Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

obtain a V1 mask.nii.gz
by lujiao luo 13 May '13

13 May '13

Hello, experts, I am trying to obtain a V1 mask and use it as a seed of my fiber tracking. But I do not know how to get the BA.nii.gz file, and I've obtained BA.ctab and lh.BA.annot files by using flag recon_all. Would someone give me some suggestions about this? Thanks so much for your help! Yours Lulu

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thickness
by Tudor Popescu 13 May '13

13 May '13

Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while factoring out age and gender be built? I didn't quite understand the example in the tutorial <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Contrasts>based on intercept/offset. In my case, shouldn't I have 4 elements in the vector (group1, group2, age, gender), with the first two elements receiving perhaps 1 and -1, since they are directly compared, and the last two elements 0 and 0 since I am not directly interested in their effect on the dependent variable? 2) Are the structures described in the .label files produced by mri_annotation2label in common (MNI) or in that subject's individual space? 3) For my thickness analysis, I have in mind an ROI for which I have a set of centre coordinates from a meta-analysis of relevant functional studies. What is the best way of defining the mask for this ROI as a function of those coordinates, rather than taking the eponymous region from the Destrieux or the Desikan atlas? 4) Exactly which of recon-all's outputs has to be inspected, for each subject, in order to tell whether the surface reconstruction has gone well? 5) Is it statistically correct to run the same design both with a DODS FSGD and with a DOSS FSGD? It's not entirely clear to me what assumptions each one (DODS, DOSS) makes of the data, and which one I should select in my case. Thank you very much indeed. Tudor

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Centos vs. Ubuntu
by Katie Surrence 10 May '13

10 May '13

Dear all, I know you run Centos at the Martinos center. Are there any known issues or concerns that differentiate between running Freesurfer on Centos or Ubuntu? Reasons to prefer one or the other? Thanks for your help, Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

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Re: [Freesurfer] Working with MEMPRAGE
by Jonathan Holt 10 May '13

10 May '13

$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh it's entirely possible I'm specifying the wrong mgz? After running recon-all on the RMS the usual directories were created, etc... including 001.mgz which is in s_MEMPRAGE/mri/orig. On Fri, May 10, 2013 at 12:39 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: > $ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer > $ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh > > it's entirely possible I'm specifying the wrong mgz? After running > recon-all on the RMS the usual directories were created, etc... including > 001.mgz which is in s_MEMPRAGE/mri/orig. > > > On Fri, May 10, 2013 at 12:33 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > wrote: > >> can you send details about the steps you carried out including full >> command lines? >> >> On Fri, 10 May 2013, Jonathan Holt wrote: >> >> I've gotten as far as running the mris_make_surfaces on the RMS, but >>> after running for a bit it stopped with this error >>> >>> mghRead (file/path/s_MEMPRAGE/mri/**0010.mgz -1): coult not open file >>> mris_make_surfaces: could not read 0th echo for dura localization from >>> file/path/s_MEMPRAGE/mri/0010.**mgz >>> >>> for reference, the RMS file name is 001.mgz >>> >>> jon >>> On May 9, 2013, at 8:44 PM, Douglas Greve wrote: >>> >>> >>>> the dcmunpack command is right. You should make sure to analyze only the >>>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>>> doug >>>> >>>> >>>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> >>>>> Hi Kayle >>>>> >>>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>>> >>>>> cheers >>>>> Bruce >>>>> On Thu, >>>>> 9 May 2013, Kayle Sawyer wrote: >>>>> >>>>> Hi all, >>>>>> >>>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have >>>>>> been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>>>>> instead specify the multiecho scans for recon-all, do we need to give any >>>>>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>>>>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>>>>> described below? Or would we have to run recon-all with the RMS, then after >>>>>> it finishes re-run mris_make_surfaces manually with the -dura flag to >>>>>> refine the pial surface? >>>>>> >>>>>> Also, I'd like to make sure we are using dcmunpack properly. We take >>>>>> the >>>>>> >>>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso >>>>> run >>>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one >>>>> mgz >>>>> file, and the RMS gets put into a separate mgz file. >>>>> >>>>>> Thanks, >>>>>> -Kayle >>>>>> >>>>>> On May 9, 2013, at 12:00 PM, freesurfer-request(a)nmr.mgh.**harvard.edu<freesurfer-request(a)nmr.mgh.harvard.edu>wrote: >>>>>> >>>>>>> Message: 35 >>>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>>> To: Jonathan Holt <whatsdac(a)umich.edu> >>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>> Message-ID: >>>>>>> <alpine.LRH.2.02.**1305091043500.13418(a)gate.nmr.** >>>>>>> mgh.harvard.edu<alpine.LRH.2.02.1305091043500.13418(a)gate.nmr.mgh.harvard.edu> >>>>>>> > >>>>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>>>> >>>>>>> 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 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>> ______________________________**_________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> >>>> 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. >>>> >>>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> >>> >

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awk issues on MacOS and RegionSettings
by Lukas.Scheef＠ukb.uni-bonn.de 10 May '13

10 May '13

Hi folks! I just like to send some information regarding "awk" problems under MacOs which occurs at least on "German" systems. I am not quite sure if FS uses awk at any point - but it might help when processing FS results: With the Region Setting "Germany" in the general settings of MacOs ( system-> Language&text->region), awk gets into trouble when dealing with floatings points: echo "1 0.2 3.1" | awk '{ print $3*$2 }' --> 0!!! The work around would be using "bc" for the calculations: awk '{ print $3 " * " $2 }' | bc -l However, if you change the regional settings to "GB" or "US" echo "1 0.2 3.1" | awk '{ print $3*$2 }' works as expected. At this point I have to thank Mark Jenkinson from the Oxford FSL team who suggested the work around and came up with the idea that the regional setting might cause the problems ... Best wishes, Luke

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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?
by Douglas N Greve 09 May '13

09 May '13

Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug ps. Please remember to send to the list and not to me directly. That way others can benefit from the exchange and the record goes into our mail archive. On 05/09/2013 11:07 AM, Glen Lee wrote: > Hi Doug > > See below for the command line that I used. > > smoothK=4; > > mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ... > num2str(smoothK) ' --cortex --sval ' > Functional_dir Subj '/GLM/all_base-sym_R.mgh '... > > > > > On Wed, May 8, 2013 at 11:31 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Glen, can you give us more information about what you did? Eg, > command line? > doug > > > > On 5/8/13 8:53 PM, Glen Lee wrote: >> 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. >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > -- 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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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 >>> >>> >>> > > > >

2 6

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..

2 6

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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