get the chance. Laura

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atlases labels coordinates
by maria estanqueiro 11 Oct '13

11 Oct '13

Dear all, I need the center coordinates of the anatomical labels from the desikan and destrieux atlases. I saw a similar post a while ago in which it was recommended the following: #1 Convert the annotation to a set of labels. This is for the Desikan atlas, but you can spec the destrieux instead mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc # For each label, run mri_surfcluster to get the centroid mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel lh.pericalcarine.label --sum sum.lh.pericalcarine --centroid --thmin 0 --hemi lh --subject fsaverage I did the last step step for 2 different labels, one in the temporal and the other in the occipital cortex. However, the coordinates that were generated in the sum files were the same. Does anyone know why? Is this the right procedure for what I want to do? Thanks!

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Normalization for brain/head size differences in a pediatric population
by David O Kamson 11 Oct '13

11 Oct '13

FreeSurfers, I have a couple of questions regarding normalization for brain/head size. We are trying to analyze a pediatric population with subjects between age 4 and 16 with variable brain (and head) sizes. We are mainly interested in measuring cortical thickness in these children, but not sure whether volumetric normalization should be performed or the output of the recon-all -all script is already comparable among subjects with different ages and brain sizes. As per the eTIV page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV) of the FreeSurfer website, cortical thickness information cannot be normalized using volumetric information. Does this mean it doesn't have to be normalized in our population at all? If normalization for cortical thickness is necessary, what approach at what stage would you suggest to use? For volumetric information, is there any data suggesting normalization to the estimated intracranial volume does not work in children? Your help is much appreciated! David Olayinka Kamson, MD Research Associate PET Center Children's Hospital of Michigan 3901 Beaubien, Detroit, MI 48201 Phone: 313-745-0668 FAX: 313-966-9228 david.kamson(a)pet.wayne.edu

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Re: [Freesurfer] V1 Labels (fwd)
by krista kelly 11 Oct '13

11 Oct '13

Hi again, I apologize for all of the emails, but I'm really trying to figure out what this labelling problem is. I've gone through all of my participants and for most of them, the talairach is fine and the voxel size is 1 x 1 x 1mm, so having a high resolution cannot be the problem, unless the problem is with the fact that it was a 3T scanner and not 1.5T. Could this be it? Can I upload a participant who's talairaching is fine and voxel size is 1 x 1 x 1mm so that you might be able to figure out what the problem with mapping the labels is? Also, I'd like to do a whole brain analyses prior to a ROI analysis with the atlases and labels, but I want to make sure that I can trust the data that I have without having to rerun all of my participants. Thanks! Krista On Wed, Oct 9, 2013 at 9:15 PM, krista kelly <krista.kelly16(a)gmail.com>wrote: > Hi again Allison, > > After going through a few of my subjects' data, I've realized that only > that one person has problems with the talairach.xfm, all of the others look > fine yet the problem with the labels still persists. Could it still be the > high resolution problem that's causing the label problem? I can upload a > participant's data that does not have a bad tal transform if that helps. > Just let me know. > > Thanks! > Krista > > > On Wed, Oct 9, 2013 at 9:04 PM, krista kelly <krista.kelly16(a)gmail.com>wrote: > >> Sorry, just one last thing. If the pial matter and white matter borders >> came out fine initially, is it necessary to rerun the whole recon-all >> automatic pipeline? I'm just asking because I have about 40 people that i >> will need to rerun because of this problem. >> >> Thanks again! >> Krista >> >> >> On Wed, Oct 9, 2013 at 8:47 PM, krista kelly <krista.kelly16(a)gmail.com>wrote: >> >>> Also, just to add to this, if I rerun recon in 5.1 starting from the >>> normalization stage when I initially ran all subjects in 5.0, will this be >>> a problem? >>> >>> >>> >>> >>> On Wed, Oct 9, 2013 at 8:05 PM, krista kelly <krista.kelly16(a)gmail.com>wrote: >>> >>>> Thanks Allison, >>>> >>>> So to be clear, I just need to rename talairach.auto.xfm as >>>> talairach.xfm and then rerun recon-all from the normalization step? However, >>>> I'm not sure how to run recon starting from the normalization stage. Would >>>> you be able to help with that? >>>> >>>> Also, I've been doing manual edits to the brain extraction as well as >>>> adding control points on all of my subjects and I'm wondering if this will >>>> negate any edits I've made. So I'm pretty much starting from scratch? >>>> >>>> Thanks so much for looking into this for me! >>>> >>>> Best, >>>> Krista >>>> >>>> >>>> On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < >>>> astevens(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> Hi Krista, >>>>> I took a look at your subject and think I have determined the problem. >>>>> Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the >>>>> talairach registration step failed. If you look at the talairach.xfm, >>>>> you'll see it is way off: >>>>> tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig >>>>> >>>>> But the talairach.auto.xfm is correct. You can copy the >>>>> talairach.auto.xfm to talairach.xfm and rerun from the -normalization step. >>>>> >>>>> You might also want to look at these instructions: >>>>> https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon> >>>>> >>>>> They might not all apply to you but could potentially. >>>>> Allison >>>>> >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>>> Date: Thu, 03 Oct 13 22:55:12 -0400 >>>>>> From: krista.kelly16(a)gmail.com >>>>>> To: fischl(a)nmr.mgh.harvard.edu >>>>>> Subject: V1 Labels >>>>>> >>>>>> Hey! >>>>>> >>>>>> Krista (krista.kelly16(a)gmail.com) has uploaded some files for you >>>>>> at the Martinos Center FileDrop: >>>>>> >>>>>> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** >>>>>> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4> >>>>>> > >>>>>> >>>>>> Also, they left this message for you: >>>>>> Hi Bruce, >>>>>> >>>>>> Here is a zipped file of one of the subjects that I'm having label >>>>>> troubles with. The lh.v1.label isn't mapping correctly. I find the same >>>>>> goes for the aparc atlas as well (I haven't checked out anything else). If >>>>>> you could help me figure out why this is happening, that would be great! >>>>>> >>>>>> Thanks, >>>>>> Krista >>>>>> >>>>>> Please be aware, your upload will expire on December 31st. If you'd >>>>>> like to download these files, feel free to use the link below: >>>>>> >>>>>> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf> >>>>>> >>>>>> Cheers, >>>>>> The NMR Team >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> 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<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. >>>>> >>>>> >>>> >>> >> >

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ANOVA in QDEC
by Muhammad Naveed Iqbal Qureshi 11 Oct '13

11 Oct '13

Dear Experts, Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM for ANOVA testing? Is there any way to convert Freesurfer thickness files to SPM readable format? Waiting for a precise reply. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi

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Job opening: Biomedical Imaging Laboratory at Hospital Gregorio Marañon (Madrid, Spain)
by Susanna Carmona Cañabate 11 Oct '13

11 Oct '13

Job available at the “Biomedical Imaging and Instrumentation Group (BiiG)<http://image.hggm.es/index.php?lang=english>”, Madrid. The “Biomedical Imaging and Instrumentation Group (BiiG)<http://image.hggm.es/index.php?lang=english> ”, is offering a position in system administration and programming to support neuroimaging data processing. The BiiG is a research organization located in Madrid (Spain) and affiliated with the “Instituto de Investigación Sanitaria Gregorio Marañon” and the “Universidad Carlos III”. The group is markedly multidisciplinary and has broad research interest, from the development of new imaging techniques to processing methodologies and their application in practice. The candidate will support the neuroimaging subdivision of the group and will be responsible of the development, maintenance and optimization of a neuroimaging platform that manages DTI, structural and functional MRI data. He/She will work together with researchers on the implementation of software, hardware, and storage, as well as the processing and analysis of large data sets. *Qualifications:* - *Biomedical Engineering,** **Computational Neuroscience** or related field **with a strong computational background. * - *Proficiency in **o**ral and written English.* - *Experience with **Matlab and other **programming languages (C, C++, bash **and** **Python**.)* - *I**nterest **in** neuroimaging **research.* - *Ability to effectively interact with a multi-disciplinary team of investigators and staff.* - *Ability to work independently and as part of a team. * *Preferences**:* - *Familiarity with stimuli presentation softwares such as Eprime, Presentation or Psychtoolbox as well as with neuroimaging processing software**s** (**FreeSurfer, FSL, SPM, AFNI, ANTs, **GIFT, BrainVoyager or** BrainVisa**).* - *Methods background (statistics/SPSS).* *Salary based upon experience and qualifications. Interested applicants should submit a cover letter and resume to **scarmona(a)hggm.es.*

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using multiple functional ROIs in fcseed-config
by SHAHIN NASR 10 Oct '13

10 Oct '13

Hi, I know that we can have multiple segments (segIDs) in fcseed-config. Is there anyway to use multiple ROIs (functionally defined) in fcseed-config? If no, what is the alternative? Is there anyway to average the .dat output files generated by separate fcseed commands? Is it OK to manually average the .dat files? Should we consider anything in this averaging? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] trac-all -tensor error
by Anastasia Yendiki 10 Oct '13

10 Oct '13

Hi Jenn - I think there was a problem in one of the scripts in the case where CVS registration is used. Can you please try replacing your current version of trac-preproc with the attached version and see if this solves the problem? Please let me know. Thanks! a.y On Thu, 10 Oct 2013, Jenn Segawa wrote: > Thanks, Anastasia. The files are attached. > > > > On Thu, Oct 10, 2013 at 2:37 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Jenn - Can you please send the scripts/trac-all.log and your > tracula.cfg? I don't have permission to access them. > > Thanks, > a.y > > On Mon, 7 Oct 2013, Jennifer Segawa wrote: > > Hello! > I'm having problems running the trac-all -tensor > step. dtifit appears to > run correctly; the problem seems to be in mapping > the output files to the > template space. The command I run is: > > trac-all -tensor -c > /cluster/manoach/dod/BU_pipeline/data/DOD_DODCON004/tracula.cfg > > ----------------------------------------------- > > And the error I get is (the move file doesn't exist, > but dtifit_FA.nii.gz > does exist): > > mri_vol2vol--mov/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_F > A.flt > .nii.gz --targ > /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz > --o/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.n > ii. > gz--m3z/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/xfms/cvs/final_CV > Smorp > h_tocvs_avg35.m3z --noDefM3zPath --interp trilin > --no-save-reg > niiRead(): error openingfile/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA > .flt > .nii.gz > Using the m3z file as it is; no assumed location. > movvol/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_ > FA.flt > .nii.gz > targvol > /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz > outvol/cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.fl > t.nii. > gz > invert 0 > tal 0 > talres 2 > regheader 0 > noresample 0 > interp trilin (1) > precision float (3) > Gdiag_no -1 > Morphing > InvertMorph 0 > Synth 0 > SynthSeed 1381542765 > Linux huygens 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed > Mar 13 00:26:49 UTC 2013 > x86_64 x86_64 x86_64 GNU/Linux > > trac-preproc exited with ERRORS at Sun Oct 6 > 12:04:16 EDT 2013 > > > --------------------------------------------------------------------- > And here is the output of bugr: > > FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > > Build stamp: > freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > > RedHat release: CentOS release 6.4 (Final) > > Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64 > > NMR Center info (/space/freesurfer exists): > > machine: huygens > > SUBJECTS_DIR: /cluster/manoach/dod/subjects > > PWD: /cluster/manoach/dod/BU_pipeline/dti_scripts > > ssh huygens > setenv SUBJECTS_DIR /cluster/manoach/dod/subjects > cd /cluster/manoach/dod/BU_pipeline/dti_scripts > --------------------------------------------------------------------- > Additionally, the subject is DODCON004 and the > script directory can be found > at > /cluster/manoach/dod/BU_pipeline/data/DODCON004/scripts > > Thanks for your help! Any advice would be > appreciated. > Jenn Segawa > > > > > 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. > > > >

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FSL masks applied to Freesurfer surfaces?
by Ruth Carper 10 Oct '13

10 Oct '13

Hi Doug, mri_label2vol says it creates an mgz from a label, I need to do the reverse. I'm starting with a mask_MNI.mgz (brought from FSL's MNI space via mri_convert) and I need to be able to use that mask to extract thickness from the individual subject. Also, mni152reg fails because it expects to write a tmp file into an FSL directory rather than a Freesurfer directory. The FSL standards directory is write protected for obvious reasons. Can I redirect the temporary file? Error message: “mkdir: /usr/local/fsl/data/standard/tmp.fslregister.9446: Permission denied” Message: 17 Date: Mon, 07 Oct 2013 11:01:23 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? 116(14) To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5252CCC3.5070601(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ruth, run mni152reg for each subject to create a registration from the subject to the 152. Then use mri_label2vol to map the mask into each subject's space. doug On 10/05/2013 04:08 PM, Ruth Carper wrote: > Doug, > I'd like to get them into the individual's space, but I assume I have > to get there by way of fsaverage? Final goal is to have a regional > thickness measure for each individual subject. > Ruth Carper > > > ------------------------------------------------------------------------ > *From:* "freesurfer-request(a)nmr.mgh.harvard.edu" > <freesurfer-request(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Sent:* Saturday, October 5, 2013 9:00 AM > *Subject:* Freesurfer Digest, Vol 116, Issue 14 > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 04 Oct 2013 12:21:32 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <524EEB0C.8050400(a)nmr.mgh.harvard.edu > <mailto:524EEB0C.8050400@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Do you want to transfer them to fsaverage space or to the individual > anatomical space? > doug > > > On 10/04/2013 01:42 AM, Ruth Carper wrote: > > Hi, > > I'd like to take some masks that I have in MNI standard space in FSL > > and map them to Freesurfer surface space. The goal is to extract > > measures of average cortical thickness (or area or etc) for those > > regions for each subject. Is there a standard way to do this? > > > > > > Ruth Carper, PhD Assoc. Project Scientist, UCSD Adjunct Professor, SDSU

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