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Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
by Antonin Skoch 20 Apr '17

20 Apr '17

Dear Bruce, I am uploading 3 example subjects processed both by v5.3 and v6.0 I referred to in the screenshots in my previous posts: Subj 1 - large leak of white surface outside brain in v6.0, not present in v5.3. RAS coords -53,-1,75 Subj 2 - another measurement of identical subject - white surface is leaking at three spots dramatically outwards towards pial surface in v6.0. RAS coords -48,-2,64 Subj 3 - leak of white surface outside brain. Both v5.3 and v6.0 has error in white surface, but the error is much larger in v6.0. RAS coords 48,5,78 The v6.0 version is without removing -mprage. Removing -mprage in v6.0 caused only very small change in brain.mgz, the filtering is still much higher than in v5.3 and still causes the white matter surface leak. The subjects are in files mri_normalize_v5.3.tar.gz and mri_normalize_v6.0.tar.gz. I would very welcome any suggestions how to: 1. Prevent new white surface errors in v6.0 in subjects previously processed and edited by v5.3 2. How to make edits to modify white/pial surface location where wm.mgz editing is not sufficient. I tried workaround of directly editing 001.mgz as I discussed in thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html This is very time consuming. Better way is maybe to consider implementation of option for mris_make_surfaces similar to -overlay option for cases where wm.mgz voxels have value 1 as I discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52730.html Antonin Hi Antonin yes, the -mprage flag is likely to be at least one source of the differences. It makes the normalization more aggressive (since mprage trades higher CNR for lower SNR). I'm surprised removing it didn't help. I think that changing things like wlo could also help depending on how wrong the normalization is. Upload a subject and I'll take a look cheers Bruce On Thu, 20 Apr 2017, Antonin Skoch wrote: Dear David, thank you for the feedback; I saw your posts concerning edits and responded to them, see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html Just my case is not concerning poor response to the edits (which I believe is not systematically different between 5.3 and 6.0), my concern is that the data processed by v6.0 need much more wm.mgz edits than data processed by v5.3. I think that my issue lies in -normalization2 step of recon-all. One of the difference between v5.3 and v6.0 is that by default the -mprage flag is passed to mri_normalize. This affects several parameters inside mri_normalize. I tried to reprocess my subjects using v6.0 with -no-mprage, but unfortunately this did not help. See the example screenshots processed by v5.3 and v6.0 with -no-mprage: The brain.mgz is still more aggressively filtered in v6.0 and there is much more prominent leak of ?h.white outside brain, which is probably caused by extended filtration which affects GM/WM contrast. Looking at the source code of mri_normalize.c I did not comprehend where the basis of the issue lies, but in any case there are big differences in mri_normalize.c code between versions. Antonin From: David Semanek <seman...(a)nyspi.columbia.edu> To: Antonin Skoch <a...(a)ikem.cz>, "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: 4/20/2017 3:41 PM Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast Agreed. A validated protocol run on a very large group of subjects in 5.3 was attempted with similar data in 6.0 and not only was the longitudinal edit stream nearly non-functional for white matter edits, cross edit performance was disappointing. I am currently waiting on a response to these potential issues before pursuing further work with 6.0. Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From: Antonin Skoch <a...(a)ikem.cz> Date: Wednesday, April 19, 2017 at 5:23 PM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast Dear experts, I am sending just one more example to illustrate issue with white surface estimation in v6.0. See the attached screenshots: In v6.0 there seems to be insufficient contrast in brain.finalsurfs.mgz, so the white surface is leaking at three spots dramatically outwards towards pial surface. The white surface in v5.3 looks much more anatomically relevant in the same spot. Could you please comment on how to avoid such issues in v.6.0? Regards, Antonin Skoch

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R: Re: R: Re: R: Re: FSGD file FS-FAST
by stdp82＠virgilio.it 20 Apr '17

20 Apr '17

I would look for differences among 4 different groups (A, B, C, D). e.g. I expected that the impaiment is A<B<C<D. Thus, I should opt for G1+G3 vs G2+G4 or G1+G2 vs G3+G4? Other option? Sorry, I'm confused on this matter and worried to produce correct results. Thank you very much. Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 20-apr-2017 17.07 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: FSGD file FS-FAST > > > >On 04/19/2017 04:37 PM, stdp82(a)virgilio.it wrote: >> I'm sorry but it not clear to me. There are 2 factors, 2 levels, while I have 1 >> Factor, 4 Levels >It is still four groups. >> In particular, have I looked to difference between Group1+Group2 vs >> Group3+Group4? >> Is it correct 0.5 -0.5 0.5 -0.5? >That will give you G1+G3 vs G2+G4 >> Thanks >> >> Stefano >> >>> ----Messaggio originale---- >>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> Data: 19-apr-2017 19.23 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: FSGD file FS-FAST >>> >>> There is one for 4 Groups with 1 covariate. Use that one and do not >>> include the covariate. >>> >>> >>> On 04/19/2017 02:37 AM, stdp82(a)virgilio.it wrote: >>>> I did not find it for for 4 Groups (1 Factor, 4 Levels), Zero Covariates. >>>> >>>> I need for check to avoid error on my analysis. >>>> Please could you say me whether the followed codes are correct. >>>> >>>> A) Group effect >>>> 1 -1 0 0 >>>> 1 0 -1 0 >>>> 1 0 0 -1 >>> This will generate an F test for the group effect >>>> B) 0.5 0.5 -0.5 -0.5 >>> This looks like it will test a difference between Group1-and-2 vs >>> Group3-and-4 >>>> Many thanks. >>>> >>>> Stefano >>>> >>>> >>>> >>>> ----Messaggio originale---- >>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>> Data: 19-apr-2017 3.50 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] FSGD file FS-FAST >>>> >>>> Have you looked at >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? >>>> >>>> >>>> On 4/17/17 5:32 PM, stdp82(a)virgilio.it wrote: >>>>> Hi list, >>>>> please could you suggest me the group.effect.mtx and the file.mtx >>>>> relative to Null Hypothesis for 4 Groups (1 Factor, 4 Levels), >>>>> Zero Covariates. DODS or DOSS. >>>>> Thanks >>>>> Stefano >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the e- mail >>> contains patient information, please contact the Partners Compliance HelpLine >> at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >>> but does not contain patient information, please contact the sender and >> properly >>> dispose of the e-mail. >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"
by Taylor, Johnmark 20 Apr '17

20 Apr '17

The contents of the runlist file are: 014 016 018 026 028 030 040 042 044 052 054 056 As a reminder, the error involved is: "ERROR: cannot find [subject_path]/bold/014/fmc.sm0". On Thu, Apr 20, 2017 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)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-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)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: Worse determination of ?h.white with v6.0 in comparison > to v5.3 - worse GM/WM contrast (Bruce Fischl) > 2. Re: White matter atrophy (Douglas N Greve) > 3. Re: Worse determination of ?h.white with v6.0 in comparison > to v5.3 - worse GM/WM contrast (Bruce Fischl) > 4. Re: mri_glmfit error with aparc table flag (Douglas N Greve) > 5. Re: plot-twf-sess display error (Douglas N Greve) > 6. Re: 5. Re: Selxavg3-sess Looking for (and can't find) > "fmc.sm0" (Douglas N Greve) > 7. Re: Using registration.dat to register a dataset (Jacobson, Aaron) > 8. Re: Using registration.dat to register a dataset (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Apr 2017 11:09:58 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in > comparison to v5.3 - worse GM/WM contrast > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: David Semanek <SemanekD(a)nyspi.columbia.edu> > Message-ID: > <alpine.LRH.2.20.1704201108490.32551(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Antonin > > yes, the -mprage flag is likely to be at least one source of the > differences. It makes the normalization more aggressive (since mprage > trades higher CNR for lower SNR). I'm surprised removing it didn't help. I > think that changing things like wlo could also help depending on how wrong > the normalization is. Upload a subject and I'll take a look > > cheers > Bruce > > > On Thu, 20 Apr 2017, > Antonin Skoch wrote: > > > Dear David, > > > > thank you for the feedback; I saw your posts concerning edits and > responded > > to them, see > > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html > > > > Just my case is not concerning poor response to the edits (which I > believe > > is not systematically different between 5.3 and 6.0), my concern is that > the > > data processed by v6.0 need much more wm.mgz edits than data processed by > > v5.3. > > > > I think that my issue lies in -normalization2 step of recon-all. One of > the > > difference between v5.3 and v6.0 is that by default the -mprage flag is > > passed to mri_normalize. This affects several parameters inside > > mri_normalize. I tried to reprocess my subjects using v6.0 with > -no-mprage, > > but unfortunately this did not help. > > > > See the example screenshots processed by v5.3 and v6.0 with -no-mprage: > > > > The brain.mgz is still more aggressively filtered in v6.0 and there is > much > > more prominent leak of ?h.white outside brain, which is probably caused > by > > extended filtration which affects GM/WM contrast. > > > > Looking at the source code of mri_normalize.c I did not comprehend where > the > > basis of the issue lies, but in any case there are big differences in > > mri_normalize.c code between versions. > > > > Antonin > > > > From: David Semanek <SemanekD(a)nyspi.columbia.edu> > > To: Antonin Skoch <ansk(a)ikem.cz>, "freesurfer(a)nmr.mgh.harvard.edu" > > <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: 4/20/2017 3:41 PM > > Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in > > comparison to v5.3 - worse GM/WM contrast > > > > Agreed. A validated protocol run on a very large group of > > subjects in 5.3 was attempted with similar data in 6.0 and not > > only was the longitudinal edit stream nearly non-functional for > > white matter edits, cross edit performance was disappointing. > > > > ? > > > > I am currently waiting on a response to these potential issues > > before pursuing further work with 6.0. > > > > ? > > > > Best, > > > > ? > > > > David P. Semanek, HCISPP > > > > Research Technician, Posner Lab > > > > Division of Child and Adolescent Psychiatry > > > > Columbia University Medical Center > > > > New York State Psychiatric Institute > > > > 1051 Riverside Drive, Pardes Bldg. Rm. 2424 > > > > New York, NY 10032 > > > > PH: (646) 774-5885 > > > > ? > > > > IMPORTANT NOTICE:? This e-mail is meant only for the use of the > > intended recipient.? It may contain confidential information which is > > legally privileged or otherwise protected by law.? If you received > > this e-mail in error or from someone who was not authorized to send it > > to you, you are strictly prohibited from reviewing, using, > > disseminating, distributing or copying the e-mail.? PLEASE NOTIFY US > > IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM > > YOUR SYSTEM.? Thank you for your cooperation. > > > > ? > > > > From: Antonin Skoch <ansk(a)ikem.cz> > > Date: Wednesday, April 19, 2017 at 5:23 PM > > To: <freesurfer(a)nmr.mgh.harvard.edu> > > Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in > > comparison to v5.3 - worse GM/WM contrast > > > > ? > > > > Dear experts, > > > > I am sending just one more example to illustrate issue with white > > surface estimation in v6.0. See the attached screenshots: In v6.0 > > there seems to be insufficient contrast in brain.finalsurfs.mgz, so > > the white surface is leaking at three spots dramatically outwards > > towards pial surface. The white surface in v5.3 looks much more > > anatomically relevant in the same spot. > > > > Could you please comment on how to avoid such issues in v.6.0? > > > > Regards, > > > > Antonin Skoch > > > > > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 20 Apr 2017 11:14:20 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] White matter atrophy > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <f1cefc9e-424e-4cdb-0721-d19a83caf4da(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Not other than just comparing the total WM volume. I guess you could do > some type of VBM analysis, but I would recommend using a package that > specializes in that type of analysis > > > On 04/20/2017 07:42 AM, John Anderson wrote: > > Dear Freesurfer experts, > > I know how to do cortical thickness group analysis using Freesurfer, > > also I know how to use Qdec to compare groups regarding gray matter > > volume differences, cortical thickness, curvatures, area,... etc. > > I am wondering if there is any way in Freesurfer to study the > > difference in white matter volume between two groups? > > > > I highly appreciate any suggestion! > > John > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 3 > Date: Thu, 20 Apr 2017 11:14:45 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in > comparison to v5.3 - worse GM/WM contrast > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: Antonin Skoch <ansk(a)ikem.cz> > Message-ID: > <alpine.LRH.2.20.1704201113370.32551(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi David > > I can take a look at a subject of yours as well if you upload it (both 5.3 > and 6.0 processed versions if you have them) and point me at voxel coords. > The white surface is by design insensitive to local variations which is > what makes it robust, but also makes it more difficult to modify. I'll take > a look and think about how to make it easier > > cheers > Bruce > > > On Thu, 20 Apr 2017, David Semanek > wrote: > > > > > Thank you for looking into the deeper mechanics of this issue. In my > case I > > am dealing with motion contaminated 1.5T data which require extensive and > > somewhat intricate edits to the white matter bleed into the pial > surface, as > > well as into dura. In working with a past dataset of similar > characteristics > > I was consistently impressed with fs 5.3?s ability to properly segment > white > > matter in most cases and the robustness of the editing response. I was > left > > with the overall impression that freesurfer handled noisy data quite well > > with a little bit of help. Our results from the analysis of corrected vs > > uncorrected data were very strong in favor of the editing protocol. > > > > ? > > > > My experience with 6.0, aside from any issues of information not > propagating > > through the longitudinal stream, is that there are many more cases in > which > > the white matter surface will not conform to the edits suggested in the > > white matter volume. A number of tricks to ?convince? the software in > cases > > of non-response used in 5.3, such as making sure to complete edits on > > adjacent slices, are simply not effective. I am left with the overall > > impression that I have very little control over the white matter surfaces > > really, beyond making suggestions which may only slightly change the > degree > > of error, but does not fundamentally change the structure of the white > > matter surface enough to remove the misclassification entirely in many > > cases. > > > > ? > > > > Best, > > > > ? > > > > David P. Semanek, HCISPP > > > > Research Technician, Posner Lab > > > > Division of Child and Adolescent Psychiatry > > > > Columbia University Medical Center > > > > New York State Psychiatric Institute > > > > 1051 Riverside Drive, Pardes Bldg. Rm. 2424 > > > > New York, NY 10032 > > > > PH: (646) 774-5885 > > > > ? > > > > IMPORTANT NOTICE:? This e-mail is meant only for the use of the intended > > recipient.? It may contain confidential information which is legally > > privileged or otherwise protected by law.? If you received this e-mail in > > error or from someone who was not authorized to send it to you, you are > > strictly prohibited from reviewing, using, disseminating, distributing or > > copying the e-mail.? PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM.? Thank you for your > > cooperation. > > > > ? > > > > From: Antonin Skoch <ansk(a)ikem.cz> > > Date: Thursday, April 20, 2017 at 10:25 AM > > To: David Semanek <SemanekD(a)nyspi.columbia.edu>, > > "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in > > comparison to v5.3 - worse GM/WM contrast > > > > ? > > > > Dear David, > > > > thank you for the feedback; I saw your posts concerning edits and > responded > > to them, see > > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html > > > > Just my case is not concerning poor response to the edits (which I > believe > > is not systematically different between 5.3 and 6.0), my concern is that > the > > data processed by v6.0 need much more wm.mgz edits than data processed by > > v5.3. > > > > I think that my issue lies in -normalization2 step of recon-all. One of > the > > difference between v5.3 and v6.0 is that by default the -mprage flag is > > passed to mri_normalize. This affects several parameters inside > > mri_normalize. I tried to reprocess my subjects using v6.0 with > -no-mprage, > > but unfortunately this did not help. > > > > See the example screenshots processed by v5.3 and v6.0 with -no-mprage: > > > > The brain.mgz is still more aggressively filtered in v6.0 and there is > much > > more prominent leak of ?h.white outside brain, which is probably caused > by > > extended filtration which affects GM/WM contrast. > > > > Looking at the source code of mri_normalize.c I did not comprehend where > the > > basis of the issue lies, but in any case there are big differences in > > mri_normalize.c code between versions. > > > > Antonin > > > > From: David Semanek <SemanekD(a)nyspi.columbia.edu> > > To: Antonin Skoch <ansk(a)ikem.cz>, "freesurfer(a)nmr.mgh.harvard.edu" > > <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: 4/20/2017 3:41 PM > > Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in > > comparison to v5.3 - worse GM/WM contrast > > > > Agreed. A validated protocol run on a very large group of > > subjects in 5.3 was attempted with similar data in 6.0 and not > > only was the longitudinal edit stream nearly non-functional for > > white matter edits, cross edit performance was disappointing. > > > > ? > > > > I am currently waiting on a response to these potential issues > > before pursuing further work with 6.0. > > > > ? > > > > Best, > > > > ? > > > > David P. Semanek, HCISPP > > > > Research Technician, Posner Lab > > > > Division of Child and Adolescent Psychiatry > > > > Columbia University Medical Center > > > > New York State Psychiatric Institute > > > > 1051 Riverside Drive, Pardes Bldg. Rm. 2424 > > > > New York, NY 10032 > > > > PH: (646) 774-5885 > > > > ? > > > > IMPORTANT NOTICE:? This e-mail is meant only for the use of the > > intended recipient.? It may contain confidential information which is > > legally privileged or otherwise protected by law.? If you received > > this e-mail in error or from someone who was not authorized to send it > > to you, you are strictly prohibited from reviewing, using, > > disseminating, distributing or copying the e-mail.? PLEASE NOTIFY US > > IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM > > YOUR SYSTEM.? Thank you for your cooperation. > > > > ? > > > > From: Antonin Skoch <ansk(a)ikem.cz> > > Date: Wednesday, April 19, 2017 at 5:23 PM > > To: <freesurfer(a)nmr.mgh.harvard.edu> > > Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in > > comparison to v5.3 - worse GM/WM contrast > > > > ? > > > > Dear experts, > > > > I am sending just one more example to illustrate issue with white > > surface estimation in v6.0. See the attached screenshots: In v6.0 > > there seems to be insufficient contrast in brain.finalsurfs.mgz, so > > the white surface is leaking at three spots dramatically outwards > > towards pial surface. The white surface in v5.3 looks much more > > anatomically relevant in the same spot. > > > > Could you please comment on how to avoid such issues in v.6.0? > > > > Regards, > > > > Antonin Skoch > > > > > > > > ------------------------------ > > Message: 4 > Date: Thu, 20 Apr 2017 11:16:16 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_glmfit error with aparc table flag > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <9a07f2b3-c9b9-cfba-8450-036c83a8b6ba(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 04/20/2017 11:08 AM, miracle ozzoude wrote: > > Thank very much Doug. Also, I was looking into the > > annotval2surfoverlay file and I have couple of questions. > > % Run these commands in matlab > > % annotnames = strvcat('superiortemporal','insula','postcentral'); > > % annotvals = [1.1 2.2 3.7]; > > % annotfile = '~/paul_analysis/fsaverage/label/lh.aparc.annot'; > > % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); > > % clear mri > > % mri.vol = surfoverlay; > > % MRIwrite(mri,'vals.mgh'); > > % > > 1) Correct me if I am wrong, the annotation values (annotvals) are > > from results after correcting for multiple comparisons using mri_fdr? > They can be anything that you have one value per annotation. > > 2) Is this correct way to add octave path to freesurfer's path? > Sorry, I have no idea > > setenv FS_USE_OCTAVE 4.0.3 > > > > setenv FS_OCTAVE_LIB /Applications/octave/lib > > setenv FS_OCTAVE_BIN /Application/octave/binary > > Thanks, > > Best, > > Paul > > > > On Thu, Apr 20, 2017 at 10:55 AM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > you can get it here > > > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/ > annotval2surfoverlay.m > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/ > annotval2surfoverlay.m> > > > > On 04/20/2017 10:10 AM, miracle ozzoude wrote: > > > Hello Doug, > > > I downloaded and installed octave. However, I can't find the > > > annotval2surfoverlay.m file in the matlab directory of freesurfer. > > > Does it come with FS v6 or do i need to download the file? Also, > > I was > > > looking into the annotval2surfoverlay file and I have couple of > > > questions. > > > % Run these commands in matlab > > > % annotnames = strvcat('superiortemporal','insula','postcentral'); > > > % annotvals = [1.1 2.2 3.7]; > > > % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; > > > % surfoverlay = > > annotval2surfoverlay(annotvals,annotnames,annotfile); > > > % clear mri > > > % mri.vol = surfoverlay; > > > % MRIwrite(mri,'vals.mgh'); > > > % > > > 1) Are the annotation values (annotvals) from results after > > correcting > > > for multiple comparisons using mri_fdr? > > > 2) Do I need to add octave path to freesurfer PATH like the example > > > below? > > > setenv FS_USE_OCTAVE 4.0.3 > > > > > > setenv FS_OCTAVE_LIB /Applications/octave/lib > > > setenv FS_OCTAVE_BIN /Application/octave/binary > > > > > > On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve > > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > > > I think that will work > > > > > > > > > On 04/19/2017 03:33 PM, miracle ozzoude wrote: > > > > Hello Doug, > > > > Do you think writing the script with octave can substitute > for > > > matlab? > > > > I am using FS v6.0 and I have the annotval2surfoverlay.m. > > Thanks > > > > Best, > > > > Paul > > > > > > > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve > > > > <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu > >> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto: > greve(a)nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > > > Sorry, I don't have another solution for you. > > > > > > > > > > > > On 04/19/2017 01:42 PM, miracle ozzoude wrote: > > > > > Thanks Doug. However, I am running freesurfer > > analysis on my > > > > personal > > > > > computer and I don't have matlab. Also, I don't know > how > > > this matlab > > > > > script works/ matlab works. Any instructions on how > > to use > > > it or > > > > > alternate? Please and thank you. > > > > > Best, > > > > > Paul. > > > > > > > > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > > > > > <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu > >>> > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > > It is a table of data, so you can't visualize it > > > directly on > > > > anything. > > > > > You can try using annotval2surfoverlay.m to create > a > > > surface > > > > > overlay of > > > > > the data. > > > > > > > > > > > > > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > > > > > Hello Doug, > > > > > > It worked. The issue was due to formatting error > > > with the > > > > aparc > > > > > file. > > > > > > Also, I was trying to visualize the result on the > > > surface > > > > using > > > > > > freeview -f fsaverage/lh.pial -viewport 3d > > (clicking > > > > overlay on > > > > > > freeview and loading the sig.mgh). However, i > > got an > > > error " > > > > > failed to > > > > > > display overlay". How can I visualize the > > result? Thanks > > > > > > Best, > > > > > > Paul > > > > > > > > > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > > > > > <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>> > > > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > > > > > > > > > > > You have a table of data, so no template is > > > needed. If you > > > > > put the > > > > > > --surf before the --table, it probably > > runs, but it > > > > will ignore > > > > > > the surface > > > > > > > > > > > > > > > > > > On 4/18/17 9:58 PM, miracooloz(a)gmail.com > > <mailto:miracooloz@gmail.com> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > > > <mailto:miracooloz@gmail.com > > <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com > > <mailto:miracooloz@gmail.com>>> > > > > > <mailto:miracooloz@gmail.com > > <mailto:miracooloz@gmail.com> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > > > <mailto:miracooloz@gmail.com > > <mailto:miracooloz@gmail.com> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > > <mailto:miracooloz@gmail.com > > <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com > > <mailto:miracooloz@gmail.com>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> > wrote: > > > > > >> Thanks doug. Does it mean when using the > > --table > > > > flag, you > > > > > can't > > > > > >> use the fsaverage template? I came across > > several > > > > post in the > > > > > >> forum that used "--surf fsaverage lh "? > > and it > > > worked. > > > > > >> Best, > > > > > >> Paul > > > > > >> > > > > > >> Sent from my BlackBerry 10 smartphone. > > > > > >> *From: *Douglas Greve > > > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > > > > >> *To: *freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > >> *Reply To: *Freesurfer support list > > > > > >> *Subject: *Re: [Freesurfer] mri_glmfit error > > > with aparc > > > > > table flag > > > > > >> > > > > > >> > > > > > >> Don't include --surf fsaverage lh. It > > thinks the > > > > input is a > > > > > >> surface, not a table > > > > > >> > > > > > >> > > > > > >> > > > > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > > > > > >>> Hello freesurfer, > > > > > >>> I am trying to run mri_glmfit with the > > --table > > > flag. My > > > > > >>> aparc_lh_thick_stats.txt contain entorhinal and > > > > > parahippocampal > > > > > >>> thickness values for 32 subjects. I ran > > the glm > > > > command and > > > > > >>> received an error. Please, how can i > > solve this > > > > issue? I have > > > > > >>> included my command, fsgd file, contrast > > > matrix and > > > > error > > > > > below. > > > > > >>> Thanks > > > > > >>> Best, > > > > > >>> Paul > > > > > >>> > > > > > >>> GLM command: mri_glmfit --table > > > aparc_lh_thick_stats.txt > > > > > --fsgd > > > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf > > > fsaverage lh > > > > > --cortex > > > > > >>> --glmdir lh.thickness.glmdir > > > > > >>> > > > > > >>> > > > > > >>> ERROR= "gdfRead(): reading age.fsgd > > > > > >>> > > > > > >>> INFO: DeMeanFlag keyword not found, > > DeMeaning will > > > > NOT be > > > > > done. > > > > > >>> > > > > > >>> Continuous Variable Means (all subjects) > > > > > >>> > > > > > >>> 0 Age 39.9375 17.3312 > > > > > >>> > > > > > >>> Class Means of each Continuous Variable > > > > > >>> > > > > > >>> 1 Group1 35.6316 > > > > > >>> > > > > > >>> 2 Group2 46.2308 > > > > > >>> > > > > > >>> INFO: gd2mtx_method is dods > > > > > >>> > > > > > >>> Reading source surface > > > > > >>> > > > > > > > > > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/ > fsaverage/surf/lh.white > > > > > >>> > > > > > >>> Number of vertices 163842 > > > > > >>> > > > > > >>> Number of faces 327680 > > > > > >>> > > > > > >>> Total area 65416.984375 > > > > > >>> > > > > > >>> AvgVtxArea 0.399269 > > > > > >>> > > > > > >>> AvgVtxDist 0.721953 > > > > > >>> > > > > > >>> StdVtxDist 0.195470 > > > > > >>> > > > > > >>> > > > > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 > > 22:02:40 > > > > zkaufman > > > > > Exp $ > > > > > >>> > > > > > >>> cwd > > > /Users/MiracleOz/Documents/improvervsdeclinermri > > > > > >>> > > > > > >>> cmdline mri_glmfit.bin --table > > > > aparc_lh_thick_stats.txt --fsgd > > > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf > > > fsaverage lh > > > > > --cortex > > > > > >>> --glmdir lh.thickness.glmdir > > > > > >>> > > > > > >>> sysname Darwin > > > > > >>> > > > > > >>> hostname MacBook-Pro.local > > > > > >>> > > > > > >>> machine x86_64 > > > > > >>> > > > > > >>> user MiracleOz > > > > > >>> > > > > > >>> FixVertexAreaFlag = 1 > > > > > >>> > > > > > >>> UseMaskWithSmoothing 1 > > > > > >>> > > > > > >>> OneSampleGroupMean 0 > > > > > >>> > > > > > >>> y > > > > > >>> > > > > > > > > > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ > lh_thick_stats.txt > > > > > >>> > > > > > >>> logyflag 0 > > > > > >>> > > > > > >>> usedti 0 > > > > > >>> > > > > > >>> FSGD age.fsgd > > > > > >>> > > > > > >>> labelmask > > > > > >>> > > > > > > > > > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/ > fsaverage/label/lh.cortex.label > > > > > >>> > > > > > >>> maskinv 0 > > > > > >>> > > > > > >>> glmdir lh.thickness.glmdir > > > > > >>> > > > > > >>> IllCondOK 0 > > > > > >>> > > > > > >>> ReScaleX 1 > > > > > >>> > > > > > >>> DoFFx 0 > > > > > >>> > > > > > >>> Creating output directory > > lh.thickness.glmdir > > > > > >>> > > > > > >>> Loading y from > > > > > >>> > > > > > > > > > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ > lh_thick_stats.txt > > > > > >>> > > > > > >>> Found 66 data colums > > > > > >>> > > > > > >>> Found 0 data rows > > > > > >>> > > > > > >>> INFO: gd2mtx_method is dods > > > > > >>> > > > > > >>> Saving design matrix to > > lh.thickness.glmdir/Xg.dat > > > > > >>> > > > > > >>> Computing normalized matrix > > > > > >>> > > > > > >>> Normalized matrix condition is 32.2165 > > > > > >>> > > > > > >>> Matrix condition is 20734.7 > > > > > >>> > > > > > >>> Found 149955 points in label. > > > > > >>> > > > > > >>> ERROR: mri_reshape: number of elements > > cannot > > > change > > > > > >>> > > > > > >>> nv1 = 163842, nv1 = 66 > > > > > >>> > > > > > >>> search space = 82219.962936 > > > > > >>> > > > > > >>> ERROR: dimension mismatch between y and X. > > > > > >>> > > > > > >>> y has 0 inputs, X has 32 rows." > > > > > >>> > > > > > >>> FSGD file: GroupDescriptorFile 1 > > > > > >>> > > > > > >>> Title MOT > > > > > >>> > > > > > >>> Class Group1 > > > > > >>> > > > > > >>> Class Group2 > > > > > >>> > > > > > >>> Variables Age > > > > > >>> > > > > > >>> Input 01053p Group1 23 > > > > > >>> > > > > > >>> Input 01054p Group1 43 > > > > > >>> > > > > > >>> Input 01061p Group2 39 > > > > > >>> > > > > > >>> Input 01062p Group2 19 > > > > > >>> > > > > > >>> Input 01074p Group2 28 > > > > > >>> > > > > > >>> .............. (I have more participants) > > > > > >>> > > > > > >>> > > > > > >>> CONTRAST MATRIX: 1 -1 0 0 > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> ______________________________ > _________________ > > > > > >>> Freesurfer mailing list > > > > > >>> Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > >>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > >>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> > > > > > >> > > > > > >> _______________________________________________ > > > > > >> Freesurfer mailing list > > > > > >> Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > >> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > >> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> > > > > > > _______________________________________________ > > > Freesurfer > > > > > mailing > > > > > > list Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> > The > > > > > > information in this e-mail is intended > > only for > > > the person > > > > > to whom > > > > > > it is addressed. If you believe this > > e-mail was sent > > > > to you in > > > > > > error and the e-mail contains patient > > > information, please > > > > > contact > > > > > > the Partners Compliance HelpLine at > > > > > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>> > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>>> > > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>> > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>>>> > > > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>> > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>>> > > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>> > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>>>>> . If the e-mail was > sent > > > > > > to you in error but does not contain patient > > > > information, please > > > > > > contact the sender and properly dispose of > the > > > e-mail. > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu > >>> > > > > <mailto:greve@nmr.mgh.harvard.edu <mailto: > greve(a)nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > > Phone Number:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 > > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>>> > > > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > > > <tel:617-724-2358 <tel:617-724-2358>>>> > > > > > Fax: 617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > > <tel:617-726-7422> > > > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 > > <tel:617-726-7422> > > > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > > > > > Bugs: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > > > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > > > > > FileDrop: > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > > > > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > > > > Outgoing: > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > > > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>> > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > -- > > > > Douglas N. Greve, Ph.D. > > > > MGH-NMR Center > > > > greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu > >> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu > >>> > > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > > <tel:617-724-2358 <tel:617-724-2358>> > > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > > <tel:617-726-7422>> > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > > > Outgoing: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 5 > Date: Thu, 20 Apr 2017 11:25:22 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] plot-twf-sess display error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <825e6f41-0aea-10be-af32-005d2c9aa780(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > display is an imagemagick program. It is used to display the images > created by gnuplot. If you have xv installed, you can add -xv to the > command line. Otherwise, install imagemagick > > > https://www.imagemagick.org/script/index.php > > > > On 04/19/2017 04:03 PM, Xie, Wenting wrote: > > Hi all, > > > > > > I am trying to use plot-twf-sess to create the motion plots as > > specified in the FsFast Tutorial, but I keep getting the error of > > "cannot find display." The command was copy-pasted from the FsFast > > tutorial > > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/ > FsFastPreProc_freeview?highlight=%28plot\-twf\-sess%29), > > and Gnuplot works on this computer (CentOS 6.8; GNOME 2.28.2) with the > > default terminal type set to "wxt". I've looked at the plot-twf-sess > > code in an attempt to troubleshoot but do not entirely understand what > > "display" means here where this error is generated: > > > > which display > /dev/null > > if($status) then > > echo "ERROR: cannot find display" > > exit 1; > > endif > > > > I've searched the archives but it seems that no one has encountered > > this problem yet (or at least written about it), so I can't tell if > > I'm just missing something glaringly obvious. Thank you for your time > > and please let me know if any further information is needed to solve > this! > > > > > > Thanks again, > > > > Wenting Xie > > > > Clinical Research Coordinator > > > > MGH Neurology | Boston, MA > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 6 > Date: Thu, 20 Apr 2017 11:30:25 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] 5. Re: Selxavg3-sess Looking for (and can't > find) "fmc.sm0" > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <b8dfcdc4-2cc7-4255-30f1-6ac01c9bb09d(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > What are the contents of the run list file? > > > On 04/19/2017 09:32 AM, Taylor, Johnmark wrote: > > Here's the contents of analysis.info <http://analysis.info>: > > > > # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve > > Exp $ > > # MKACMD /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/mkanalysis-sess > > -analysis glm_single_all_ps_0 -fsd bold -runlistfile > > runlist_single.txt -native -nuisreg mcprextreg 3 -fwhm 0 > > -event-related -nconditions 8 -paradigm spiralpara.par -spmhrf 0 > > -per-session -refeventdur 12 -TR 1.5 -polyfit 2 -force -nskip 8 > > # DATE Sat Apr 1 18:30:53 EDT 2017 > > > > analysis glm_single_all_ps_0 > > mcstem fmc > > fsd bold > > runlistfile runlist_single.txt > > TR 1.5 > > RegDOF 6 > > PerSession 1 > > RawSpace volume native > > mask brain > > RawFWHM 0 > > RawSTC none > > UseB0DC 0 > > ApplySubCortMask 1 > > inorm 100 > > acfbins 30 > > fixacf 1 > > acffwhm 20 > > acfsvd 0 > > designtype event-related > > nskip 8 > > polyfit 2 > > HPFCutoffHz 0 > > HeteroGCor 0 > > nconditions 8 > > parname spiralpara.par > > RefEventDur 12 > > timewindow 40.000000 > > prestim 0 > > TER 0.050000 > > spmhrf 0 > > stimulusdelay -.75000000000000000000 > > Condition 1 Condition01 > > Condition 2 Condition02 > > Condition 3 Condition03 > > Condition 4 Condition04 > > Condition 5 Condition05 > > Condition 6 Condition06 > > Condition 7 Condition07 > > Condition 8 Condition08 > > nuisreg mcprextreg 3 > > > > > > On Tue, Apr 18, 2017 at 9:49 PM, > > <freesurfer-request(a)nmr.mgh.harvard.edu > > <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: > > > > Send Freesurfer mailing list submissions toAl > > freesurfer(a)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 > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > > <mailto:freesurfer-request@nmr.mgh.harvard.edu> > > > > You can reach the person managing the list at > > freesurfer-owner(a)nmr.mgh.harvard.edu > > <mailto:freesurfer-owner@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. Fwd: fix topology problem (miracle ozzoude) > > 2. mri_glmfit error with aparc table flag (miracle ozzoude) > > 3. Re: Any advices for hires surface reconstruction? (Douglas > > Greve) > > 4. Re: Inconsistency in SI axis coordinate between FreeSurfer > > recon-all seg image and BrainVoyager (Douglas Greve) > > 5. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0" > > (Douglas Greve) > > > > > > ------------------------------------------------------------ > ---------- > > > > Message: 1 > > Date: Tue, 18 Apr 2017 21:06:00 -0400 > > From: miracle ozzoude <miracooloz(a)gmail.com > > <mailto:miracooloz@gmail.com>> > > Subject: [Freesurfer] Fwd: fix topology problem > > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Message-ID: > > > > <CANfOk0hQPdgzKMGQRRfFCvUZ8X+tmP=mL9r-mtQDMpWQVH4MyA(a)mail.gmail.com > > <mailto:mL9r-mtQDMpWQVH4MyA@mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > > > ---------- Forwarded message ---------- > > From: miracle ozzoude <miracooloz(a)gmail.com > > <mailto:miracooloz@gmail.com>> > > Date: Mon, Apr 17, 2017 at 8:40 AM > > Subject: fix topology problem > > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > > > Hello freesurfer, > > I am running recon-all on a scan and for the past 4 days, it hasn't > > finished the fix topology step of recon-all. I have attached the > > recon.log > > in the email. Thanks > > Best, > > Paul > >

2 1

White matter atrophy
by John Anderson 20 Apr '17

20 Apr '17

Dear Freesurfer experts, I know how to do cortical thickness group analysis using Freesurfer, also I know how to use Qdec to compare groups regarding gray matter volume differences, cortical thickness, curvatures, area,... etc. I am wondering if there is any way in Freesurfer to study the difference in white matter volume between two groups? I highly appreciate any suggestion! John

3 4

Using registration.dat to register a dataset
by Jacobson, Aaron 20 Apr '17

20 Apr '17

Hello, I am new to freesurfer. I have been looking for an answer to this issue for days. I ran bbregister to align a dti scan to a t1 struc. It worked beautifully. I am trying to register a very abnormal looking dataset to the t1 using the registration parameters created during the first bbregister (dti to t1). I have been unable to figure this out, but it seems like it must be a common procedure. Any advice would be greatly appreciated.

2 5

5. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0"
by Taylor, Johnmark 20 Apr '17

20 Apr '17

Here's the contents of analysis.info: # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve Exp $ # MKACMD /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/mkanalysis-sess -analysis glm_single_all_ps_0 -fsd bold -runlistfile runlist_single.txt -native -nuisreg mcprextreg 3 -fwhm 0 -event-related -nconditions 8 -paradigm spiralpara.par -spmhrf 0 -per-session -refeventdur 12 -TR 1.5 -polyfit 2 -force -nskip 8 # DATE Sat Apr 1 18:30:53 EDT 2017 analysis glm_single_all_ps_0 mcstem fmc fsd bold runlistfile runlist_single.txt TR 1.5 RegDOF 6 PerSession 1 RawSpace volume native mask brain RawFWHM 0 RawSTC none UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 8 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 8 parname spiralpara.par RefEventDur 12 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay -.75000000000000000000 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 Condition 6 Condition06 Condition 7 Condition07 Condition 8 Condition08 nuisreg mcprextreg 3 On Tue, Apr 18, 2017 at 9:49 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions toAl > freesurfer(a)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-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)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. Fwd: fix topology problem (miracle ozzoude) > 2. mri_glmfit error with aparc table flag (miracle ozzoude) > 3. Re: Any advices for hires surface reconstruction? (Douglas Greve) > 4. Re: Inconsistency in SI axis coordinate between FreeSurfer > recon-all seg image and BrainVoyager (Douglas Greve) > 5. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0" > (Douglas Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Apr 2017 21:06:00 -0400 > From: miracle ozzoude <miracooloz(a)gmail.com> > Subject: [Freesurfer] Fwd: fix topology problem > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CANfOk0hQPdgzKMGQRRfFCvUZ8X+tmP=mL9r-mtQDMpWQVH4MyA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > ---------- Forwarded message ---------- > From: miracle ozzoude <miracooloz(a)gmail.com> > Date: Mon, Apr 17, 2017 at 8:40 AM > Subject: fix topology problem > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu> > > > Hello freesurfer, > I am running recon-all on a scan and for the past 4 days, it hasn't > finished the fix topology step of recon-all. I have attached the recon.log > in the email. Thanks > Best, > Paul >

2 1

plot-twf-sess display error
by Xie, Wenting 20 Apr '17

20 Apr '17

Hi all, I am trying to use plot-twf-sess to create the motion plots as specified in the FsFast Tutorial, but I keep getting the error of "cannot find display." The command was copy-pasted from the FsFast tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc_…) and Gnuplot works on this computer (CentOS 6.8; GNOME 2.28.2) with the default terminal type set to "wxt". I've looked at the plot-twf-sess code in an attempt to troubleshoot but do not entirely understand what "display" means here where this error is generated: which display > /dev/null if($status) then echo "ERROR: cannot find display" exit 1; endif I've searched the archives but it seems that no one has encountered this problem yet (or at least written about it), so I can't tell if I'm just missing something glaringly obvious. Thank you for your time and please let me know if any further information is needed to solve this! Thanks again, Wenting Xie Clinical Research Coordinator MGH Neurology | Boston, MA

2 1

R: Re: R: Re: FSGD file FS-FAST
by stdp82＠virgilio.it 20 Apr '17

20 Apr '17

I'm sorry but it not clear to me. There are 2 factors, 2 levels, while I have 1 Factor, 4 Levels In particular, have I looked to difference between Group1+Group2 vs Group3+Group4? Is it correct 0.5 -0.5 0.5 -0.5? Thanks Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 19-apr-2017 19.23 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: FSGD file FS-FAST > >There is one for 4 Groups with 1 covariate. Use that one and do not >include the covariate. > > >On 04/19/2017 02:37 AM, stdp82(a)virgilio.it wrote: >> I did not find it for for 4 Groups (1 Factor, 4 Levels), Zero Covariates. >> >> I need for check to avoid error on my analysis. >> Please could you say me whether the followed codes are correct. >> >> A) Group effect >> 1 -1 0 0 >> 1 0 -1 0 >> 1 0 0 -1 >This will generate an F test for the group effect >> >> B) 0.5 0.5 -0.5 -0.5 >This looks like it will test a difference between Group1-and-2 vs >Group3-and-4 >> >> Many thanks. >> >> Stefano >> >> >> >> ----Messaggio originale---- >> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >> Data: 19-apr-2017 3.50 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] FSGD file FS-FAST >> >> Have you looked at >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? >> >> >> On 4/17/17 5:32 PM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> please could you suggest me the group.effect.mtx and the file.mtx >>> relative to Null Hypothesis for 4 Groups (1 Factor, 4 Levels), >>> Zero Covariates. DODS or DOSS. >>> Thanks >>> Stefano >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >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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Re: [Freesurfer] Any advices for hires surface reconstruction?
by Damien MARIE 20 Apr '17

20 Apr '17

Hi, Thank you for your reply Douglas, I will talk with my supervisor about an eventual contribution. Best, Damien Douglas Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Tue, 18 Apr 2017 18:41:59 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> That looks pretty good to me considering the resolution and 7T. We will be re-evaluating the hires stream over the next year. If you want to contribute a problem data set to our test suite, that would be appreciated. doug On 4/17/17 1:45 PM, Damien MARIE wrote: Hi, I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, skull strip was done despite a slight piece of dura is still present. For the data processed at native resolution, with the hires flag, I mainly used this: recon-all -subject -i -parallel -expert -hires The expert file indicating only mris_inflate -n 50 As a result, skull strip had to be fixed for 5 subjects (missing brain pieces). Bilateral temporal pole is missing in the reconstructed surfaces in 19 subjects. For the downsampled data, without the hires flag : recon-all -subject -i -parallel Bilateral temporal pole is missing in the reconstructed surfaces in only 1 subject. Surfaces are way smoother. I guess such differences between the classic pipeline and the pipeline tuned for hires data are expected. I was just wondering if I was missing something somewhere, some additional options that I would need to tweak, to get better surfaces with the hires data especially in the temporal pole. For now the only things I see that I could do are adding checkpoints or play with this command line: mris_make_surfaces -max_gray_at_csf_border X -max_csf Y Thank you and best, *Damien*

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Worse determination of ?h.white with v6.0 in comparison to v5.3 - more aggressive filtering during normalization in v6.0?
by Antonin Skoch 19 Apr '17

19 Apr '17

Dear experts, I was rerunning recon-all on quite large group of subjects previously reconstructed and edited with v5.3. I was disappointed to see quite large amount of new surface errors in subjects after rerun with v6.0 which need many new manual time consuming interventions. Most pronounced issue seems to me worse determination of wm.mgz, i.e. more regions of gray matter and "dura" is left in wm.mgz voxels. This is not primarily related to skullstrip, since I used brainmask.mgz from v5.3 for recon-all in v6.0 (to keep edits). The possible reason of worse wm.mgz is probably related by the filtering during normalization steps: I found that there is much more aggressive signal intensity filtering during normalization in v.6.0. See the screenshots with brain.mgz and white surface in one of the problematic regions. The white surface is OK with v5.3, whereas white surface is leaking out of the brain in v6.0 and there is much lower variance of signal in white matter regions in v6.0 in comparison to v5.3. Could you please comment on? Regards, Antonin Skoch

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