Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Fwd: Qdec error
by Z K 03 Jul '13

03 Jul '13

Begin forwarded message: > From: Anupa AV <av.anupa(a)yahoo.com> > Date: July 3, 2013, 2:03:26 AM EDT > To: "zkaufman(a)nmr.mgh.harvard.edu" <zkaufman(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Qdec error > Reply-To: Anupa AV <av.anupa(a)yahoo.com> > > Thank you so much.. > It worked.. :) > > > From: "zkaufman(a)nmr.mgh.harvard.edu" <zkaufman(a)nmr.mgh.harvard.edu> > To: Anupa AV <av.anupa(a)yahoo.com> > Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, July 1, 2013 9:53 PM > Subject: Re: [Freesurfer] Qdec error > > Hello, > > Is this running in Ubuntu? If so, it should be solved by running the > following command: > > $ sudo apt-get install libjpeg62 > > -Zeke > > > Dear All, > > > > When I tried to running qdec, I'm getting the following error. > > > > qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open > > shared object file: No such file or directory > > > > > > What is the solution for this.? > > > > Any help will be greatly appreciated. > > _______________________________________________ > > 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. > >

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Interior white matter surfaces
by Jason Reed 02 Jul '13

02 Jul '13

Dear FreeSurfer Experts, I am attempting to construct surfaces that are 1, 2, 3, and 4 mm interior from the GM/WM boundary (?h.white). So going gradually deeper into white matter from the GM/WM boundary. I have successfully used mris_fill to fill the ?h.white surface and mri_morphology to erode the resulting volume, but I'm not sure on the correct procedure to create the new surfaces. Any advice or suggestions on tools with options to use will be greatly appreciated! My eventual goal is to project coregistered DTI data onto these more interior white matter surfaces. Thanks! -Jason -- Jason Reed VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2946 Fax: (858) 642-3836 jreed(a)vapop.ucsd.edu

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mri_ca_normalize error
by Mark Plantz 02 Jul '13

02 Jul '13

Hello, I am currently having some difficulties with the mri_ca_normalize command. I am attempting to create a normalized volume file using an input brain with the following command: mri_ca_normalize /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/ /Applications/freesurfer/subjects/CMH-7259/mri/transforms/talairach.lta /Volumes/Wong_Lab/norm.mgz However, I am getting an error that my seg.mgz file could not be read: Operation not permitted dhcp-165-124-23-240:~ IngvalsonLab$ mri_ca_normalize /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/ /Applications/freesurfer/subjects/CMH-7259/mri/transforms/talairach.lta /Volumes/Wong_Lab/neo-atlas.gca reading 2 input volumes reading atlas from '/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/'... GCAread(/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/): could not read file Operation not permitted mri_ca_normalize: could not open GCA /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/. I don't believe it is a permissions issue. Any ideas? Thanks, Mark

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[tracula] running into trouble with nifti data
by Satrajit Ghosh 02 Jul '13

02 Jul '13

hi anastasia, i'm trying to debug a seg fault that some folks are seeing deep into a tracula run. process: 1. feed dicoms to a script that runs DTIPrep and outputs a nifti file, bvec, bval (among checking for many artifacts, this reduces the b=0 volumes to a single registered mean volume, runs eddy correction, discards bad directions, reorients the gradients appropriately and generates a report of the quality) 2. run tracula on this nifti file observation: when i run fsl/dtifit on the same nifti file + bvec + bval, i get the proper orientation for eigvec1 lines. however, when i feed this into tracula, the output of the dtifit step looks terrible - i.e. the lines are not oriented as how one might expect water to diffuse. suspicion: although i have not reached the crash yet, i believe it might be related to this fact that the gradients are not oriented properly relative to the volume. i also suspect that this has something to do with the flip4fsl step inside tracula, which is possibly unnecessary because fsl already likes the input files. but it seems this step is encoded quite heavily within the trac-all scripts. questions: a. is there a quick way to turn the flip4fsl step off? b. alternatively do you have any suggestions for what to do here? the whole point of running through DTIPrep is to clean up the data before giving it to tracula or other programs, so i would really like to keep that step. cheers, satra

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Difference between recon-all -autorecon2-wm and recon-all -autorecon2-wm -autorecon3
by ye tian 02 Jul '13

02 Jul '13

Dear Freesurfers, I just realize that in the tutorial example of "geometric accuracy", *recon-all -autorecon2-wm *is used to recreate the final surfaces; while in "lateral ventricle", *recon-all -autorecon2-wm -autorecon3 *is used. However, the modification steps look the same to me -- fill in the "hole" of white matter in wm.mgz. Why do they use different commands after all? What's the difference between -autorecon2-wm and -autorecon2-wm -autorecon3? Thank you very much! Sincerely, Ye

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Re: [Freesurfer] importing from nifti
by Martin Reuter 02 Jul '13

02 Jul '13

Probably the script was necessary to fix this problem. Look up the command for mri_convert, it could be that it adjusts the direction cosines directly. Best, Martin On 07/02/2013 02:36 PM, Jonathan Holt wrote: > OK, > > so while the structures look normal in tkmedit the orientations are > mixed up. Coronal view shows horizontal, horizontal shows coronal, and > sagittal has been rotated 90 degrees clockwise. > > Not entirely sure what to do here! This is the first I've seen of this > issue. keep in mind I processed this subject without an issue using > scripts that essentially pump the nifti through mri_convert and then > recon-all -s > > So I'm a bit confused > On Jul 2, 2013, at 2:24 PM, Martin Reuter wrote: > >> In the meantime you can check how the mri/orig/001.mgz and the >> mri/orig.mgz and mri/orig_nu.mgz look. >> >> Best, Martin >> >> On 07/02/2013 02:16 PM, Jonathan Holt wrote: >>> Thanks Martin, >>> >>> I have attached recon-all.log. I tried to run the process several >>> times, I clearly forgot to pass -all that time but I know for >>> certain the first time I tried I passed -all and it provided the >>> same issue. I can pass the dicom images but I'll have to wait for my >>> PI to return in lab. >>> >>> >>> >>> On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter >>> <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> >>> wrote: >>> >>> Hi Jonathan, >>> >>> I changed the subject of the thread, to better reflect this >>> problem, it (so far) has nothing to do with longitudinal processing. >>> >>> Next time, can you send the log file, it is in >>> /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log >>> not the output on the screen. >>> >>> But first lets check these: >>> >>> - your command in the email below seems to be missing "-all"? >>> Probably you passed it? >>> >>> - and from your screen output it looks like there is a problem >>> importing the nifit: >>> >>> WARNING: neither NIfTI-1 qform or sform are valid >>> WARNING: your volume will probably be incorrectly oriented >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>> reading from >>> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... >>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 >>> WARNING: it does not appear that there was sufficient information >>> in the input to assign orientation to the volume... >>> >>> So you need to check the orientation of your >>> /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz... >>> >>> Not sure why your nifti files are incomplete. Can you point -i >>> to the original dicom? >>> >>> >>> Best, Martin >>> >>> On 07/02/2013 01:13 PM, Jonathan Holt wrote: >>>> and the command >>>> >>>> nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii >>>> >>>> >>>> >>>> On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt >>>> <whatsdac(a)umich.edu <mailto:whatsdac@umich.edu>> wrote: >>>> >>>> Here ya go (to list) >>>> >>>> >>>> On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt >>>> <whatsdac(a)umich.edu <mailto:whatsdac@umich.edu>> wrote: >>>> >>>> Here ya go. >>>> >>>> >>>> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter >>>> <mreuter(a)nmr.mgh.harvard.edu >>>> <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: >>>> >>>> No, it's not nifti, that should work. >>>> >>>> Can you send me your log file and the command you >>>> issued. >>>> >>>> Thanks, Martin >>>> >>>> >>>> On 07/01/2013 03:13 PM, Jonathan Holt wrote: >>>>> Martin, >>>>> >>>>> definitely passing my images and naming time >>>>> points appropriately. I have been passing nifti as >>>>> opposed to dicom and it's entirely possible that >>>>> may be the issue? >>>>> >>>>> jon >>>>> On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote: >>>>> >>>>>> Hi Jon, >>>>>> >>>>>> are you passing your images? >>>>>> <tpNid> is a placeholder for the id of your >>>>>> subject+time point, for example it could be >>>>>> jon_01 the "path_to_tpN_dcm" needs to specify the >>>>>> path to the dicom files, point it to the first >>>>>> file in the MPRAGE series (or multi echo mprage >>>>>> or what you are using). This is the full path on >>>>>> your file system to that file. >>>>>> >>>>>> Best, Martin >>>>>> >>>>>> On 07/01/2013 02:29 PM, Jonathan Holt wrote: >>>>>>> I have tried to inspect the tal xfms that were >>>>>>> created in the brief time this string was running >>>>>>> >>>>>>> recon-all -all -s <tpNid> -i path_to_tpN_dcm >>>>>>> >>>>>>> while viewing orig.mgz in tkmedit. they were >>>>>>> talairach.xfm and talairach.auto.xfm, both were >>>>>>> empty and the tkmedit window was empty. >>>>>>> >>>>>>> upon further inspection the log file is >>>>>>> complaining about my nifty. >>>>>>> >>>>>>> WARNING: neither NIfTI-1 qform or sform are valid >>>>>>> WARNING: your volume will probably be >>>>>>> incorrectly oriented >>>>>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 >>>>>>> 21:55:16 mreuter Exp $ >>>>>>> reading from >>>>>>> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... >>>>>>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>>>> WARNING: it does not appear that there was >>>>>>> sufficient information >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl >>>>>>> <fischl(a)nmr.mgh.harvard.edu >>>>>>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>>>>>> >>>>>>> can you cc the list so that others can answer? >>>>>>> >>>>>>> On Mon, 1 Jul 2013, Jonathan Holt wrote: >>>>>>> >>>>>>> I have not and I am not certain how to >>>>>>> do so >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Jul 1, 2013, at 1:03 PM, Bruce Fischl >>>>>>> wrote: >>>>>>> >>>>>>> Hi Jon >>>>>>> >>>>>>> have you visually inspected the >>>>>>> results of the tal xform? >>>>>>> Bruce >>>>>>> On Mon, 1 Jul 2013, Jonathan Holt wrote: >>>>>>> >>>>>>> Log file indicates manual >>>>>>> talairach alignment may be >>>>>>> necessary. >>>>>>> ERROR: talairach_afd: Talairach >>>>>>> Transform: >>>>>>> transforms/talairach.xfm >>>>>>> ***FAILED*** (p=0.0079, >>>>>>> pval=0.0000 < threshold=0.0050) >>>>>>> Manual Talairach alignment may >>>>>>> be necessary >>>>>>> Can anyone provide direction. >>>>>>> Alternatively, the error >>>>>>> indicates talairach alignment >>>>>>> can be skipped >>>>>>> with -notal-check flag. Is this >>>>>>> step completely necessary? >>>>>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> -- >>>>>> Martin Reuter, Ph.D. >>>>>> Assistant in Neuroscience - Massachusetts General Hospital >>>>>> Instructor in Neurology - Harvard Medical School >>>>>> MGH / HMS / MIT >>>>>> >>>>>> A.A.Martinos Center for Biomedical Imaging >>>>>> 149 Thirteenth Street, Suite 2301 >>>>>> Charlestown, MA 02129 >>>>>> >>>>>> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >>>>>> Email: >>>>>> mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> >>>>>> reuter(a)mit.edu <mailto:reuter@mit.edu> >>>>>> Web :http://reuter.mit.edu <http://reuter.mit.edu/> >>>>> >>>> >>>> -- >>>> Martin Reuter, Ph.D. >>>> Assistant in Neuroscience - Massachusetts General Hospital >>>> Instructor in Neurology - Harvard Medical School >>>> MGH / HMS / MIT >>>> >>>> A.A.Martinos Center for Biomedical Imaging >>>> 149 Thirteenth Street, Suite 2301 >>>> Charlestown, MA 02129 >>>> >>>> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >>>> Email: >>>> mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> >>>> reuter(a)mit.edu <mailto:reuter@mit.edu> >>>> Web :http://reuter.mit.edu <http://reuter.mit.edu/> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Martin Reuter, Ph.D. >>> Assistant in Neuroscience - Massachusetts General Hospital >>> Instructor in Neurology - Harvard Medical School >>> MGH / HMS / MIT >>> >>> A.A.Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, MA 02129 >>> >>> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >>> Email: >>> mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> >>> reuter(a)mit.edu <mailto:reuter@mit.edu> >>> Web :http://reuter.mit.edu <http://reuter.mit.edu/> >>> >>> >> >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> reuter(a)mit.edu >> Web :http://reuter.mit.edu > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Loosing data when using mri_convert
by Ray, Siddharth 02 Jul '13

02 Jul '13

Hi all, So I am trying to reorient my sagittal scans (with messed up labels) to axial using mri_convert (to get right label), I am able to do so but I am loosing some data (some slices). When I checked voxel-to-ras transform for the original and reorient image, they were different. How can I fix this? Thanks in advance. ~Siddharth

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Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
by Martin Reuter 02 Jul '13

02 Jul '13

Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn <bohn-peter(a)gmx.de> wrote: >Thanks a lot! Do I have to repeat >creating the base and the longitudinal runs once I use the new version >or are >they compatible concerning this aspect? > > > >Thank you very much! > > > >Best regards > > > >Peter > > > >From: mreuter(a)nmr.mgh.harvard.edu >Date: Thu, 20 Jun 2013 02:46:05 -0700 >To: bohn-peter(a)gmx.de; freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not >found > >Yes, those scripts are available since 5.2. You need to update to a >newer version. > >Best Martin > >Peter Bohn <bohn-peter(a)gmx.de> wrote: > > > >Hi Martin, > >thanks a lot fort he quick reply! When I type freesurfer into the >window it shows me v5.0.0 as the version. Sorry for my prior mistake >concerning the version’s name. All other commands I use run perfectly >fine. > >Thanks once again! > >Best regards > >Peter > >From: mreuter(a)nmr.mgh.harvard.edu >Date: Thu, 20 Jun 2013 05:21:39 -0400 >To: bohn-peter(a)gmx.de >CC: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not >found > >Hi Peter, >can you run any free surfer command at all? Looks to me that you did >not source free surfer. What happens if you typefreesurferinto the >terminal window? It should print the version. >Best, Martin >On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter(a)gmx.de> wrote: > > >Dear Freesurfer experts, > >I was trying to run some longitudinal analysis but whenever I want to >use the commands “long_mris_slopes” or “long_qdec_table” I just get >“command not found” as an answer. When I try to look up a package that >might include the command, by typing “cnf long_mris_slopes”, >I also just get “command not found” as an answer. We are currently >using version v 1.313.2.6. > >Does anyone of you know if the two commands that I would like to run, >are included in this version? Where would I have to look for the >additional package if it exists? Or am I by any chance just typing the >commands incorrect? > >Many thanks for the help! > >Sincerely yours > >Peter_______________________________________________Freesurfer mailing >listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >---------------------------------Dr. Martin ReuterAssistant in >Neuroscience - Massachusetts General Hospital >Instructor in Neurology - Harvard Medical School >MGH / HMS / MIT > >A.A.Martinos Center for Biomedical Imaging >149 Thirteenth Street, Suite 2301 >Charlestown, MA 02129 > >Phone: +1-617-724-5652 >Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.eduWeb : >http://reuter.mit.edu > > > > >_______________________________________________ >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. > > >-- > >Sent from my phone, please excuse brevity. >_______________________________________________ >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. -- Sent from my phone, please excuse brevity.

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Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates
by Douglas N Greve 02 Jul '13

02 Jul '13

It is hard to say, since 4.5 came out 3 years ago:). It is ok to do group analysis in a different version of FS. doug ps. Please remember to copy the list instead of sending emails directly to us. thanks! On 07/02/2013 01:53 PM, Emily Boeke wrote: > Strange, I have run simulations before in 4.5 and gotten talairach coords. Are you sure there isn't any other reason the coordinates are in this format in this simulation? > > Is it generally ok to do a group analysis in a later version of freesurfer if the first level analyses have been done in 4.5? Or would you recommend redoing the individual analyses as well? > > Thanks! > Emily > > On Jul 2, 2013, at 12:18 PM, Douglas N Greve wrote: > >> OK, in later versions it will give you the talairach coords. I would >> download 5.3 and run your group analysis in that, just be careful not to >> run recon-all using 5.3 (unless you want to upgrade all your subjects). >> doug >> >> On 07/02/2013 11:48 AM, Emily Boeke wrote: >>> 4.5 >>> >>> Emily >>> On Jul 2, 2013, at 11:45 AM, Douglas N Greve wrote: >>> >>>> Hi Emily, what version of FS are you using? >>>> doug >>>> >>>> >>>> On 07/02/2013 11:41 AM, Emily Boeke wrote: >>>>> Hi Doug, >>>>> >>>>> Sorry to be overly persistent, but I just wanted to make sure you saw this email! >>>>> >>>>> Thanks, >>>>> Emily >>>>> >>>>> On Jul 1, 2013, at 9:20 AM, Emily Boeke wrote: >>>>> >>>>>> This was the command I ran: >>>>>> >>>>>> mri_glmfit-sim --glmdir tal.sm.wls.pct.rfx --sim mc-z 10000 2 HvL.SBQ.2.10000.pos --stim-sign pos >>>>>> >>>>>> On Jun 28, 2013, at 3:29 PM, Douglas N Greve wrote: >>>>>> >>>>>>> Hi Emily, what is your mri_glmfit-sim command line? >>>>>>> doug >>>>>>> >>>>>>> >>>>>>> On 06/28/2013 02:40 PM, Emily Boeke wrote: >>>>>>>> Any thoughts on why this file turned out this way? >>>>>>>> >>>>>>>> Thanks! >>>>>>>> Emily >>>>>>>> >>>>>>>> On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote: >>>>>>>> >>>>>>>>> Sure, here it is: >>>>>>>>> >>>>>>>>> # Cluster Growing Summary (mri_volcluster) >>>>>>>>> # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ >>>>>>>>> # cwd /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car >>>>>>>>> # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask tal.sm.wls.pct.rfx//mask.mgh --cwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat >>>>>>>>> # sysname Linux >>>>>>>>> # hostname compute-0-114 >>>>>>>>> # machine x86_64 >>>>>>>>> # user eboeke01 >>>>>>>>> # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh >>>>>>>>> # Frame Number: 0 >>>>>>>>> # Minimum Threshold: 2 >>>>>>>>> # Maximum Threshold: inifinity >>>>>>>>> # Threshold Sign: pos >>>>>>>>> # AdjustThreshWhenOneTail 1 >>>>>>>>> # Size Threshold: 0 mm^3 >>>>>>>>> # Size Threshold: 0 voxels >>>>>>>>> # Voxel Size: 8 mm^3 >>>>>>>>> # Registration: None : Tal Coords invalid >>>>>>>>> # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh >>>>>>>>> # Mask Thresh: 0.500000 >>>>>>>>> # Mask Sign: abs >>>>>>>>> # Mask Invert: 0 >>>>>>>>> # AllowDiag: 0 >>>>>>>>> # NClusters 192 >>>>>>>>> # CSD thresh 2.000000 >>>>>>>>> # CSD nreps 10000 >>>>>>>>> # CSD simtype mc-z >>>>>>>>> # CSD contrast group >>>>>>>>> # CSD confint 90.000000 >>>>>>>>> # >>>>>>>>> # Reporting Coordinates in Voxel Indices >>>>>>>>> # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max# CWP CWPLow CWPHi >>>>>>>>> 1 597 4776.0 30.00 50.00 65.00 5.94673 0.02490 0.02290 0.02690 >>>>>>>>> 2 730 5840.0 27.00 28.00 86.00 5.56628 0.00720 0.00610 0.00830 >>>>>>>>> 3 1124 8992.0 5.00 18.00 38.00 5.01850 0.00010 0.00000 0.00020 >>>>>>>>> 4 259 2072.0 59.00 20.00 78.00 5.01465 0.68360 0.67760 0.68960 >>>>>>>>> 5 279 2232.0 18.00 22.00 73.00 3.94952 0.58840 0.58210 0.59470 >>>>>>>>> 6 194 1552.0 35.00 66.00 76.00 3.94297 0.93630 0.93320 0.93940 >>>>>>>>> 7 664 5312.0 32.00 15.00 60.00 3.68551 0.01400 0.01250 0.01550 >>>>>>>>> 8 293 2344.0 28.00 5.00 58.00 3.66686 0.52560 0.51920 0.53200 >>>>>>>>> 9 49 392.0 12.00 52.00 58.00 3.63351 1.00000 -0.00010 1.00000 >>>>>>>>> 10 150 1200.0 5.00 4.00 28.00 3.62637 0.99560 0.99470 0.99640 >>>>>>>>> 11 298 2384.0 12.00 47.00 86.00 3.58250 0.50260 0.49620 0.50900 >>>>>>>>> 12 343 2744.0 13.00 39.00 60.00 3.57829 0.33900 0.33290 0.34510 >>>>>>>>> 13 467 3736.0 21.00 42.00 49.00 3.53307 0.09590 0.09210 0.09970 >>>>>>>>> 14 276 2208.0 49.00 36.00 56.00 3.51549 0.60280 0.59650 0.60910 >>>>>>>>> 15 134 1072.0 70.00 17.00 34.00 3.38623 0.99890 0.99850 0.99930 >>>>>>>>> 16 75 600.0 5.00 25.00 55.00 3.09334 1.00000 -0.00010 1.00000 >>>>>>>>> 17 74 592.0 13.00 10.00 49.00 3.03017 1.00000 -0.00010 1.00000 >>>>>>>>> 18 45 360.0 65.00 39.00 62.00 3.00205 1.00000 -0.00010 1.00000 >>>>>>>>> 19 15 120.0 72.00 7.00 42.00 2.96283 1.00000 -0.00010 1.00000 >>>>>>>>> 20 55 440.0 62.00 9.00 23.00 2.93121 1.00000 -0.00010 1.00000 >>>>>>>>> 21 79 632.0 46.00 60.00 87.00 2.92199 1.00000 -0.00010 1.00000 >>>>>>>>> 22 35 280.0 2.00 41.00 48.00 2.84065 1.00000 -0.00010 1.00000 >>>>>>>>> 23 44 352.0 6.00 35.00 27.00 2.80109 1.00000 -0.00010 1.00000 >>>>>>>>> 24 14 112.0 50.00 3.00 54.00 2.75399 1.00000 -0.00010 1.00000 >>>>>>>>> 25 71 568.0 0.00 22.00 9.00 2.75160 1.00000 -0.00010 1.00000 >>>>>>>>> 26 5 40.0 28.00 0.00 36.00 2.72535 1.00000 -0.00010 1.00000 >>>>>>>>> 27 130 1040.0 40.00 1.00 45.00 2.71826 0.99920 0.99880 0.99950 >>>>>>>>> 28 81 648.0 33.00 61.00 86.00 2.70040 1.00000 -0.00010 1.00000 >>>>>>>>> 29 73 584.0 67.00 26.00 52.00 2.68744 1.00000 -0.00010 1.00000 >>>>>>>>> 30 16 128.0 64.00 48.00 72.00 2.67636 1.00000 -0.00010 1.00000 >>>>>>>>> 31 28 224.0 75.00 35.00 88.00 2.65193 1.00000 -0.00010 1.00000 >>>>>>>>> 32 11 88.0 15.00 21.00 82.00 2.61771 1.00000 -0.00010 1.00000 >>>>>>>>> 33 5 40.0 45.00 0.00 27.00 2.61424 1.00000 -0.00010 1.00000 >>>>>>>>> 34 16 128.0 9.00 13.00 70.00 2.58842 1.00000 -0.00010 1.00000 >>>>>>>>> 35 23 184.0 15.00 27.00 48.00 2.57410 1.00000 -0.00010 1.00000 >>>>>>>>> 36 28 224.0 15.00 31.00 44.00 2.57219 1.00000 -0.00010 1.00000 >>>>>>>>> 37 23 184.0 29.00 56.00 78.00 2.55890 1.00000 -0.00010 1.00000 >>>>>>>>> 38 7 56.0 0.00 42.00 92.00 2.55525 1.00000 -0.00010 1.00000 >>>>>>>>> 39 49 392.0 52.00 40.00 88.00 2.54894 1.00000 -0.00010 1.00000 >>>>>>>>> 40 42 336.0 7.00 31.00 63.00 2.52160 1.00000 -0.00010 1.00000 >>>>>>>>> 41 37 296.0 22.00 43.00 81.00 2.50557 1.00000 -0.00010 1.00000 >>>>>>>>> 42 21 168.0 22.00 58.00 72.00 2.49912 1.00000 -0.00010 1.00000 >>>>>>>>> 43 32 256.0 59.00 45.00 91.00 2.44918 1.00000 -0.00010 1.00000 >>>>>>>>> 44 12 96.0 31.00 29.00 36.00 2.42939 1.00000 -0.00010 1.00000 >>>>>>>>> 45 50 400.0 14.00 34.00 26.00 2.42102 1.00000 -0.00010 1.00000 >>>>>>>>> 46 22 176.0 6.00 15.00 55.00 2.41349 1.00000 -0.00010 1.00000 >>>>>>>>> 47 12 96.0 9.00 43.00 42.00 2.40593 1.00000 -0.00010 1.00000 >>>>>>>>> 48 27 216.0 64.00 17.00 31.00 2.38351 1.00000 -0.00010 1.00000 >>>>>>>>> 49 16 128.0 25.00 49.00 81.00 2.37500 1.00000 -0.00010 1.00000 >>>>>>>>> 50 37 296.0 12.00 18.00 54.00 2.36836 1.00000 -0.00010 1.00000 >>>>>>>>> 51 22 176.0 43.00 50.00 63.00 2.35072 1.00000 -0.00010 1.00000 >>>>>>>>> 52 39 312.0 31.00 39.00 46.00 2.31633 1.00000 -0.00010 1.00000 >>>>>>>>> 53 7 56.0 75.00 60.00 84.00 2.28945 1.00000 -0.00010 1.00000 >>>>>>>>> 54 6 48.0 33.00 25.00 67.00 2.28154 1.00000 -0.00010 1.00000 >>>>>>>>> 55 10 80.0 49.00 40.00 33.00 2.27301 1.00000 -0.00010 1.00000 >>>>>>>>> 56 13 104.0 26.00 65.00 88.00 2.27017 1.00000 -0.00010 1.00000 >>>>>>>>> 57 6 48.0 13.00 25.00 26.00 2.26583 1.00000 -0.00010 1.00000 >>>>>>>>> 58 15 120.0 54.00 9.00 20.00 2.25868 1.00000 -0.00010 1.00000 >>>>>>>>> 59 16 128.0 63.00 14.00 19.00 2.21490 1.00000 -0.00010 1.00000 >>>>>>>>> 60 4 32.0 9.00 25.00 61.00 2.21056 1.00000 -0.00010 1.00000 >>>>>>>>> 61 37 296.0 25.00 37.00 62.00 2.21055 1.00000 -0.00010 1.00000 >>>>>>>>> 62 10 80.0 59.00 51.00 51.00 2.20982 1.00000 -0.00010 1.00000 >>>>>>>>> 63 20 160.0 66.00 41.00 51.00 2.19863 1.00000 -0.00010 1.00000 >>>>>>>>> 64 2 16.0 53.00 66.00 72.00 2.18410 1.00000 -0.00010 1.00000 >>>>>>>>> 65 9 72.0 37.00 38.00 66.00 2.17739 1.00000 -0.00010 1.00000 >>>>>>>>> 66 6 48.0 6.00 44.00 62.00 2.17461 1.00000 -0.00010 1.00000 >>>>>>>>> 67 39 312.0 50.00 35.00 70.00 2.16322 1.00000 -0.00010 1.00000 >>>>>>>>> 68 11 88.0 52.00 6.00 21.00 2.16002 1.00000 -0.00010 1.00000 >>>>>>>>> 69 6 48.0 26.00 0.00 43.00 2.15030 1.00000 -0.00010 1.00000 >>>>>>>>> 70 8 64.0 41.00 16.00 19.00 2.14875 1.00000 -0.00010 1.00000 >>>>>>>>> 71 4 32.0 51.00 8.00 39.00 2.14592 1.00000 -0.00010 1.00000 >>>>>>>>> 72 3 24.0 47.00 9.00 21.00 2.14285 1.00000 -0.00010 1.00000 >>>>>>>>> 73 8 64.0 67.00 19.00 27.00 2.14034 1.00000 -0.00010 1.00000 >>>>>>>>> 74 12 96.0 3.00 59.00 86.00 2.13879 1.00000 -0.00010 1.00000 >>>>>>>>> 75 3 24.0 15.00 6.00 19.00 2.13024 1.00000 -0.00010 1.00000 >>>>>>>>> 76 9 72.0 59.00 41.00 41.00 2.12204 1.00000 -0.00010 1.00000 >>>>>>>>> 77 18 144.0 35.00 48.00 55.00 2.10334 1.00000 -0.00010 1.00000 >>>>>>>>> 78 6 48.0 40.00 57.00 92.00 2.08841 1.00000 -0.00010 1.00000 >>>>>>>>> 79 7 56.0 43.00 1.00 17.00 2.07371 1.00000 -0.00010 1.00000 >>>>>>>>> 80 6 48.0 41.00 55.00 69.00 2.07007 1.00000 -0.00010 1.00000 >>>>>>>>> 81 14 112.0 23.00 35.00 88.00 2.06307 1.00000 -0.00010 1.00000 >>>>>>>>> 82 11 88.0 40.00 73.00 82.00 2.05213 1.00000 -0.00010 1.00000 >>>>>>>>> 83 5 40.0 39.00 19.00 51.00 2.04809 1.00000 -0.00010 1.00000 >>>>>>>>> 84 10 80.0 38.00 24.00 69.00 2.04252 1.00000 -0.00010 1.00000 >>>>>>>>> 85 9 72.0 30.00 32.00 67.00 2.04237 1.00000 -0.00010 1.00000 >>>>>>>>> 86 7 56.0 54.00 58.00 72.00 2.03645 1.00000 -0.00010 1.00000 >>>>>>>>> 87 10 80.0 30.00 13.00 22.00 2.03577 1.00000 -0.00010 1.00000 >>>>>>>>> 88 8 64.0 0.00 25.00 72.00 2.03193 1.00000 -0.00010 1.00000 >>>>>>>>> 89 5 40.0 7.00 23.00 6.00 2.02805 1.00000 -0.00010 1.00000 >>>>>>>>> 90 4 32.0 59.00 28.00 21.00 2.02245 1.00000 -0.00010 1.00000 >>>>>>>>> 91 11 88.0 43.00 18.00 63.00 2.01764 1.00000 -0.00010 1.00000 >>>>>>>>> 92 5 40.0 14.00 41.00 87.00 2.01255 1.00000 -0.00010 1.00000 >>>>>>>>> 93 3 24.0 28.00 50.00 55.00 2.01226 1.00000 -0.00010 1.00000 >>>>>>>>> 94 6 48.0 35.00 0.00 43.00 1.99869 1.00000 -0.00010 1.00000 >>>>>>>>> 95 1 8.0 59.00 57.00 79.00 1.99505 1.00000 -0.00010 1.00000 >>>>>>>>> 96 1 8.0 25.00 2.00 51.00 1.99394 1.00000 -0.00010 1.00000 >>>>>>>>> 97 4 32.0 55.00 4.00 36.00 1.98505 1.00000 -0.00010 1.00000 >>>>>>>>> 98 2 16.0 66.00 21.00 6.00 1.97461 1.00000 -0.00010 1.00000 >>>>>>>>> 99 3 24.0 31.00 51.00 90.00 1.97154 1.00000 -0.00010 1.00000 >>>>>>>>> 100 3 24.0 12.00 11.00 23.00 1.95664 1.00000 -0.00010 1.00000 >>>>>>>>> 101 5 40.0 38.00 43.00 50.00 1.95222 1.00000 -0.00010 1.00000 >>>>>>>>> 102 2 16.0 28.00 22.00 7.00 1.95066 1.00000 -0.00010 1.00000 >>>>>>>>> 103 4 32.0 20.00 17.00 69.00 1.94669 1.00000 -0.00010 1.00000 >>>>>>>>> 104 5 40.0 1.00 8.00 46.00 1.94587 1.00000 -0.00010 1.00000 >>>>>>>>> 105 4 32.0 42.00 15.00 49.00 1.94354 1.00000 -0.00010 1.00000 >>>>>>>>> 106 4 32.0 4.00 41.00 54.00 1.93906 1.00000 -0.00010 1.00000 >>>>>>>>> 107 3 24.0 15.00 9.00 33.00 1.93848 1.00000 -0.00010 1.00000 >>>>>>>>> 108 6 48.0 61.00 28.00 72.00 1.92516 1.00000 -0.00010 1.00000 >>>>>>>>> 109 1 8.0 49.00 26.00 88.00 1.92457 1.00000 -0.00010 1.00000 >>>>>>>>> 110 3 24.0 65.00 37.00 41.00 1.92365 1.00000 -0.00010 1.00000 >>>>>>>>> 111 3 24.0 69.00 29.00 25.00 1.91576 1.00000 -0.00010 1.00000 >>>>>>>>> 112 2 16.0 70.00 15.00 9.00 1.89931 1.00000 -0.00010 1.00000 >>>>>>>>> 113 2 16.0 65.00 24.00 70.00 1.89719 1.00000 -0.00010 1.00000 >>>>>>>>> 114 1 8.0 41.00 24.00 36.00 1.89653 1.00000 -0.00010 1.00000 >>>>>>>>> 115 7 56.0 71.00 32.00 91.00 1.89529 1.00000 -0.00010 1.00000 >>>>>>>>> 116 6 48.0 24.00 38.00 69.00 1.88993 1.00000 -0.00010 1.00000 >>>>>>>>> 117 4 32.0 6.00 22.00 34.00 1.88833 1.00000 -0.00010 1.00000 >>>>>>>>> 118 3 24.0 41.00 45.00 51.00 1.87881 1.00000 -0.00010 1.00000 >>>>>>>>> 119 2 16.0 18.00 58.00 91.00 1.87841 1.00000 -0.00010 1.00000 >>>>>>>>> 120 3 24.0 44.00 10.00 17.00 1.87792 1.00000 -0.00010 1.00000 >>>>>>>>> 121 4 32.0 7.00 38.00 71.00 1.87444 1.00000 -0.00010 1.00000 >>>>>>>>> 122 2 16.0 39.00 12.00 65.00 1.87242 1.00000 -0.00010 1.00000 >>>>>>>>> 123 7 56.0 25.00 35.00 38.00 1.87054 1.00000 -0.00010 1.00000 >>>>>>>>> 124 3 24.0 14.00 28.00 25.00 1.86776 1.00000 -0.00010 1.00000 >>>>>>>>> 125 4 32.0 64.00 23.00 76.00 1.86629 1.00000 -0.00010 1.00000 >>>>>>>>> 126 7 56.0 58.00 44.00 43.00 1.86598 1.00000 -0.00010 1.00000 >>>>>>>>> 127 1 8.0 40.00 44.00 63.00 1.86487 1.00000 -0.00010 1.00000 >>>>>>>>> 128 1 8.0 19.00 8.00 55.00 1.84677 1.00000 -0.00010 1.00000 >>>>>>>>> 129 1 8.0 59.00 58.00 80.00 1.84162 1.00000 -0.00010 1.00000 >>>>>>>>> 130 1 8.0 16.00 40.00 92.00 1.83828 1.00000 -0.00010 1.00000 >>>>>>>>> 131 2 16.0 21.00 42.00 63.00 1.83258 1.00000 -0.00010 1.00000 >>>>>>>>> 132 6 48.0 2.00 19.00 69.00 1.82733 1.00000 -0.00010 1.00000 >>>>>>>>> 133 1 8.0 25.00 45.00 73.00 1.81604 1.00000 -0.00010 1.00000 >>>>>>>>> 134 1 8.0 6.00 10.00 48.00 1.81496 1.00000 -0.00010 1.00000 >>>>>>>>> 135 2 16.0 9.00 7.00 43.00 1.80712 1.00000 -0.00010 1.00000 >>>>>>>>> 136 1 8.0 36.00 2.00 53.00 1.80667 1.00000 -0.00010 1.00000 >>>>>>>>> 137 1 8.0 19.00 43.00 60.00 1.80358 1.00000 -0.00010 1.00000 >>>>>>>>> 138 1 8.0 24.00 0.00 25.00 1.80337 1.00000 -0.00010 1.00000 >>>>>>>>> 139 2 16.0 25.00 5.00 42.00 1.79990 1.00000 -0.00010 1.00000 >>>>>>>>> 140 4 32.0 69.00 18.00 40.00 1.79854 1.00000 -0.00010 1.00000 >>>>>>>>> 141 1 8.0 62.00 48.00 85.00 1.79309 1.00000 -0.00010 1.00000 >>>>>>>>> 142 4 32.0 61.00 43.00 84.00 1.78916 1.00000 -0.00010 1.00000 >>>>>>>>> 143 1 8.0 13.00 13.00 34.00 1.78877 1.00000 -0.00010 1.00000 >>>>>>>>> 144 1 8.0 34.00 28.00 78.00 1.78826 1.00000 -0.00010 1.00000 >>>>>>>>> 145 3 24.0 69.00 32.00 83.00 1.78152 1.00000 -0.00010 1.00000 >>>>>>>>> 146 1 8.0 14.00 11.00 33.00 1.78004 1.00000 -0.00010 1.00000 >>>>>>>>> 147 1 8.0 70.00 19.00 25.00 1.77961 1.00000 -0.00010 1.00000 >>>>>>>>> 148 1 8.0 24.00 1.00 50.00 1.77625 1.00000 -0.00010 1.00000 >>>>>>>>> 149 1 8.0 3.00 35.00 84.00 1.77073 1.00000 -0.00010 1.00000 >>>>>>>>> 150 1 8.0 22.00 43.00 64.00 1.77048 1.00000 -0.00010 1.00000 >>>>>>>>> 151 1 8.0 25.00 63.00 83.00 1.76957 1.00000 -0.00010 1.00000 >>>>>>>>> 152 1 8.0 52.00 57.00 72.00 1.76913 1.00000 -0.00010 1.00000 >>>>>>>>> 153 1 8.0 6.00 24.00 31.00 1.76905 1.00000 -0.00010 1.00000 >>>>>>>>> 154 1 8.0 7.00 37.00 72.00 1.76885 1.00000 -0.00010 1.00000 >>>>>>>>> 155 2 16.0 75.00 24.00 12.00 1.76788 1.00000 -0.00010 1.00000 >>>>>>>>> 156 1 8.0 64.00 38.00 42.00 1.76533 1.00000 -0.00010 1.00000 >>>>>>>>> 157 1 8.0 54.00 32.00 84.00 1.76446 1.00000 -0.00010 1.00000 >>>>>>>>> 158 1 8.0 23.00 38.00 88.00 1.76098 1.00000 -0.00010 1.00000 >>>>>>>>> 159 1 8.0 6.00 40.00 33.00 1.75765 1.00000 -0.00010 1.00000 >>>>>>>>> 160 1 8.0 22.00 25.00 9.00 1.75009 1.00000 -0.00010 1.00000 >>>>>>>>> 161 2 16.0 67.00 3.00 52.00 1.74760 1.00000 -0.00010 1.00000 >>>>>>>>> 162 2 16.0 28.00 67.00 70.00 1.74531 1.00000 -0.00010 1.00000 >>>>>>>>> 163 1 8.0 4.00 33.00 30.00 1.74303 1.00000 -0.00010 1.00000 >>>>>>>>> 164 1 8.0 69.00 20.00 74.00 1.74160 1.00000 -0.00010 1.00000 >>>>>>>>> 165 1 8.0 18.00 21.00 55.00 1.74153 1.00000 -0.00010 1.00000 >>>>>>>>> 166 2 16.0 31.00 25.00 80.00 1.73939 1.00000 -0.00010 1.00000 >>>>>>>>> 167 2 16.0 22.00 40.00 63.00 1.73425 1.00000 -0.00010 1.00000 >>>>>>>>> 168 2 16.0 68.00 21.00 74.00 1.72982 1.00000 -0.00010 1.00000 >>>>>>>>> 169 2 16.0 7.00 18.00 27.00 1.72964 1.00000 -0.00010 1.00000 >>>>>>>>> 170 1 8.0 11.00 29.00 60.00 1.72963 1.00000 -0.00010 1.00000 >>>>>>>>> 171 1 8.0 25.00 65.00 86.00 1.72933 1.00000 -0.00010 1.00000 >>>>>>>>> 172 1 8.0 40.00 10.00 56.00 1.72897 1.00000 -0.00010 1.00000 >>>>>>>>> 173 2 16.0 40.00 56.00 61.00 1.72244 1.00000 -0.00010 1.00000 >>>>>>>>> 174 1 8.0 17.00 67.00 74.00 1.72103 1.00000 -0.00010 1.00000 >>>>>>>>> 175 1 8.0 42.00 67.00 70.00 1.71913 1.00000 -0.00010 1.00000 >>>>>>>>> 176 1 8.0 25.00 64.00 85.00 1.71646 1.00000 -0.00010 1.00000 >>>>>>>>> 177 1 8.0 9.00 38.00 73.00 1.71532 1.00000 -0.00010 1.00000 >>>>>>>>> 178 1 8.0 4.00 34.00 31.00 1.71458 1.00000 -0.00010 1.00000 >>>>>>>>> 179 1 8.0 3.00 22.00 7.00 1.71416 1.00000 -0.00010 1.00000 >>>>>>>>> 180 1 8.0 31.00 50.00 89.00 1.71002 1.00000 -0.00010 1.00000 >>>>>>>>> 181 1 8.0 51.00 7.00 19.00 1.70870 1.00000 -0.00010 1.00000 >>>>>>>>> 182 1 8.0 43.00 1.00 48.00 1.70621 1.00000 -0.00010 1.00000 >>>>>>>>> 183 1 8.0 22.00 36.00 41.00 1.70538 1.00000 -0.00010 1.00000 >>>>>>>>> 184 1 8.0 1.00 22.00 71.00 1.70431 1.00000 -0.00010 1.00000 >>>>>>>>> 185 1 8.0 65.00 20.00 5.00 1.70426 1.00000 -0.00010 1.00000 >>>>>>>>> 186 1 8.0 70.00 10.00 43.00 1.70299 1.00000 -0.00010 1.00000 >>>>>>>>> 187 1 8.0 11.00 17.00 62.00 1.70210 1.00000 -0.00010 1.00000 >>>>>>>>> 188 1 8.0 1.00 21.00 70.00 1.70207 1.00000 -0.00010 1.00000 >>>>>>>>> 189 1 8.0 35.00 26.00 63.00 1.70166 1.00000 -0.00010 1.00000 >>>>>>>>> 190 1 8.0 11.00 37.00 66.00 1.70059 1.00000 -0.00010 1.00000 >>>>>>>>> 191 1 8.0 22.00 37.00 70.00 1.70035 1.00000 -0.00010 1.00000 >>>>>>>>> 192 1 8.0 25.00 14.00 22.00 1.69897 1.00000 -0.00010 1.00000 >>>>>>>>> >>>>>>>>> >>>>>>>>> Date: Tue, 25 Jun 2013 12:22:23 -0400 >>>>>>>>> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>>>>>>> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach >>>>>>>>> coordinates >>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> Message-ID: <51C9C3BF.7000000(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:51C9C3BF.7000000@nmr.mgh.harvard.edu>> >>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>>>> >>>>>>>>> can you send the file? >>>>>>>>> >>>>>>>>> On 06/25/2013 10:08 AM, Emily Boeke wrote: >>>>>>>>>> Hi All, >>>>>>>>>> >>>>>>>>>> I'm running Monte Carlo simulations on functional data, and the >>>>>>>>>> coordinate information outputted in the cluster.summary file isn't >>>>>>>>>> making sense. Usually the coordinates for the clusters listed are >>>>>>>>>> Talairach coordinates, but in the .summary files I'm getting, the >>>>>>>>>> coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" >>>>>>>>>> and the numbers are clearly not Talairach coordinates. Above the >>>>>>>>>> table, it says "Reporting Coordinates in Voxel Indices." I also >>>>>>>>>> noted that in the descriptive information above the table, it says >>>>>>>>>> "Registration: None: Tal Coords invalid." >>>>>>>>>> >>>>>>>>>> However, the .nii files I'm seeing look like I would expect them too. >>>>>>>>>> >>>>>>>>>> I'm using the same command line I've run before, so I have no idea >>>>>>>>>> why the .summary file looks different. Does anyone know why this >>>>>>>>>> would be? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Emily >>>>>>>> _______________________________________________ >>>>>>>> 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: 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/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>> -- >>>> 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/ >>>> >>>> >>> _______________________________________________ >>> 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: 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/ >> >> _______________________________________________ >> 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: 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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Order of Edits + Intensity Normalization
by Peter Boulos 02 Jul '13

02 Jul '13

Resending, would greatly appreciate some input so I can move forward: I have a fairly basic question regarding the order in which I should perform the edits. After running the full recon on all of my subjects I have now completed the Talairach edits and the skull strip edits on my subjects. At this point I am attempting to seek out help in terms of performing the edits on white/grey matter border from a more experienced user but have a couple of days before I can meet with them. Therefore, can I go ahead and do the pial surface edits before or does the intensity normalization and white/grey boundary edits need to be done first before the pial surface? As in will those edits alter what I do in later steps? Also, I am having a hard time understanding what I am doing with intensity normalization. Am I just ensuring that there are sections of an intensity of 110 in the white matter boundaries of each subject? Am I only looking for white matter that appears to be left out in a disastrous way in this step or should I be very meticulous about this? I am confused because I have areas considered white matter in free surfer that appear to be white matter by visual inspection that have intensities as low as 70 but then areas of the same intensity outside of the boundary. I realize that the program is probably using intensity data along with location data but do not understand how I am supposed to ensure that whether something with an intensity lower than 110 is indeed white matter by visual inspection alone. I apologize for the simplicity of my understanding at this point and thank you for your time. Peter

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Freesurfer July 2013