Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

Trouble performing Monte Carlo simulation constrained to label
by Susan Alice McLaughlin 07 Jan '13

07 Jan '13

Hi, I am trying to run a Monte Carlo simulation on functional data constrained to a label using Freesurfer 4.0.1. I did not use Qdec for data analysis. Looking at a previous post - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290… - I see that I should: 1) constrain when running mri_glmfit, then 2) use mri_glmfit-sim (as opposed to running mri_glmfit with the simulation options). I have done step 1, however when I try to mri_glmfit-sim, I receive a "command not found" message. Is mri_glmfit-sim not available in 4.0.1? Can I copy a workable version of mri_glmfit-sim into 4.0.1? Thanks, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Rejoindre mon réseau sur LinkedIn
by didac vidal via LinkedIn 07 Jan '13

07 Jan '13

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Re: [Freesurfer] aparc stats file; missing 'mean cortical thickness' value
by Douglas N Greve 07 Jan '13

07 Jan '13

Oh, I see now, you are including -noaseg and that is causing the problem. Why are you including that? You can rerun like recon-all -parcstats -parcstats2 -s subject and it should regenerate the stats with the mean cortical thickness doug On 01/07/2013 02:32 PM, Deirdre O Shea wrote: > sure, here it is > > On Mon, Jan 7, 2013 at 2:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > hmmm, that is bizarre. Can you send me the recon-all.log file for > this subject? > > > On 01/07/2013 02:23 PM, Deirdre O Shea wrote: > > I just ran ran recon-all myself. I have attached the script i > have been using for all my subjects. > > thanks, > deirdre > > On Mon, Jan 7, 2013 at 1:45 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > I can see that the command line is not set up to create > the mean > cortical thickness, but I don't know why the arguments for the > command are not being set up properly. Did you run > mris_anatomical_stats yourself or did you just run recon-all > again? If you ran recon-all, can you send me your > recon-all script? > > doug > > > > On 01/07/2013 01:25 PM, Deirdre O Shea wrote: > > Thanks Doug, > > I have attached two files. You will see in > 'aparc.stats' that > there is no mean for cortical thickness and in the > aparc.stats2 file there is. > > thanks > Deirdre > > On Mon, Jan 7, 2013 at 12:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Can you send the aparc.stats file in question? > doug > On 01/07/2013 11:44 AM, Deirdre O Shea wrote: > > Dear FreeSurfers, > > > > My query relates to the aparc stats file in > FreeSurfer. > Upon the > > editing and reconstruction of my subjects I have > noticed > that > the Mean > > Thickness for the cortex was missing, i.e., no > value was > provided > > despite it being there before I ran another > reconstruction. > While this > > has only occurred in a couple of my subjects (out of > many) I'm > > wondering what may be the cause and how I may I > now go > about getting > > this value? > > > > > > Best, > > Deirdre > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: 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/ > > -- 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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expected directory structure
by Satrajit Ghosh 07 Jan '13

07 Jan '13

hi folks, happy new year. we are trying to create an object model for the freesurfer directory. is there a function/script in freesurfer that would return me effectively something `ls -lR` but only the items that are mandatory for a subjects' directory? if not, is there a document that lists the relevant outputs along the lines of something like this: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#FEAT_Output and if anybody is interested, here is our work in progress in cataloging freesurfer directory structure and stats (coming soon) in the w3c-prov model format. http://nbviewer.ipython.org/urls/dl.dropbox.com/s/1ssv4i1dyraa46h/freesurfe… (the link doesn't have versioning yet - but will keep changing as we work on it) cheers, satra

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Re: [Freesurfer] aparc stats file; missing 'mean cortical thickness' value
by Douglas N Greve 07 Jan '13

07 Jan '13

I can see that the command line is not set up to create the mean cortical thickness, but I don't know why the arguments for the command are not being set up properly. Did you run mris_anatomical_stats yourself or did you just run recon-all again? If you ran recon-all, can you send me your recon-all script? doug On 01/07/2013 01:25 PM, Deirdre O Shea wrote: > Thanks Doug, > > I have attached two files. You will see in 'aparc.stats' that there is > no mean for cortical thickness and in the aparc.stats2 file there is. > > thanks > Deirdre > > On Mon, Jan 7, 2013 at 12:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Can you send the aparc.stats file in question? > doug > On 01/07/2013 11:44 AM, Deirdre O Shea wrote: > > Dear FreeSurfers, > > > > My query relates to the aparc stats file in FreeSurfer. Upon the > > editing and reconstruction of my subjects I have noticed that > the Mean > > Thickness for the cortex was missing, i.e., no value was provided > > despite it being there before I ran another reconstruction. > While this > > has only occurred in a couple of my subjects (out of many) I'm > > wondering what may be the cause and how I may I now go about getting > > this value? > > > > > > Best, > > Deirdre > > > > > > _______________________________________________ > > 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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: 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 <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: 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] 回复: 回复: about ROI to SPSS
by Douglas N Greve 07 Jan '13

07 Jan '13

what was your command line? On 01/05/2013 01:43 AM, xiangbo_2010 wrote: > Dear doug > Using the command to only obtain the size of volume from every > subject, however, I want to obtain the size of surface area from every > subject, what should I do? thanks! > Bo Xiang > > > > > > At 2013-01-05 13:12:18,"Douglas Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > > Drawing the ROI as a label is fine. Just don't transfer the label > to each individual subject. The y.mgh is all the data for all the > subjects in the fsaverage space (where the label is defined). You > can use mri_segstats, something like > > mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1 > > avg.dat will have one column and number of rows equal to the > number of subjects > > doug > > > On 1/4/13 11:20 PM, xiangbo_2010 wrote: >> Dear doug >> I am sorry to disturb you again, I still do not know how to >> direct obtain the label of two significant clusters, is not to >> draw the ROI? thanks! >> Bo Xiang >> >> >> >> >> >> At 2013-01-05 06:49:14,"Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> wrote: >> >yes y.mgh >> >On 01/04/2013 05:13 PM,xiangbo_2010(a)126.com wrote: >> >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! >> >> Bo Xiang >> >> 发送自我的HTC One SUJ >> >> >> >> ----- Reply message ----- >> >> 发件人： "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >> >> 收件人：<xiangbo_2010(a)126.com> >> >> 抄送： "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> >> >> 主题： [Freesurfer] 回复: about ROI to SPSS >> >> 日期：周六, 1 月 5 日, 2013 年 05:48 >> >> >> >> >> >> >> >> >> >>> That technique can yield inconsistent results when the ROI is small (as >> >>> in your case). You are better off extracting the data directly from the >> >>> input to mri_glmfit. This is created by QDEC and is called y.mgh. This >> >>> will be a file with number of frames equal to the number of subjects. >> >>> >> >>> doug >> >>> >> >>> >> >>> >> >>> >> >>> On 01/04/2013 04:13 PM,xiangbo_2010(a)126.com wrote: >> >>>> I drawing two ROIs in two clusters, and mapping two labels to all subjects, following extract the average surface area of two ROIs from every subject. Anyway, whether have command to direct obtain the label of two clusters, not to drawing the ROIs from these clusters, then there have exactly data to be obtained. Thanks! >> >>>> Ho Xiang >> >>>> >> >>>> 发送自我的HTC One SU >> >>>> >> >>>> ----- Reply message ----- >> >>>> 发件人： "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >> >>>> 收件人：<freesurfer(a)nmr.mgh.harvard.edu> >> >>>> 主题： [Freesurfer] about ROI to SPSS >> >>>> 日期：周六, 1 月 5 日, 2013 年 02:42 >> >>>> >> >>>> >> >>>> >> >>>> >> >>>>> Hi Bo, you need to make sure that you have exactly the same design >> >>>>> matrix in SPSS. The design matrix for qdec is Xg.dat in the output >> >>>>> directory. How did you extract the data out of the ROIs? >> >>>>> >> >>>>> doug >> >>>>> >> >>>>> >> >>>>> >> >>>>> On 01/02/2013 11:46 PM, xiangbo_2010 wrote: >> >>>>>> Dear experts >> >>>>>> I has obtained two ROIs (corrected FDR) difference between AA and >> >>>>>> GG regressing out the effect of age and gender using the QDEC with >> >>>>>> attachment, following extract the average surface area of two ROIs to >> >>>>>> analysis using SPSS, in which I used the >> >>>>>> Univariate Analysis of Variance to find the difference between AA and >> >>>>>> GG, gender and age as covariates, but find that there no significant >> >>>>>> in these ROIs, I want to know why there were significant difference in >> >>>>>> QDEC, but no significant difference in SPSS? I hope that have experts >> >>>>>> to help me, thanks! >> >>>>>> Bo Xiang >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> 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/ >> >>>>> >> >>>>> _______________________________________________ >> >>>>> 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. >> >>>>> >> >>>> >> >>> -- >> >>> 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/ >> >>> >> >>> _______________________________________________ >> >>> 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/ >> > >> >> > > > -- 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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aparc stats file; missing 'mean cortical thickness' value
by Deirdre O Shea 07 Jan '13

07 Jan '13

Dear FreeSurfers, My query relates to the aparc stats file in FreeSurfer. Upon the editing and reconstruction of my subjects I have noticed that the Mean Thickness for the cortex was missing, i.e., no value was provided despite it being there before I ran another reconstruction. While this has only occurred in a couple of my subjects (out of many) I'm wondering what may be the cause and how I may I now go about getting this value? Best, Deirdre

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Checking cerebellar segmentations
by charles laidi 07 Jan '13

07 Jan '13

Dear freesurfers, I just finished cerebellar segmentation on almost 100 subjects. I have read the usual checking procedure that should be performed on freesurfer website. However I wasn't able to find if there is a specific checking workflow that can be performed when freesurfer is used for 100 / a lot of subjects. For example FSL provides a tool called slicesdir that allows to check segmentation faster. Is there such a feature with freesurfer ? What kind of checking would you recommend for cerebellar segmentation on 100 subjects ? Thank you very much and happy new year ! Charles

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Differences between avg33 and avg32 in dpath folders
by Alessia Sarica 06 Jan '13

06 Jan '13

Dear Freesurfer Experts, i'm here again, maybe for a trivial question, but I didn't find any information about my doubt. I'm doing tractography on 36 patients and I noticed that some of them have dpath folders named "_avg33_mni_flt" and in other patients, they are named "_avg32_mni_flt". Which is the reason for this? Something has gone wrong? Thanks a lot, Alessia. -- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193

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Freesurfer 5.2 release date?
by Mehul Sampat 05 Jan '13

05 Jan '13

Hi Folks, I just wanted to inquire about the estimated release date for Freesurfer 5.2 ? Is there a beta version we could try out ? Thanks Mehul

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Freesurfer January 2013