Can you send me the aparc.annot.ctab and label files? On 08/03/2016 12:25 PM, Caroline Beelen wrote: > My command line is: > mris_label2annot --subject fsaverage --hemi lh --ctab aparc.annot.ctab > --annot myaparc --l lh.fusiform.label > --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh > (I have version 5.3) > > Regards, Caroline > > Message: 3 > Date: Wed, 3 Aug 2016 09:30:48 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mapping error > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > what is your command line? > > > On 8/3/16 6:00 AM, Caroline Beelen wrote: >> Dear FS, >> >> An aparc.annot ctab file was created but I got the following error: >> >> Colortable:aparc.annot.ctab >> >> Annotname: myaparc >> >> Nhitsfile nhits.mgh >> >> Nlabels 6 >> >> Labeltresh 0 0.00000 >> >> Loading freesurfer/fsaverage/surf/lh.orig >> >> 1 -1 not found >> >> 2 -1 not found >> >> 3 -1 not found >> >> Etc? >> >> Mapping unhit to unknown >> >> Found 132101 unhit vertices >> >> Writing annot to freesurfer/fsaverage/lh.myaparc.annot >> >> I guess my ctab file is incorrect? I included an example of a label >> with it. >> >> Thanks again for your help. >> >> Caroline >> >> > -----Oorspronkelijk bericht----- > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens > freesurfer-requ...@nmr.mgh.harvard.edu > Verzonden: woensdag 3 augustus 2016 18:00 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Freesurfer Digest, Vol 150, Issue 6 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: brain mask and T1 are not the same size (Isabelle Deschamps) > 2. Re: Coordinates in TRACULA group analysis (Anri WATANABE) > 3. Re: mapping error (Douglas Greve) > 4. Re: Multiple Comparison Question for surface-based analyses > (Douglas Greve) > 5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki) > 6. Re: brain mask and T1 are not the same size (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Aug 2016 10:50:30 +0000 > From: Isabelle Deschamps <isabelle.deschamp...@ulaval.ca> > Subject: Re: [Freesurfer] brain mask and T1 are not the same size > To: "<freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <8f31a8f6-59c6-4d12-a2a4-2ef526465...@ulaval.ca> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/fc0fed11/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 3 Aug 2016 20:19:09 +0900 > From: Anri WATANABE <z2aa...@koto.kpu-m.ac.jp> > Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <caaw-jjeawc33oax6oameuect3q06ah8zyfd6nuuo32bn-eh...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Anastasia, > > Thank you for your kind explanation. I can be understanding how TRACULA > tracts white matter pathways. > At each position (in training subjects, not in new subjects of my data) > probability that next goes for which direction to every labels in the > aparc+aseg (not with setting a certain ROI) is computed with use of > training subjects. The prior probabilities are made from training subjects > (your publication in 2011) and they are based on manual labeling (the > manual labeling tracts are referred to Wakana et al. 2007). Then when white > matter pathways are reconstructed in my subjects, TRACULA computes > anatomical priors in each subjects in my data in pre-processing and > probability distributions from anatomical priors and by fitting > ball-and-stick model. > Is this comprehension ok? > > Best Regards, > Anri > > > > ********************************************************************** > ???????????? > ???????? > ?? ?? > ********************************************************************** > Anri WATANABE, M.D. > Department of Psychiatry, > University Hospital, Kyoto Prefectural University of Medicine > ********************************************************************** > > 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > >> Hi Anri - Instead of hard-coding some ROIs in the white matter that the >> tract is forced to go through, TRACULA uses information like "what is the >> probability that this tract goes lateral/anterior/etc to XXX", where XXX >> any of the labels in the aparc+aseg. TRACULA computes these prior >> probabilities from a set of training subjects, where the tracts have been >> labeled manually. So it knows how likely a tract is to go through a certain >> aparc+aseg label, or to he left, right, anterior, etc of a certain >> aparc+aseg label. This is computed separately at each position along the >> tract. It's computed from the training subjects, and then used when >> reconstructing the tract in the new subject that you run TRACULA on. >> >> Hope this helps, >> a.y >> >> On Sun, 31 Jul 2016, Anri WATANABE wrote: >> >> Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if >>> ROIs are not >>> >>> set how determine the origin and the end of a certain tract? I think that >>> the first we >>> have to determine the origin and the end of the tract, the second it >>> constructs possible >>> pathway not with the deterministic way (only 1 direction / 1 voxel) but >>> with the >>> probabilistic way (considering which direction should be next to). Is >>> this comprehension >>> wrong? >>> Thank you. >>> >>> Anri >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto Prefectural University of Medicine >>> ********************************************************************** >>> >>> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki < >>> ayend...@nmr.mgh.harvard.edu>: >>> >>> Hi Anri - TRACULA does not use deterministic ROIs. It uses a >>> probabilistic >>> model of how likely each tract is to go through or next to each of >>> the labels >>> of the freesurfer subcortical segmentation and cortical >>> parcellation, as a >>> function of position along the trajectory of the tract. >>> >>> Best, >>> a.y >>> >>> On Sun, 31 Jul 2016, Anri WATANABE wrote: >>> >>> Hi Anastasia, >>> Thank you! It seems work well!! >>> I have another question. Are ROIs for automatic tractography >>> in >>> TRACULA the same ROIs >>> presented in Wakana et al. 2007? >>> >>> Anri >>> >>> >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto Prefectural University of Medicine >>> >>> ********************************************************************** >>> >>> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> Hi Anri - The problem is in this line: >>> >>> set cmd = ($cmd --ref $cvstempdir/$cvstemp) >>> >>> It should be changed to this: >>> >>> set cmd = ($cmd --ref >>> $cvstempdir/$cvstemp/mri/norm.mgz) >>> >>> For this to take effect, you need to run "which >>> trac-all" >>> and make the change in >>> the trac-all file that the which commands shows you. >>> >>> Hope this helps, >>> >>> a.y >>> >>> On Fri, 15 Jul 2016, Anri WATANABE wrote: >>> >>> Hi, AnastasiaThis is trac-all.local-copy from 1 >>> subject. Thank you! >>> >>> Anri >>> >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> >>> >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto Prefectural University >>> of >>> Medicine >>> >>> >>> ********************************************************************** >>> >>> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> Hi Anri - This may be a bug that was fixed >>> at >>> some point. Can >>> you send me the scripts/trac-all.local-copy >>> from >>> one of your >>> subjects? Thanks! >>> >>> a.y >>> >>> On Mon, 11 Jul 2016, Anri WATANABE wrote: >>> >>> Hi Anastasia,There is an error in .log >>> files of left >>> corticospinal tract in cvs template >>> and I >>> attached >>> one >>> of file. In addition .log files of >>> right >>> corticospinal tract in cvs template >>> doesn't exist. >>> Thanks in advance. >>> >>> Anri >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> >>> >>> >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto Prefectural >>> University of >>> Medicine >>> >>> >>> >>> ********************************************************************** >>> >>> 2016-07-07 20:12 GMT+09:00 Anastasia >>> Yendiki >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> Hi Anri - Is there an error in >>> the >>> stats/*.log >>> files for the different tracts? >>> >>> a.y >>> >>> On Tue, 5 Jul 2016, Anri >>> WATANABE >>> wrote: >>> >>> Dear Anastasia, >>> >>> I use TRACULA to obtain >>> diffusion >>> measures at each voxel in a certain >>> pathway for >>> group analysis, but >>> there aren't >>> stats/*.path.mean.txt >>> files. I found .log files >>> >>> (<tract>_PP.avg33_mni_bbr.log) >>> which >>> exist >>> 1 file per 1 tract, except >>> corticospinal >>> tract which has 2 .log files. >>> >>> Command: trac-all ?stat ?c >>> >>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >>> >>> Error log: Loading output >>> reference >>> volume from >>> >>> >>> /Applications/freesurfer/subjects/cvs_avg35 >>> >>> corRead(): can't open file >>> >>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >>> >>> ERROR: Could not read >>> >>> /Applications/freesurfer/subjects/cvs_avg35 >>> >>> >>> I attached dmrirc.example >>> (configuration >>> file) and >>> <subjd>/scripts/trac-all.log. >>> >>> >>> Thanks in advance, >>> Anri >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> >>> >>> >>> >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto >>> Prefectural >>> University of Medicine >>> >>> >>> >>> >>> ********************************************************************** >>> >>> 2016-06-03 9:51 GMT+09:00 >>> Anri >>> WATANABE >>> <z2aa...@koto.kpu-m.ac.jp>: >>> Hi, Anastasia. >>> There aren't any .log >>> files >>> but text >>> files like >>> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. >>> I guess text >>> files complete all >>> pathways >>> and >>> measures. >>> >>> >>> >>> >>> >>> ********************************************************************** >>> ???????????? >>> ???????? >>> ?? ?? >>> >>> >>> >>> >>> ********************************************************************** >>> Anri WATANABE, M.D. >>> Department of Psychiatry, >>> University Hospital, Kyoto >>> Prefectural >>> University of Medicine >>> >>> >>> >>> >>> ********************************************************************** >>> >>> 2016-06-02 3:03 GMT+09:00 >>> Anastasia >>> Yendiki <ayend...@nmr.mgh.harvard.edu >>>> : >>> Thanks, Anri. So the >>> previous >>> steps seem to have run fine. Are >>> there any >>> .log >>> files >>> created in the >>> stats/ >>> folder, >>> which is created by trac-all -stat? >>> >>> On Wed, 1 Jun 2016, >>> Anri >>> WATANABE >>> wrote: >>> >>> Hi >>> Anastasia, This >>> is a >>> <subjid>/scripts/trac-all.log of one >>> subject of >>> the group. >>> >>> Thanks, >>> Anri >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> ???????????? >>> ???????? >>> ?? ?? >>> >>> >>> >>> >>> ********************************************************************** >>> Anri WATANABE, >>> M.D. >>> Department of >>> Psychiatry, >>> University >>> Hospital, Kyoto >>> Prefectural University of Medicine >>> >>> >>> >>> >>> ********************************************************************** >>> >>> 2016-05-31 >>> 22:55 >>> GMT+09:00 >>> Anastasia Yendiki >>> >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> Hi Anri >>> - >>> Can you also >>> send your log file >>> (scripts/trac-all.log)? >>> I'll need to >>> see >>> what >>> exactly >>> was >>> running >>> when the error occurred. Thanks! >>> >>> a.y >>> >>> On Sat, >>> 28 >>> May 2016, >>> Anri WATANABE wrote: >>> >>> >>> Hello >>> Anastasia,sorry for few information >>> and >>> let me tell >>> you >>> command and >>> >>> error >>> log. >>> >>> Command: trac-all ?stat ?c >>> >>> >>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >>> >>> >>> Error >>> log: Loading output reference volume >>> from >>> >>> >>> /Applications/freesurfer/subjects/cvs_avg35 >>> >>> >>> corRead(): can't >>> open file >>> >>> >>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >>> >>> >>> ERROR: >>> Could not >>> read >>> >>> >>> /Applications/freesurfer/subjects/cvs_avg35 >>> >>> >>> >>> dmrirc.example (configuration file) is >>> attached to >>> this >>> e-mail. >>> >>> >>> Thanks >>> in >>> advance, >>> >>> Anri >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> ???????????? >>> >>> ???????? >>> ?? >>> ?? >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> Anri >>> WATANABE, >>> M.D. >>> >>> Department of >>> Psychiatry, >>> >>> University >>> Hospital, Kyoto Prefectural >>> University of >>> Medicine >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> 2016-05-27 22:57 >>> GMT+09:00 Anastasia Yendiki >>> >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> >>> >>> Hi Anri - >>> I do not know what command line you >>> ran >>> and >>> what your >>> >>> configuration >>> file looks like, so it is very >>> >>> >>> hard for >>> me to suggest solutions. >>> >>> >>> >>> Best, >>> >>> >>> a.y >>> >>> >>> >>> On Fri, 27 >>> May 2016, Anri WATANABE wrote: >>> >>> >>> >>> Hi >>> Anastasia, >>> >>> >>> >>> Thank you for your answer. >>> >>> >>> >>> There aren't stats/*.path.mean.txt >>> files and >>> terminal says >>> 'Could >>> >>> not >>> read >>> >>> >>> >>> >>> /Applications/freesurfer/subjects/cvs_avg35.' I >>> >>> >>> >>> checked >>> >>> >>> /Application/freesurfer/subjects/cvs_avg35 >>> folder >>> and >>> >>> couldn't find >>> COR-.info file. >>> >>> >>> >>> Could you tell me any resolutions, >>> please? >>> >>> >>> >>> >>> Thanks, >>> >>> >>> Anri >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> >>> ???????????? >>> >>> >>> >>> ???????? >>> >>> >>> ?? >>> ?? >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> Anri >>> WATANABE, M.D. >>> >>> >>> >>> Department of Psychiatry, >>> >>> >>> >>> University Hospital, Kyoto Prefectural >>> University >>> of Medicine >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> >>> >>> 2016-05-21 6:48 GMT+09:00 Anastasia >>> Yendiki >>> >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> >>> >>> >>> Hi Anri - The FA values are >>> extracted in >>> the native >>> space >>> of >>> each subject, >>> which is why >>> >>> >>> >>> those are the only >>> >>> >>> >>> coordinates that you see. If you >>> want to >>> display the >>> >>> results of your >>> analysis on an average >>> >>> >>> >>> path, after >>> >>> >>> >>> running trac-all -stat, you can use >>> the >>> >>> stats/*.path.mean.txt files (see also >>> the >>> last part >>> >>> >>> of >>> the TRACULA >>> >>> >>> >>> tutorial). >>> >>> >>> >>> >>> Best, >>> >>> >>> >>> a.y >>> >>> >>> >>> >>> On Wed, 18 May 2016, Anri WATANABE >>> wrote: >>> >>> >>> >>> >>> Dear experts, >>> >>> >>> >>> I use TRACULA to examine a >>> measure >>> (FA) at each >>> voxel >>> >>> in one >>> pathway. >>> >>> >>> >>> pathstats.byvoxel.txt files >>> show >>> coordinates in >>> >>> native >>> space and >>> after converting >>> >>> >>> >>> those the new >>> >>> >>> >>> files don't show any >>> coordinates >>> which are in >>> MNI >>> >>> space. >>> >>> >>> >>> Could you tell me how can I >>> know >>> MNI >>> coordinate >>> >>> values? >>> >>> >>> >>> >>> Thank you! >>> >>> >>> >>> >>> >>> Regards, >>> >>> >>> >>> Anri >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> >>> ???????????? >>> >>> >>> >>> ???????? >>> >>> >>> >>> ?? ?? >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> >>> Anri WATANABE, M.D. >>> >>> >>> >>> Department of Psychiatry, >>> >>> >>> >>> University Hospital, Kyoto >>> Prefectural >>> University of >>> >>> Medicine >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ********************************************************************** >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> >>> >>> Freesurfer mailing list >>> >>> >>> >>> 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. >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Freesurfer >>> mailing list >>> >>> 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 >>> >>> >> ... >> >> [???????????] >> _______________________________________________ >> Freesurfer mailing list >> 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. >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/550a8010/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 3 Aug 2016 09:30:48 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mapping error > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > what is your command line? > > > On 8/3/16 6:00 AM, Caroline Beelen wrote: >> Dear FS, >> >> An aparc.annot ctab file was created but I got the following error: >> >> Colortable:aparc.annot.ctab >> >> Annotname: myaparc >> >> Nhitsfile nhits.mgh >> >> Nlabels 6 >> >> Labeltresh 0 0.00000 >> >> Loading freesurfer/fsaverage/surf/lh.orig >> >> 1 -1 not found >> >> 2 -1 not found >> >> 3 -1 not found >> >> Etc? >> >> Mapping unhit to unknown >> >> Found 132101 unhit vertices >> >> Writing annot to freesurfer/fsaverage/lh.myaparc.annot >> >> I guess my ctab file is incorrect? I included an example of a label >> with it. >> >> Thanks again for your help. >> >> Caroline >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/a468e29f/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 3 Aug 2016 09:41:24 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Multiple Comparison Question for > surface-based analyses > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <dcd38d26-01cd-721e-9b52-81382d318...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > > > On 8/3/16 3:45 AM, Ajay Kurani wrote: >> Hi Doug, >> Thank you very much for your update regarding this issue. >> >> 1)Just curious, will LGI be included in this report as this is another >> analysis of interest? > I was not planning to. The 809 subjects that I used for thickness do not > have lGI run on them, but I think it is possible to run it on a subset > without too much trouble. Not sure when I'll get to it. >> 2)As for the cortical thickness I originally used 15mm in the analysis >> so based on your email I think using 5-10mm may be more prudent in >> order to minimize FPR. From your email, I understand that >> mris_surf2surf (command I use to convert individual subject to >> fsaverage or template and smooth to 10-15mm) assumes an ACF estimation >> of smoothness which DOES NOT take into account the long tail >> distribution. Does this mean that when using mri_mcsim on my own >> template, the cluster extents for a given smoothness will be >> undersampled due to the fact that the "true" smoothness is more than >> what is estimated in the simulation, correct? For instance, when I >> select 15mm in qdec, it would point to the 21mm folder >> (fwhm.dat=20.8mm estimate), and I would select a given cluster extent >> for p=0.05. However, in this case, 15mm may translate to a larger >> FWHM than the estimated 21mm, correct? > Sort of. It is the Gaussian assumption that is incorrect, so there is no > one FWHM that is correct (it is not a question of it simply being too > small). >> 3)You mentioned that I can use mri_glmfit-sim which is permutation >> testing based. I am struggling a bit in understanding how this >> differs from the simulation ran with mri_mcsim/qdec? Does qdec monte >> carlo simulation option run mri_glmfit-sim in the background to >> estimate the smoothness which looks up the cluster extent within the >> mri_mcsim based on the estimated FWHM? If so, is this estimate >> incorrect due to the fact that the long tails are not taken into account? > Permutation uses your data and permutes (ie, randomly swaps) the class > label associated with a subject, the data with this new labeling are > analyzed and clusters computed. Under the null, the label is irrelevant, > so clusters are interpreted as false positives. After several thousand > of these swaps, one builds a list of the probability of seeing a cluster > of a certain size under the null, and this is used to generate the > p-value. Permutation will then naturally take into account all the > non-Gaussian aspects of the data. The monte carlo (MC) simulation is > similar, but it uses smoothed synthesized gaussian noise instead of the > real data and so the gaussian assumption is built into it. >> >> Thanks, >> Ajay >> >> On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kur...@gmail.com >> <mailto:dr.ajay.kur...@gmail.com>> wrote: >> >> Hello Freesurfer Experts, >> Recently there were two article published regarding clusterwise >> simulations for volumetric fmri analyses and potential errors for >> underestimating clusterwise extent thresholds. >> >> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >> 2) biorxiv.org/content/early/2016/07/26/065862 >> <http://biorxiv.org/content/early/2016/07/26/065862> >> >> One issue pointed out from these articles seems software specific, >> however the second issue is determining the proper clustersize. >> The heavy-tail nature of spatial smoothness seems to be ignored >> and a gaussian shape is generally assumed, leading to an >> underestimation of the spatial smoothness which can affect cluster >> size calculations. The issues are highlighted in the second >> article above. >> >> I created my own monte carlo simulation in Freesurfer for a >> specific brain template and I wanted to find out if these concerns >> also apply to my surface based simulations? I am not sure if it >> does since the monte carlo tool is a GRF simulation as opposed to >> an analytic equation, however given that these articles were >> highlighted very recently, I wanted to ensure I am running things >> appropriately for surface based cortical thickness/dti analyses. >> >> Thanks, >> Ajay >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/86fe71de/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 3 Aug 2016 10:15:53 -0400 (EDT) > From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1608031015470.22...@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > That's correct! > > On Wed, 3 Aug 2016, Anri WATANABE wrote: > >> Hi Anastasia, >> Thank you for your kind explanation. I can be understanding how TRACULA >> tracts white matter pathways.? >> At each position (in training subjects, not in new subjects of my data) >> probability that next goes for >> which direction to every labels in the aparc+aseg (not with setting a >> certain ROI) is computed with use of >> training subjects. The prior probabilities are made from training subjects >> (your publication in 2011) and >> they are based on manual labeling (the manual labeling tracts are referred >> to Wakana et al. 2007). Then >> when white matter pathways are reconstructed in my subjects, TRACULA >> computes anatomical priors in each >> subjects in my data in pre-processing and probability distributions from >> anatomical priors and by fitting >> ball-and-stick model.? >> Is this comprehension ok? >> >> Best Regards,? >> Anri >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ********************************************************************** >> >> 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >> >> Hi Anri - Instead of hard-coding some ROIs in the white matter that >> the tract is forced to go >> through, TRACULA uses information like "what is the probability that >> this tract goes >> lateral/anterior/etc to XXX", where XXX any of the labels in the >> aparc+aseg. TRACULA computes >> these prior probabilities from a set of training subjects, where the >> tracts have been labeled >> manually. So it knows how likely a tract is to go through a certain >> aparc+aseg label, or to he >> left, right, anterior, etc of a certain aparc+aseg label. This is >> computed separately at each >> position along the tract. It's computed from the training subjects, >> and then used when >> reconstructing the tract in the new subject that you run TRACULA on. >> >> Hope this helps, >> a.y >> >> On Sun, 31 Jul 2016, Anri WATANABE wrote: >> >> Thanks, AnastasiaI know that TRACULA use probabilistic >> tractography but if ROIs >> are not >> set how determine the origin and the end of a certain tract? I >> think that the >> first we >> have to determine the origin and the end of the tract, the >> second it constructs >> possible >> pathway not with the deterministic way (only 1 direction / 1 >> voxel) but with the >> probabilistic way (considering which direction should be next >> to). Is this >> comprehension >> wrong? >> Thank you. >> >> Anri >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> >> ********************************************************************** >> >> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? Hi Anri - TRACULA does not use deterministic ROIs. It >> uses a probabilistic >> ? ? ? model of how likely each tract is to go through or next >> to each of the >> labels >> ? ? ? of the freesurfer subcortical segmentation and cortical >> parcellation, as a >> ? ? ? function of position along the trajectory of the tract. >> >> ? ? ? Best, >> ? ? ? a.y >> >> ? ? ? On Sun, 31 Jul 2016, Anri WATANABE wrote: >> >> ? ? ? ? ? ? Hi Anastasia, >> ? ? ? ? ? ? Thank you! It seems work well!! >> ? ? ? ? ? ? I have another question. Are ROIs for automatic >> tractography in >> ? ? ? ? ? ? TRACULA the same ROIs >> ? ? ? ? ? ? presented in Wakana et al. 2007? >> >> ? ? ? ? ? ? Anri >> >> >> >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ?? ?? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? Anri WATANABE, M.D. >> ? ? ? ? ? ? Department of Psychiatry, >> ? ? ? ? ? ? University Hospital, Kyoto Prefectural University >> of Medicine >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki >> ? ? ? ? ? ? <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? Hi Anri - The problem is in this line: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?set cmd = ($cmd --ref >> $cvstempdir/$cvstemp) >> >> ? ? ? ? ? ? ? ? ? It should be changed to this: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?set cmd = ($cmd --ref >> ? ? ? ? ? ? $cvstempdir/$cvstemp/mri/norm.mgz) >> >> ? ? ? ? ? ? ? ? ? For this to take effect, you need to run >> "which trac-all" >> ? ? ? ? ? ? and make the change in >> ? ? ? ? ? ? ? ? ? the trac-all file that the which commands >> shows you. >> >> ? ? ? ? ? ? ? ? ? Hope this helps, >> >> ? ? ? ? ? ? ? ? ? a.y >> >> ? ? ? ? ? ? ? ? ? On Fri, 15 Jul 2016, Anri WATANABE wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? Hi, AnastasiaThis is >> trac-all.local-copy from 1 >> ? ? ? ? ? ? subject. Thank you! >> >> ? ? ? ? ? ? ? ? ? ? ? ? Anri >> >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ?? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto Prefectural >> University of >> ? ? ? ? ? ? Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? 2016-07-13 6:16 GMT+09:00 Anastasia >> Yendiki >> ? ? ? ? ? ? ? ? ? ? ? ? <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri - This may be a bug that >> was fixed at >> ? ? ? ? ? ? some point. Can >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? you send me the >> scripts/trac-all.local-copy from >> ? ? ? ? ? ? one of your >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? subjects? Thanks! >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? a.y >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Mon, 11 Jul 2016, Anri >> WATANABE wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anastasia,There is an >> error in .log >> ? ? ? ? ? ? files of left >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? corticospinal tract in cvs >> template and I >> ? ? ? ? ? ? attached >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? one >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? of file. In addition .log >> files of right >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? corticospinal tract in cvs >> template >> ? ? ? ? ? ? doesn't exist.? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks in advance. >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri >> >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto >> Prefectural >> ? ? ? ? ? ? University of >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-07-07 20:12 GMT+09:00 >> Anastasia >> ? ? ? ? ? ? Yendiki >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri - Is there an >> error in the >> ? ? ? ? ? ? stats/*.log >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files for the different >> tracts? >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? a.y >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Tue, 5 Jul 2016, >> Anri WATANABE >> ? ? ? ? ? ? wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Dear Anastasia,? >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I use TRACULA >> to obtain >> ? ? ? ? ? ? diffusion >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? measures at each voxel in a >> certain >> ? ? ? ? ? ? pathway for >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? group analysis, >> but >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? there aren't >> ? ? ? ? ? ? stats/*.path.mean.txt >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files. I found .log files >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> (<tract>_PP.avg33_mni_bbr.log) >> ? ? ? ? ? ? which >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? exist >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 file per 1 >> tract, except >> ? ? ? ? ? ? corticospinal >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? tract which has 2 .log >> files. >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> Command:?trac-all ?stat ?c >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Error >> log:?Loading output >> ? ? ? ? ? ? reference >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? volume from >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35 >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? corRead(): >> can't open file >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ERROR: Could >> not read >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35 >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I attached >> dmrirc.example >> ? ? ? ? ? ? (configuration >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? file) and >> <subjd>/scripts/trac-all.log. >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks in >> advance, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri >> >> >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, >> M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of >> Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University >> Hospital, Kyoto >> ? ? ? ? ? ? Prefectural >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University of Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-06-03 9:51 >> GMT+09:00 Anri >> ? ? ? ? ? ? WATANABE >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <z2aa...@koto.kpu-m.ac.jp>: >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi, >> Anastasia. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? There aren't >> any .log files >> ? ? ? ? ? ? but text >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files like >> ? ? ? ? ? ? lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I guess text >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files complete >> all pathways >> ? ? ? ? ? ? and >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? measures. >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, >> M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of >> Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University >> Hospital, Kyoto >> ? ? ? ? ? ? Prefectural >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University of Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-06-02 3:03 >> GMT+09:00 >> ? ? ? ? ? ? Anastasia >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Yendiki >> <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks, >> Anri. So the >> ? ? ? ? ? ? previous >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? steps seem to have run >> fine. Are there any >> ? ? ? ? ? ? .log >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? created >> in the stats/ >> ? ? ? ? ? ? folder, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? which is created by >> trac-all -stat? >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Wed, 1 >> Jun 2016, Anri >> ? ? ? ? ? ? WATANABE >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi >> Anastasia,?This >> ? ? ? ? ? ? is a >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> <subjid>/scripts/trac-all.log of one >> ? ? ? ? ? ? subject of >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the >> group. >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> Thanks, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? >> ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> Anri WATANABE, >> ? ? ? ? ? ? M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> Department of >> ? ? ? ? ? ? Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> University >> ? ? ? ? ? ? Hospital, Kyoto >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Prefectural University of >> Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> 2016-05-31 22:55 >> ? ? ? ? ? ? GMT+09:00 >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anastasia Yendiki >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? Hi Anri - >> ? ? ? ? ? ? Can you also >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? send your log file >> (scripts/trac-all.log)? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> I'll need to see >> ? ? ? ? ? ? what >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? exactly was >> ? ? ? ? ? ? running >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? when the error occurred. >> Thanks! >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? a.y >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? On Sat, 28 >> ? ? ? ? ? ? May 2016, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? Hello >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anastasia,sorry for few >> information and >> ? ? ? ? ? ? let me tell >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? you >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> command and >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? error >> ? ? ? ? ? ? log. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Command:?trac-all ?stat ?c >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? Error >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? log:?Loading output >> reference volume from >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35 >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? corRead(): can't >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? open file >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ERROR: >> ? ? ? ? ? ? Could not >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? read >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35 >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> dmrirc.example?(configuration file) is >> ? ? ? ? ? ? attached to >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? this >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> e-mail. >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? Thanks >> ? ? ? ? ? ? in >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? advance, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? Anri >> >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ?? >> ? ? ? ? ? ? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? Anri >> ? ? ? ? ? ? WATANABE, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? Department of >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? University >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hospital, Kyoto Prefectural >> University of >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? 2016-05-27 22:57 >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? GMT+09:00 Anastasia Yendiki >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? Hi Anri - >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I do not know what command >> line you ran >> ? ? ? ? ? ? and >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> what your >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? configuration >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? file looks like, so it is >> very >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? hard for >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? me to suggest solutions. >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? Best, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? a.y >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? On Fri, 27 >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? May 2016, Anri WATANABE >> wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? Hi >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anastasia,? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thank you for your answer. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? There >> aren't?stats/*.path.mean.txt >> ? ? ? ? ? ? files?and >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> terminal says >> ? ? ? ? ? ? 'Could >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? not >> ? ? ? ? ? ? read >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35.' I >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? checked >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> /Application/freesurfer/subjects/cvs_avg35 >> ? ? ? ? ? ? folder >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? and >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? couldn't find >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? COR-.info file. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Could you tell me any >> resolutions, please? >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks,? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? Anri >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? Anri >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? WATANABE, M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto >> Prefectural >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? of >> Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-05-21 6:48 GMT+09:00 >> Anastasia >> ? ? ? ? ? ? Yendiki >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> <ayend...@nmr.mgh.harvard.edu>: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri - The FA values >> are extracted in >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the >> native space >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? of >> ? ? ? ? ? ? each subject, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? which is why >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? those are the only >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? coordinates that you see. >> If you want to >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> display the >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? results of your >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? analysis on an average >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? path, after >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? running trac-all -stat, >> you can use the >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? stats/*.path.mean.txt files >> (see also the >> ? ? ? ? ? ? last part >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? of >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the TRACULA >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? tutorial). >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Best, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? a.y >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Wed, 18 May 2016, Anri >> WATANABE >> ? ? ? ? ? ? wrote: >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Dear experts,? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I use TRACULA to >> examine a measure >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> (FA) at each voxel >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? in one >> ? ? ? ? ? ? pathway. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> pathstats.byvoxel.txt files show >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> coordinates in >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? native >> ? ? ? ? ? ? space and >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? after converting >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? those the new >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files don't show >> any coordinates >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> which are in MNI >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? space. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Could you tell me >> how can I know >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? MNI >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> coordinate >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? values? >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thank you! >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Regards,? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri >> >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???????? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ?? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D. >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of >> Psychiatry, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University >> Hospital, Kyoto >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> Prefectural >> ? ? ? ? ? ? University of >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? Medicine >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? >> ********************************************************************** >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? _______________________________________________ >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer mailing list >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> 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. >> >> >> >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? _______________________________________________ >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? >> ? ? ? ? ? ? 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If the >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? e-mail was >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> sent to you in >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> ? ? ? ? error >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> >> ... >> >> [???????????]?? >> _______________________________________________ >> Freesurfer mailing list >> 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. >> >> >> >> > ------------------------------ > > Message: 6 > Date: Wed, 3 Aug 2016 10:43:56 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] brain mask and T1 are not the same size > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <57a2032c.4050...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Sorry, I did not see that one of the volumes was 256x256x255. I cannot > replicate here on your data using 5.3 under linux. Can you say exactly > what you do in freeview? Also, what version of FS are you using? And > what platform? > > On 08/03/2016 06:50 AM, Isabelle Deschamps wrote: >> I had the problem before and was told the the output of mri_info >> should be 256 x 256 x 256 for the dimensions of the brainmask and T1. >> When I run mri_info on the brainmask.mgz that I modified I have 256 x >> 256 x 255 but the T1 I have 256 x 256 x 256. The zstart and zend are >> also different between the brainmask and T1. Could that be the source >> of the problem? >> >> *Modified brainmask:* >> mri_info >> /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz >> >> Volume information for >> /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz >> type: MGH >> dimensions: 256 x 256 x 255 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: UCHAR (0) >> fov: 256.000 >> dof: 0 >> xstart: -128.0, xend: 128.0 >> ystart: -128.0, yend: 128.0 >> zstart: -127.5, zend: 127.5 >> >> *T1:* >> mri_info >> /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz >> Volume information for >> /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz >> type: MGH >> dimensions: 256 x 256 x 256 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: UCHAR (0) >> fov: 256.000 >> dof: 0 >> xstart: -128.0, xend: 128.0 >> ystart: -128.0, yend: 128.0 >> zstart: -128.0, zend: 128.0 >> >> *Non-modified brain mask:* >> mri_info /Users/Isabelle/Desktop/S14/brainmask_orig.mgz >> Volume information for /Users/Isabelle/Desktop/S14/brainmask_orig.mgz >> type: MGH >> dimensions: 256 x 256 x 256 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: UCHAR (0) >> fov: 256.000 >> dof: 0 >> xstart: -128.0, xend: 128.0 >> ystart: -128.0, yend: 128.0 >> zstart: -128.0, zend: 128.0 >> >> I am not sure why I get this error and why the change in dimensions, >> zstart and zend between the brainmask and T1. For all other >> participants that do not have an error the information of mri_info for >> dimensions, zstart and zend is the same for the brainmask and T1. So I >> am very confuse as to why these 4 participants are exiting with the >> same error. I am not sure what I am doing wrong in this case. >> >> Thanks, >> >> Isabelle >> >> On 3 Aug 2016, at 06:00, freesurfer-requ...@nmr.mgh.harvard.edu >> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >> >>> Send Freesurfer mailing list submissions to >>> freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> or, via email, send a message with subject or body 'help' to >>> freesurfer-requ...@nmr.mgh.harvard.edu >>> >>> You can reach the person managing the list at >>> freesurfer-ow...@nmr.mgh.harvard.edu >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Freesurfer digest..." >>> >>> >>> Today's Topics: >>> >>> 1. DTI of frontostriatal tracts (Ritobrato Datta) >>> 2. Re: Multiple Comparison Question for surface-based analyses >>> (Douglas N Greve) >>> 3. Re: brain mask and T1 are not the same size (Douglas N Greve) >>> 4. Save Overlay via Command Line (Jordan Chad) >>> 5. Re: MNI coordinates of all the vertices of fsaverage >>> (Douglas N Greve) >>> 6. Retinotopy questions (Xiaomin Yue) >>> 7. Re: DTI of frontostriatal tracts (Anthony Dick) >>> 8. Re: DTI of frontostriatal tracts (Ritobrato Datta) >>> 9. Re: Labels to MNI152, SPM compatible (Thomas Yeo) >>> 10. Re: Multiple Comparison Question for surface-basedanalyses >>> (Ajay Kurani) >>> 11. mapping error (Caroline Beelen) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Tue, 2 Aug 2016 12:26:43 -0400 (EDT) >>> From: Ritobrato Datta <rida...@mail.med.upenn.edu >>> <mailto:rida...@mail.med.upenn.edu>> >>> Subject: [Freesurfer] DTI of frontostriatal tracts >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Message-ID: >>> <1643573287.53129960.1470155203784.javamail.r...@zimbra.upenn.edu >>> <mailto:javamail.r...@zimbra.upenn.edu>> >>> Content-Type: text/plain; charset=utf-8 >>> >>> Hello All, >>> >>> We are studying adolescents with HIV and are interested in >>> frontostriatal tracts (anything from frontal cortex to >>> caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. >>> >>> Is anyone aware of DTI based atlases where these tracts are defined >>> in MNI or some other standard space ? >>> >>> Any suggestions will be very helpful. >>> >>> Best >>> >>> Ri >>> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Tue, 2 Aug 2016 12:54:01 -0400 >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] Multiple Comparison Question for >>> surface-based analyses >>> To: freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <57a0d029.7020...@nmr.mgh.harvard.edu >>> <http://nmr.mgh.harvard.edu>> >>> Content-Type: text/plain; charset=windows-1252; format=flowed >>> >>> I have been doing simulations similar to #1 (Eklund) using >>> surface-based analysis on both thickness and fMRI. I'll prepare a report >>> of the results, but the early indications are that the same effect is in >>> play, though it does not look like the effects are as bad as in Eklund. >>> >>> For thickness analysis using applied smoothing of 5 or 10 mm FWHM, for a >>> voxel-wise threshold of .001, the false positives are appropriate (ie, >>> 5%). For a voxel-wise threshold of .01, the false positives is only a >>> little off (about 7%); for a voxel-wise threshold of .05, the FPR is >>> about 13%. If the data are not smoothed at all, then the false positive >>> rates go way up. The reason appears to be the same as found in Eklund >>> (ie, the autocorrelation function has a heavier-than-Gaussian tail). I >>> did the analysis by randomly selecting 40 subjects from a homogeneous >>> data set of 809 subjects aged 18-25. I then made two groups of 20 >>> subjects each and ran a two-group test, then found clusters significant >>> based on our Monte Carlo (Gaussian) simulations. I repeated this several >>> thousand times. Any significant clusters were interpreted as false >>> positives. These results are much better than Eklund, but Eklund was >>> analyzing fMRI data. >>> >>> I'm still working on the fMRI data. It is much more complicated because >>> the results depend on the assumed stimulus schedule (eg, 10 sec blocks >>> vs 30 sec blocks) and whether a one-group or two-group anaysis is done; >>> nuisance variables also play a role. At very low cluster-forming >>> thresholds (ie, .05), the FPR is roughly 20-30%. At a threshold of .01, >>> the FPR is about 3-13%. At a threshold of .001 are about 1-6%. This is >>> all for an applied smoothing level of 5mm. >>> >>> All of these results are preliminary, so don't take them as true and >>> established yet. As a reminder, you can always do a permutation test >>> using mri_glmfit-sim. Eklund found that permutation did pretty well in >>> most cases. >>> >>> doug >>> >>> >>> On 8/2/16 12:43 AM, Ajay Kurani wrote: >>>> Hello Freesurfer Experts, >>>> Recently there were two article published regarding clusterwise >>>> simulations for volumetric fmri analyses and potential errors for >>>> underestimating clusterwise extent thresholds. >>>> >>>> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >>>> 2) biorxiv.org/content/early/2016/07/26/065862 >>>> <http://biorxiv.org/content/early/2016/07/26/065862> >>>> <http://biorxiv.org/content/early/2016/07/26/065862> >>>> >>>> One issue pointed out from these articles seems software specific, >>>> however the second issue is determining the proper clustersize. The >>>> heavy-tail nature of spatial smoothness seems to be ignored and a >>>> gaussian shape is generally assumed, leading to an underestimation of >>>> the spatial smoothness which can affect cluster size calculations. >>>> The issues are highlighted in the second article above. >>>> >>>> I created my own monte carlo simulation in Freesurfer for a specific >>>> brain template and I wanted to find out if these concerns also apply >>>> to my surface based simulations? I am not sure if it does since the >>>> monte carlo tool is a GRF simulation as opposed to an analytic >>>> equation, however given that these articles were highlighted very >>>> recently, I wanted to ensure I am running things appropriately for >>>> surface based cortical thickness/dti analyses. >>>> >>>> Thanks, >>>> Ajay >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Tue, 2 Aug 2016 13:18:09 -0400 >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] brain mask and T1 are not the same size >>> To: freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <57a0d5d1.20...@nmr.mgh.harvard.edu >>> <http://nmr.mgh.harvard.edu>> >>> Content-Type: text/plain; charset=windows-1252; format=flowed >>> >>> The voxel size and dimensions of all three volumes are the same: 256^3 >>> and 1mm^3. Why do you think they are not? >>> >>> On 08/02/2016 09:17 AM, Isabelle Deschamps wrote: >>>> Yes, of course. The upload is now active. >>>> >>>> Thank you again for your help, >>>> >>>> Isabelle >>>> On 2 Aug 2016, at 08:55, freesurfer-requ...@nmr.mgh.harvard.edu >>>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> >>>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >>>> >>>>> Re: [Freesurfer] brain mask and T1 are not the same size >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> 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 >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@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/ >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Tue, 2 Aug 2016 14:17:28 -0400 >>> From: Jordan Chad <jc...@research.baycrest.org> >>> Subject: [Freesurfer] Save Overlay via Command Line >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> <CA+FdjQX9T0cr50M4awGdW0YJHM3n32FrFcQ9AvGM_+=vmb1...@mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hello, >>> >>> I am trying to perform between-subject statistics on cortical DTI data in >>> certain ROIs. >>> >>> I can do this by overlaying the DTI data on the surfaces on tksurfer, >>> load >>> and mask the label with the ROI, and then go to File -> Save Overlay. >>> After >>> doing this for all subjects I can perform statistics on the output files. >>> >>> However, it is not practical to do this for all >200 subjects for >>> each ROI. >>> Is there a way to go about this process on the command line? >>> >>> Thank You, >>> Jordan Chad >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160802/080b7431/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 5 >>> Date: Tue, 2 Aug 2016 15:40:33 -0400 >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] MNI coordinates of all the vertices of >>> fsaverage >>> To: Sabin Khadka <mr.sabinkha...@gmail.com>, >>> "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <57a0f731.9050...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=utf-8; format=flowed >>> >>> By default they are in talairach. But you can get mni305 by adding >>> --nofixmni to the surfcluster command line >>> >>> On 08/02/2016 03:36 PM, Sabin Khadka wrote: >>>> Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From >>>> previous post you mentioned these are in mni305 space but if I look at >>>> the log file it say TalX, TalY, TalZ. I am a little confused. >>>> >>>> And how can I convert these coordinates to MNI152 space? >>>> >>>> thanks for your help. >>>> >>>> Cheers, >>>> Sabin Khadka >>>> >>>> On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve >>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>> >>>> ps. you can always just load the xyz in the label into matlab and >>>> compute the centroid >>>> >>>> >>>> On 8/1/16 10:23 AM, Sabin Khadka wrote: >>>>> Anyone? >>>>> >>>>> Cheers, >>>>> Sabin Khadka >>>>> >>>>> On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka >>>>> <mr.sabinkha...@gmail.com <mailto:mr.sabinkha...@gmail.com>> wrote: >>>>> >>>>> Hi Doug, I tried to pick up from the thread below to get MNI >>>>> coordinates of each destrieux parcellation region. >>>>> >>>>> >>>>> >>>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html >>>>> >>>>> I created label files from >>>>> mri_annotation2label --subject fsaverage --hemi lh(/rh) >>>>> --annotation aparc.a2009s --outdir label_destrieux # which >>>>> works fine >>>>> >>>>> And I tried to get the coordinates of each labels using >>>>> >>>>> mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness >>>>> --clabel <label file> --sum <output file> --centroid --thmin >>>>> 0 --hemi lh --subject fsaverage >>>>> >>>>> But, all left labels would produce the same coordinates and >>>>> so does right labels. (I've attached few example files here >>>>> with). Also, it says TalX, TalY, TalZ are these coordinates >>>>> in MNI or Talairach? >>>>> >>>>> Thanks for help. >>>>> >>>>> >>>> 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 >>> gr...@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/ >>> >>> >>> >>> ------------------------------ >>> >>> Message: 6 >>> Date: Tue, 2 Aug 2016 21:55:38 +0000 >>> From: Xiaomin Yue <yu...@hotmail.com> >>> Subject: [Freesurfer] Retinotopy questions >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <blu406-eas159bdb45b45ce0f30358a01b3...@phx.gbl> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi, >>> I am running a retinotopy analysis using fsfast 5.3. ?The design has >>> 15 TR blank before and after wedge presented for 30 TR with 7 >>> repeats, and ring presented ?for 24 TR with 7 repeats. ?Here is my >>> analysis:?mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip >>> 15 -TR 1.5 -retinotopy 48 -paradigm rtopy.par. >>> The data doesn't look right. ?I assume that the analysis does require >>> the stimuli presentation as a full circle, which means that the last >>> 15 TR blank was accounted as the stimuli presentation time. If I am >>> correct, ?is there simple way to take care of it in mkanalysis-sess? >>> Second, the ring and wedge were presented in different frequency. It >>> seems that the anslysis-sess does not take this into account in the >>> current configration. Is there a way to specify this?? >>> Thanks very much for the help.? >>> Xiaomin? >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160802/d25a5166/attachment-0001.html >>> -------------- next part -------------- >>> _______________________________________________ >>> Freesurfer mailing list >>> 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. >>> >>> ------------------------------ >>> >>> Message: 7 >>> Date: Tue, 2 Aug 2016 18:34:53 -0400 >>> From: Anthony Dick <ad...@fiu.edu> >>> Subject: Re: [Freesurfer] DTI of frontostriatal tracts >>> To: <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <ef9ff21a-e069-a7b7-74e8-04ab84e11...@fiu.edu> >>> Content-Type: text/plain; charset="windows-1252"; format=flowed >>> >>> Hello, >>> >>> See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832 >>> >>> Anthony >>> >>>> On 8/2/16 12:26 PM, Ritobrato Datta wrote: >>>>> Hello All, >>>>> >>>>> We are studying adolescents with HIV and are interested in >>>>> frontostriatal tracts (anything from frontal cortex to >>>>> caudate/putamen/nucleus accumbens) and tracts connected to the >>>>> amygdala. >>>>> >>>>> Is anyone aware of DTI based atlases where these tracts are defined >>>>> in MNI or some other standard space ? >>>>> >>>>> Any suggestions will be very helpful. >>>>> >>>>> Best >>>>> >>>>> Ri >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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. >>>>> >>> -- >>> Anthony Steven Dick, Ph.D. >>> Associate Professor >>> Director, Cognitive Neuroscience Program and Graduate Certificate in >>> Cognitive Neuroscience >>> Department of Psychology >>> Florida International University Modesto A. Maidique Campus AHC4 454 >>> 11200 S.W. 8th Street >>> Miami, FL 33199 >>> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 >>> Email: ad...@fiu.edu >>> Webpage: http://myweb.fiu.edu/adick >>> Join the Society for the Study of Human Development: >>> http://www.sshdonline.org >>> >>> >>> >>> ------------------------------ >>> >>> Message: 8 >>> Date: Tue, 2 Aug 2016 19:41:51 -0400 (EDT) >>> From: Ritobrato Datta <rida...@mail.med.upenn.edu> >>> Subject: Re: [Freesurfer] DTI of frontostriatal tracts >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <1403815860.53391808.1470181311536.javamail.r...@zimbra.upenn.edu> >>> Content-Type: text/plain; charset=utf-8 >>> >>> Many thanks. >>> >>> Best >>> >>> Ri >>> >>> ----- Original Message ----- >>> From: Anthony Dick <ad...@fiu.edu> >>> To: freesurfer@nmr.mgh.harvard.edu >>> Sent: Tue, 02 Aug 2016 18:34:53 -0400 (EDT) >>> Subject: Re: [Freesurfer] DTI of frontostriatal tracts >>> >>> Hello, >>> >>> See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832 >>> >>> Anthony >>> >>>> On 8/2/16 12:26 PM, Ritobrato Datta wrote: >>>>> Hello All, >>>>> >>>>> We are studying adolescents with HIV and are interested in >>>>> frontostriatal tracts (anything from frontal cortex to >>>>> caudate/putamen/nucleus accumbens) and tracts connected to the >>>>> amygdala. >>>>> >>>>> Is anyone aware of DTI based atlases where these tracts are defined >>>>> in MNI or some other standard space ? >>>>> >>>>> Any suggestions will be very helpful. >>>>> >>>>> Best >>>>> >>>>> Ri >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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. >>>>> >>> -- >>> Anthony Steven Dick, Ph.D. >>> Associate Professor >>> Director, Cognitive Neuroscience Program and Graduate Certificate in >>> Cognitive Neuroscience >>> Department of Psychology >>> Florida International University Modesto A. Maidique Campus AHC4 454 >>> 11200 S.W. 8th Street >>> Miami, FL 33199 >>> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 >>> Email: ad...@fiu.edu >>> Webpage: http://myweb.fiu.edu/adick >>> Join the Society for the Study of Human Development: >>> http://www.sshdonline.org >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> ------------------------------ >>> >>> Message: 9 >>> Date: Wed, 3 Aug 2016 10:43:40 +0800 >>> From: Thomas Yeo <ytho...@csail.mit.edu> >>> Subject: Re: [Freesurfer] Labels to MNI152, SPM compatible >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <canzvntaw8ja0f7npk9erqsqpcbhcgxrrvnm7t3wftqtnyn4...@mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi Matyas, >>> >>> In freeview, looks fine to me. See attached. >>> >>> Can you send us your screenshot? >>> >>> Regards, >>> Thomas >>> >>> On Tue, Aug 2, 2016 at 9:39 PM, Maty?? Kuhn <matyas.k...@gmail.com> >>> wrote: >>>> The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >>>> comes from >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, >>>> and the description says it is the FSL MNI152 1mm template interpolated >>>> and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume >>>> (obtained by putting the FSL MNI152 1mm template through recon-all ). So >>>> I supposed it is in MNI305 after it was processed with freesurfer. When >>>> I overlap the >>>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and >>>> Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not >>>> in MNI152. >>>> >>>> When I add the --invertmtx then the result is still the same, empty >>>> image. >>>> >>>> I uploaded those images here: >>>> https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip , >>>> if you want to try yourself. >>>> >>>> >>>> Thank you, >>>> >>>> Matyas >>>> >>>> >>>> >>>> Dne 2.8.2016 v 14:55 Douglas Greve napsal(a): >>>>> From the names, it looks like both the seg vol and the template >>>>> vol are both in mni152. Where did >>>>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >>>>> come from? One thing you can try is to invert the registration by >>>>> adding --invertmtx to the command line. >>>>> >>>>> >>>>> On 8/2/16 8:18 AM, Maty?? Kuhn wrote: >>>>>> Hi Freesurfer experts, >>>>>> >>>>>> I just started to use Freesurfer and I was wondering how can I convert >>>>>> images from MNI305 which uses Freesurfer to MNI152 which is used >>>>>> by SPM. >>>>>> We would like to get MNI152 template of Yeo parcelation >>>>>> ( ) >>>>>> so we can overlay with our results from SPM fMRI analysis. >>>>>> >>>>>> I tried this: >>>>>> mri_label2vol --seg >>>>>> /path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >>>>>> \ >>>>>> --temp >>>>>> /path_to_analysis/Template_T1_IXI555_MNI152.nii \ >>>>>> --reg >>>>>> $FREESURFER_HOME/average/mni152.register.dat \ >>>>>> --o /path_to_analysis/output_mni152.nii >>>>>> >>>>>> which resulted in image full of zeros (so maybe problem with >>>>>> registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152 >>>>>> template which is used by Computational anatomical toolbox 12 for SPM >>>>>> from Christian Gaser and his group. >>>>>> >>>>>> Thanks in advance for any suggestions, >>>>>> >>>>>> Matyas >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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. >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: Screen Shot 2016-08-03 at 10.41.31 AM.png >>> Type: image/png >>> Size: 222427 bytes >>> Desc: not available >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/b575e32f/attachment-0001.png >>> >>> ------------------------------ >>> >>> Message: 10 >>> Date: Wed, 3 Aug 2016 02:45:47 -0500 >>> From: Ajay Kurani <dr.ajay.kur...@gmail.com> >>> Subject: Re: [Freesurfer] Multiple Comparison Question for >>> surface-basedanalyses >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <CA+uskrDgnhv2SaRJHGHUQQVJseuEKQC6ov-=f7n0dyrtsge...@mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi Doug, >>> Thank you very much for your update regarding this issue. >>> >>> 1)Just curious, will LGI be included in this report as this is another >>> analysis of interest? >>> >>> 2)As for the cortical thickness I originally used 15mm in the analysis so >>> based on your email I think using 5-10mm may be more prudent in order to >>> minimize FPR. From your email, I understand that mris_surf2surf >>> (command I >>> use to convert individual subject to fsaverage or template and smooth to >>> 10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into >>> account the long tail distribution. Does this mean that when using >>> mri_mcsim on my own template, the cluster extents for a given smoothness >>> will be undersampled due to the fact that the "true" smoothness is more >>> than what is estimated in the simulation, correct? For instance, when I >>> select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm >>> estimate), and I would select a given cluster extent for p=0.05. >>> However, >>> in this case, 15mm may translate to a larger FWHM than the estimated >>> 21mm, >>> correct? >>> >>> 3)You mentioned that I can use mri_glmfit-sim which is permutation >>> testing >>> based. I am struggling a bit in understanding how this differs from the >>> simulation ran with mri_mcsim/qdec? Does qdec monte carlo simulation >>> option run mri_glmfit-sim in the background to estimate the smoothness >>> which looks up the cluster extent within the mri_mcsim based on the >>> estimated FWHM? If so, is this estimate incorrect due to the fact >>> that the >>> long tails are not taken into account? >>> >>> >>> Thanks, >>> Ajay >>> >>> On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>> wrote: >>> >>>> Hello Freesurfer Experts, >>>> Recently there were two article published regarding clusterwise >>>> simulations for volumetric fmri analyses and potential errors for >>>> underestimating clusterwise extent thresholds. >>>> >>>> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >>>> 2) biorxiv.org/content/early/2016/07/26/065862 >>>> >>>> One issue pointed out from these articles seems software specific, >>>> however >>>> the second issue is determining the proper clustersize. The heavy-tail >>>> nature of spatial smoothness seems to be ignored and a gaussian shape is >>>> generally assumed, leading to an underestimation of the spatial >>>> smoothness >>>> which can affect cluster size calculations. The issues are >>>> highlighted in >>>> the second article above. >>>> >>>> I created my own monte carlo simulation in Freesurfer for a specific >>>> brain >>>> template and I wanted to find out if these concerns also apply to my >>>> surface based simulations? I am not sure if it does since the monte >>>> carlo >>>> tool is a GRF simulation as opposed to an analytic equation, however >>>> given >>>> that these articles were highlighted very recently, I wanted to >>>> ensure I am >>>> running things appropriately for surface based cortical thickness/dti >>>> analyses. >>>> >>>> Thanks, >>>> Ajay >>>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/f75c8a4a/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 11 >>> Date: Wed, 3 Aug 2016 10:00:18 +0000 >>> From: Caroline Beelen <caroline.bee...@kuleuven.be> >>> Subject: [Freesurfer] mapping error >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <40b86b2ee4c24b96b8d585eb822a0...@icts-s-exmbx26.luna.kuleuven.be> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> >>> Dear FS, >>> >>> An aparc.annot ctab file was created but I got the following error: >>> Colortable:aparc.annot.ctab >>> Annotname: myaparc >>> Nhitsfile nhits.mgh >>> Nlabels 6 >>> Labeltresh 0 0.00000 >>> Loading freesurfer/fsaverage/surf/lh.orig >>> 1 -1 not found >>> 2 -1 not found >>> 3 -1 not found >>> Etc... >>> Mapping unhit to unknown >>> Found 132101 unhit vertices >>> Writing annot to freesurfer/fsaverage/lh.myaparc.annot >>> >>> I guess my ctab file is incorrect? I included an example of a label >>> with it. >>> >>> Thanks again for your help. >>> >>> Caroline >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/762d4854/attachment.html >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: aparc.annot.ctab >>> Type: application/octet-stream >>> Size: 782 bytes >>> Desc: aparc.annot.ctab >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/762d4854/attachment.obj >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: lh.fusiform.label >>> Type: application/octet-stream >>> Size: 223962 bytes >>> Desc: lh.fusiform.label >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/762d4854/attachment-0001.obj >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> End of Freesurfer Digest, Vol 150, Issue 5 >>> ****************************************** >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
