Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Question regarding the subject directory
by Lukas.Scheef＠ukb.uni-bonn.de 27 Mar '13

27 Mar '13

Hi folks! I would like to use a different subject dirctory (setenv SUBJECTS_DIR <full path to subject dir>). Does freesurfer still finds the folders which are located in the default subjects directory of the FS installation? Or are they simply not needed for the recon-all process ? I refer to cvs_avg35 etc. not to the test data sets. Please excuse if this question is stupid ... but considering the processsing time ... Many thanks in advance, Luke

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getting started with ROI & labels
by Fred Lado 27 Mar '13

27 Mar '13

Dear Freesurfers, I'm interested in using FS identified labels, such as Brodman areas in the anatomical volume, to measure a feature, say mean intensity in V1, in a second volume registered to the first. I'm new to the use of labels, so some advice on where to start would be appreciated. Thanks, Fred Lado, MD PhD Director, Neurology Service - Moses & North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: flado(a)montefiore.org Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately.

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iSurf BrainView now available for Windows 8 {Disarmed}
by Pedro Paulo de Magalhães Oliveira Junior 27 Mar '13

27 Mar '13

Today Microsoft approved iSurf BrainView version for Windows 8 Tablets and computers. It's a free App. http://apps.microsoft.com/windows/en-us/app/brainview/be2623f5-c5e3-4295-a2… BrainView is a Brain MRI tutor based on the MRI automatic segmentation produced by FreeSurfer. FreeSurfer is a software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging. This App uses its automatic segmentation to produce an automatic atlas of neuroimaging based on T1 MRI Images. It also displays 3D accurate models of brain cortex with automatic structure labeling. A great tool for teaching brain MRI and for learning neuroanatomy. For more reference on the educational use of iSurf BrainView: Oliveira Jr, PPM; Fischl, Bruce; Amaro, Edson "Teaching neuroanatomy using Iphone and IPad. In: Human Brain Mapping, 2011, Quebec, CA. Proc. Human Brain Mapping 2011, 2011." --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com <http://www.netfilter.com.br>

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Re: [Freesurfer] Merging PArcellation labels
by Laura M. Tully 26 Mar '13

26 Mar '13

it sounds like you want a different parcellation of the lateral prefrontal cortex than what is offered by the default atlas (aparc, AKA the desikan atlas) - I suggest you load in ?h.aparc.a2009s.annot (aka the destrieux atlas) as your annotation in tksurfer and select the annotations of the PFC that you want from there and save as labels. The aparc.a2009 annotation offers a more fine grained parcellation of the PFC - e.g. you can get the DLPFC by merging the middle frontal gyrus & middle frontal sulcus parcellations. On Mon, Mar 25, 2013 at 3:19 AM, Anupa AV <av.anupa(a)yahoo.com> wrote: > Dear Laura, > Thank you so much. > It worked well. > Do you know how to make cuts on the merged label, for eg. if I need to > seperate DLPFC from premotor cortex. > > > ------------------------------ > *From:* Laura M. Tully <tully.laura(a)googlemail.com> > *To:* Anupa AV <av.anupa(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Sunday, March 24, 2013 12:20 AM > *Subject:* Re: [Freesurfer] Merging PArcellation labels > > First save each parcellation that you want as its own separate label by > selecting it in tksurfer (simply click on it with your mouse and its > boarder will be highlighted in yellow) and then file -> label -> save > selected label... Then you can merge these separate labels into one label > at the command line using mri_mergelabels -i [labelfile1] -i [labelfile2] > -o [newlabelfile.label] > > If doing glms from the command line you can then feed mri_glmfit the label > with the --label option. This will conduct the glm in the region specified > in the label only (i.e. an roi analysis) > > There is also a quick way to turn all of the desikan parcellations into > individual label files at the command line using mri_annotation2label I > think, but I can't remember precisely. This is a lot faster than using > tksurfer as it simply dumps *all* the individual parcellations into a > specified output directory. But I don't know if you can do it with the > Destrieux atlas parcellations (if you were interested in doing that.) > > Laura. > > > > > > On Sat, Mar 23, 2013 at 2:36 AM, Anupa AV <av.anupa(a)yahoo.com> wrote: > > Dear All, > > Can anyone tell me how to merge the parcellation labels using tksurfer.? > For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and > caudal middle frontal gyrus. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > > > -- > -- > Laura M. Tully, MA > Social Neuroscience & Psychopathology, Harvard University > Center for the Assessment and Prevention of Prodromal States, UCLA Semel > Institute of Neuroscience > ltully(a)mednet.ucla.edu > ltully(a)fas.harvard.edu > 310-267-0170 > -- > My musings as a young clinical scientist: > http://theclinicalbrain.blogspot.com/ > Follow me on Twitter: @tully_laura > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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Error in Talairach transform version 5.2
by Pedro Paulo de Magalhães Oliveira Junior 26 Mar '13

26 Mar '13

I'm having some recon-all errors like this: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3505/src.mnc transforms/talairach.auto.xfm Use of uninitialized value $path in join or string at /usr/local/freesurfer/mni/bin/mritotal line 462. mritotal: Couldn't find configuration file mritotal.cfg anywhere in :/usr/local/freesurfer/mni/bin/../etc/mni_autoreg ERROR: mritotal failed, see transforms/talairach.log Linux ip-10-147-137-177 3.2.39-6.88.amzn1.i686 #1 SMP Sat Mar 2 05:13:38 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s caso765 exited with ERRORS at Mon Mar 25 19:24:29 UTC 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is this file /usr/local/freesurfer/mni/bin/../etc/mni_autoreg really missing in the distribution?

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trackstats2table error
by Jon Wieser 26 Mar '13

26 Mar '13

I am trying to convert my dti tracts stats to a table and got the following error tractstats2table --inputs fmajor_PP_avg23_mni_flt/pathstats.overall.txt --overall --tablefile table.txt Traceback (most recent call last): File "/usr/local/freesurfer/bin/tractstats2table", line 9, in <module> from fsutils import TractOverallStatsParser, TractByvoxelStatsParser, BadFileError, tractlogger ImportError: cannot import name TractOverallStatsParser -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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sort labels by lobes
by Anna Varentsova 26 Mar '13

26 Mar '13

Dear all, I have a brain segmented with Freesurfer 2009 and a list with label description looking like this: ... 11101 ctx_lh_G_and_S_frontomargin 12101 ctx_rh_G_and_S_frontomargin 11102 ctx_lh_G_and_S_occipital_inf 12102 ctx_rh_G_and_S_occipital_inf ... What is the best way to sort labels by lobes based on the name or the number? Are there any publications with this information or a table somewhere on Freesurfer web-page? Sincerely yours, Anna Varentsova

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subcortical segmentation
by Joshua Lee 26 Mar '13

26 Mar '13

A subcortical segmentation error sometimes get Freesurfer (v 5.1) is cortical areas coming over into the hippocampus, ignoring the wm inferior and lateral to the hippocmapus (coronal). See attached png. Will adding wm control points help, or do they not inform the aseg segmentation. What is the best way to (non-manually) fix this kind of issue? - Josh

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Fwd: Brodmann area thickness, surface area and volume
by _andreia_＠sapo.pt 26 Mar '13

26 Mar '13

Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia ----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- Data: Sun, 24 Mar 2013 19:11:13 +0000 De: _andreia_(a)sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>, freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Cc: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: > Sounds like centos4 is probably the safest bet for you, although you > should ask the list this question. > > Sorry, I don't know what values you want to get in a table. > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: > >> Ah ok! Anyway, I'm thinking of working with 5.2, should I download >> the version for centOS 4 then? >> >> After running the new BAxxx.thresh.label files how can I get the >> values in a table? >> >> >> >> >> Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >> >>> It doesn't matter. You just need to use those .label files from >>> the fsaverage directory in the 5.2 distritbution. You don't need >>> to run any of the executables from the 5.2 distribution. >>> >>> On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>> >>>> I'm using Centos5, which file should I download? The one for >>>> CentOS 6 or > 4? >>>>> > Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> > You'll need to go to the section of recon-all.log under the >>>>> heading "BA > > labels". You'll need to rerun the commands in >>>>> that section, but instead > > of using the BAxxx.label files, us >>>>> the BAxxx.thresh.label files, which > > you'll find in the >>>>> fsaverage subject dir in the 5.2 distribution. >>>>> > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>>>> > > > Hello Anastasia, >>>>> > > How should I proceed to get the different BAs measures >>>>> output with > > > > FS > 5.0? >>>>> > > Thank you very much! >>>>> > > Andreia >>>>> > > > Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> > > > The thresholded labels are in the 5.2 version of >>>>> fsaverage > > > > > under: >>>>> > > $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label >>>>> > > > > On Sat, 23 Mar 2013, Bruce Fischl wrote: >>>>> > > > > > Anastasia? >>>>> > > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>>>> > > > > > Ok, that was my guess... I am running against a >>>>> deadline, > > > > > > > any > > > > > news on >>>>> > > > > automatically computing the correct threshold script? >>>>> Will I > > > > > > be > > > > able to >>>>> > > > > use it in 5.0? >>>>> > > > > > > Thanks you! >>>>> > > > > > > Andreia >>>>> > > > > > > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>>> > > > > > > > yes. Surface area will be the affected much >>>>> more than > > > > > > > > > > > > > > > > thickness (and > >>>>> > > > volume of > > > > > > > > > course scales with area) >>>>> > > > > > > On Fri, 22 Mar 2013, _andreia_(a)sapo.pt wrote: >>>>> > > > > > > > Hi Bruce, >>>>> > > > > > > > > Thank you for the quick response! >>>>> > > > > > > > > In the meanwhile, does that also apply to >>>>> cortical > > > > > > > > > > > > > > > > > > thickness > >>>>> > > > > > and > > > > > > > > > > > > volume? >>>>> > > > > > > > > Thank you! >>>>> > > > > > > > > Andreia >>>>> > > > > > > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>>> > > > > > > > > > Hi Andreia >>>>> > > > > > > > > > > the issue is that the BA labels contain >>>>> every > > > > > > > > > > > > point > > > > > > > > > > >>>>> that > > > > > > > > > > > > > > > > > > > > has any > > > >>>>> non-zero >>>>> > > > > > > > probability (no matter how small!) of being in >>>>> that > > > > > > > > > label. > > > > > > > So > > > > > >>>>> the > > > > > > > > > > > > total >>>>> > > > > > > > label area is almost certainly always bigger >>>>> than the > > > > > > > > > > > > > > > > actual > > > > > >>>>> BA. > > > > > > > > > > > > Anastasia >>>>> > > > > > > > has some scripts for automatically computing >>>>> the > > > > > > > > > correct > > > > > > > > > > > > >>>>> threshold, > > > > > > > > > > > > and I >>>>> > > > > > > > believe she and Nick integrated them into 5.2 >>>>> so that > > > > > > > > > the > > > > > > > stats > > > > >>>>> > are >>>>> > > > > > > > computed both thresholded and unthresholded, > >>>>> > > > > > > > > hopefully > > > > > > > they can > > > > >>>>> > > > > > > > > > > > > > comment. >>>>> > > > > > > > Bruce >>>>> > > > > > > > > > > > > > > > > On Fri, 22 Mar 2013, > > > > >>>>> > > > > > > > > > > > > > > _andreia_(a)sapo.pt >>>>> > > > > > > > wrote: >>>>> > > > > > > > > > > > Hi all, >>>>> > > > > > > > > > > > > I'm using FS 5.0 and some time ago I >>>>> was > > > > > > > > > > > > > > told by > > > > > > > > > > >>>>> > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>> Bruce that I had > > > > > > > > > > > > > > > > > > > > > > >>>>> > > > > > > > > to >>>>> > > > > > > > > threshold the BA in order to have an >>>>> approximate > > > > > > > > > > area > > > > > > > > when >>>>> > > > > > > > > > > > > > > > > > > > > overlaying >>>>> > > > > > > > > in the inflated surface. To get surface area >>>>> values > > > > > > > > > > I > > > > > > > > also > > > > >>>>> > > need to > > > > > > > > > > > > > > use >>>>> > > > > > > > > the label_area and put a threshold >>>>> > > > > > > > > having the possibility to choose the surface >>>>> that I > > > > > > > > > > > > > > > > > > want, > > > > >>>>> > > either > > > > > > > > > > > > > > white >>>>> > > > > > > > > or pial. >>>>> > > > > > > > > > > > > But I can also get the BA stats in a >>>>> table > > > > > > > > > > > > > > for > > > > > > > > > > > >>>>> > all > > > > > > > > > > > > > > > > > > > > > > > > >>>>> subjects and > > > > > > > > > > > > > > > > > > > > > > > > >>>>> > > > > > > areas >>>>> > > > > > > > > using either mris_anatomical_stats (on each >>>>> label) > > > > > > > > > > or > > > > > > > > usinga > > >>>>> > > > > > > > > > > > > > > > > > > script by >>>>> > > > > > > > > Jamaan to get the table (since I already >>>>> have the > > > > > > > > > > > > > > > > > > ?.BA.stats > >>>>> > > > > > > > > > > > > > > > > > > > files), >>>>> > > > > > > > > right? >>>>> > > > > > > > > > > > > My question is, which is the >>>>> better/correct > > > > > > > > > > > > > > way > > > > > > > >>>>> > > > > > to > > > > > > > > > > > > > > > > > > > > > > >>>>> > > get the > > > > > > > > > > > > > > > > > > > > > > > > > >>>>> > > > > > thickness >>>>> > > > > > > > > and surface area values of the BA to export >>>>> for > > > > > > > > > > > > > > > > > > statistical > > > >>>>> > > > > > > > > > > > > > > > > > analysis >>>>> > > > > > > > > since there are the thresolds issue. >>>>> > > > > > > > > > > > > I want to study mainly cortical >>>>> thickness > > > > > > > > > > > > > > and > > > > > > > > > >>>>> > > > surface > > > > > > > > > > > > > > > > > > > > > > >>>>> > > area but > > > > > > > > > > > > > > > > > > > > > > > >>>>> > > > > > > > also >>>>> > > > > > > > > look also at the volume (which is >>>>> surface-based, > > > > > > > > > > thus >>>>> > > > > > > > > thickness*surface are will not be = volume >>>>> since > > > > > > > > > > they > > > > > > > > are an > > >>>>> > > > > > > > > > > > > > > > > > > average >>>>> > > > > > > > > from each label, right?). >>>>> > > > > > > > > > > > > I' not sure of which approach to >>>>> follow > > > > > > > > > > > > > > now... > > > > > > > > > >>>>> > > > Does > > > > > > > > > > > > > > > > > > > > > > > >>>>> > it depend on > > > > > > > > > > > > > > > > > > > > > > >>>>> > > > > > > > > the >>>>> > > > > > > > > measure I'll be using? >>>>> > > > > > > > > > > > > Thank you! >>>>> > > > > > > > > > > > > Andreia >>>>> > > > > > > > > > > > > > > > > >>>>> _______________________________________________ >>>>> > > > > > > > > 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 >>>>> > > > > > > > > > > > > > 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. >>>>> > > > > > > > > > > > > > > > > > > > > >> >> >> >> ----- Fim de mensagem reenviada -----

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Re: [Freesurfer] recon-all bad talairach
by Douglas N Greve 26 Mar '13

26 Mar '13

Hi Jon, it is not supposed to be horizontal. The anatomy in the target is just supposed to match that in the moveable. doug ps. please respond to the list. thanks! On 03/26/2013 02:35 PM, Jon Wieser wrote: > HI doug, > i viewed it with tkregister2. the transform looks poor, the ac-pc line is not horizontal. > i have attached a pic > Jon > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, March 26, 2013 11:28:01 AM > Subject: Re: [Freesurfer] recon-all bad talairach > > Hi Jon, the data are not reoriented or resliced into talairach space. It > is just the transform that is computed. To inspect whether this was done > right, use > > tkregister2 --s subject --fstal > > doug > > > On 03/26/2013 12:20 PM, Jon Wieser wrote: >> Hello >> I ran recon-all auto_recon1. and the resulting brainmask file, has a poor talairazation. the ac-pc line is not horizontal, it's tilted, and the interhemisphere fissure is tilted too. how do I fix this? >> I have attached a picture of the brain >> >> >> >> _______________________________________________ >> 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 greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer March 2013