Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

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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mri_glmfit-sim without talairach.xfm, orig.mgz and aparc
by Caspar M. Schwiedrzik 10 Oct '13

10 Oct '13

Hi Freesurfer experts, I am running a group analysis of functional data on a custom template/average subject for which I do not have a talairach.xfm file, an orig.mgz nor aparc data (it is a primate dataset). I ran into some error messages when trying to use mri_glmfit-sim. 1) I get an error message that the flag --no-cortex is not recognized. I am using --no-cortex in mri_glmfit because I do not have a cortex label file for my template subject. This error does not crash the program, but may be worth a minor bug fix in future releases. 2) For the primate data, I did not make an average volume yet, but only an average surface. Hence, I do not have an orig.mgz file for the average subject. All analyses I currently run are surface based. Can I just copy any orig.mgz into the mri folder without negatively affecting mri_glmfit-sim? 3) I do not have a Talairach.xfm file for the average subject either. Can I copy an identity matrix into mri/transforms without negatively affecting mri_glmfit-sim? Again, all analyses are surface-based. 4) I removed the --annot flag where mri_glmfit-sim where mri_surfclusters is being called. Is that expected to result in any problems? 5) Anything else I should observer? Thanks, Caspar

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Re: [Freesurfer] brain.mgz and control.dat attached
by Francesco Siciliano 10 Oct '13

10 Oct '13

Thank you for your help! I will re-run this brain and see if it reads all 53 control points and then let you know the outcome. However, the last time I ran this brain with this control point set, it only read 22 control points. ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 3:28 PM To: Francesco Siciliano Subject: RE: brain.mgz and control.dat attached but it should say "reading 53 control points". Can you verify whether this is or is not the case? And also please cc the list so that others can answer! On Mon, 7 Oct 2013, Francesco Siciliano wrote: > I can run it again - but it has already been run with the current control point set (apparently with 53 points) and some of the points have not been successful for some reason. > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Monday, October 07, 2013 2:55 PM > To: Francesco Siciliano > Subject: Re: brain.mgz and control.dat attached > > hmmm, and you reran after this? There are 53 points in it. Can you run > autorecon2-cp and see if it now reads 53 control points? > On Mon, 7 Oct 2013, > Francesco Siciliano wrote: > >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Monday, October 07, 2013 2:48 PM >> To: Francesco Siciliano >> Subject: RE: [Freesurfer] [FreeSurfer] control points >> >> can you email me the control.dat and the brain.mgz? >> >> On Mon, 7 Oct 2013, Francesco Siciliano >> wrote: >> >>> In the control.dat file it says numpoints 53. Is that referring to control points? Because I certainly don't have that many! I counted about 28 when I loaded the control.dat file onto the brainmask volume. >>> ________________________________________ >>> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Sent: Monday, October 07, 2013 2:14 PM >>> To: Francesco Siciliano >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: RE: [Freesurfer] [FreeSurfer] control points >>> >>> and how many do you see in the control.dat file? Sounds like they aren't >>> getting saved to disk somehow.... >>> On Mon, 7 Oct 2013, Francesco Siciliano >>> wrote: >>> >>>> I counted at least 28 control points on the brainmask when I loaded the set and my log indicates that freesurfer read 22 control points. I've attached part of the log below. >>>> >>>> >>>> #@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013 >>>> /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/mri >>>> \n mri_normalize -f /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz \n >>>> using control points from file /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat... >>>> using segmentation for initial intensity normalization >>>> reading from norm.mgz... >>>> normalizing image... >>>> Reading 22 control points... >>>> only using 22 control points from file, mean 84.1, scaling by 1.31... >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> removing outliers in the aseg WM... >>>> 4899 control points removed >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> 3d normalization pass 1 of 2 >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> 3d normalization pass 2 of 2 >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> writing output to brain.mgz >>>> 3D bias adjustment took 4 minutes and 46 seconds. >>>> using MR volume brainmask.mgz to mask input volume... >>>> white matter peak found at 111 >>>> white matter peak found at 102 >>>> gm peak at 66 (66), valley at 25 (25) >>>> csf peak at 33, setting threshold to 55 >>>> white matter peak found at 111 >>>> white matter peak found at 110 >>>> gm peak at 66 (66), valley at 24 (24) >>>> csf peak at 33, setting threshold to 55 >>>> >>>> >>>> >>> >>> >>> 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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Re: [Freesurfer] TRACULA question
by Anastasia Yendiki 10 Oct '13

10 Oct '13

Hi Lars - Just like you have to do before you run any freesurfer programs, you'll have to run a script that comes with freesurfer and sets up all the necessary environment variables. See: http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration Hope this helps, a.y PS: Please send emails about tracula usage to the freesurfer list (cc'd here) and not to me personally. This makes sure the answers get archived so that people can search for answers to common questions. Thanks! On Thu, 10 Oct 2013, Lars M. Rimol wrote: > Dear Dr. Yendiki, > > I am trying to learn how to do Tracula analyses and was wondering about one > thing: > > According to the tutorial, all I need to do is set up the various > configuration files. However, when I try to run the example data set, with > > trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial > > it complains: "FSLDIR: Undefined variable." > > FSL dir doesn't seem to be defined in any of the configuration files > provided in the tutorial. Is it necessary to install FSL in order to use > Tracula? And where do I set the FSLDIR variable? > > > > > Thank you! > > > > yours, > > Dr. Lars M. Rimol > >

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Freesurfer October 2013