Hi there, I have a similar problem not using longitudinal stream, just a routine recon-all analyses, this with several processed subjects, Here is my message sent several days ago. Thanks, Octavian.
Dear Bruce, I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on reruns using any of the recon-all -autorecon-wm -aitorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all For example, the complete command line for a rerun on this particular subject is recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 -parallel > output.txt & Here are some of the edited voxels which are not excluded from the wm on rerun: -40.14, -2.67, 116.29 coronal slice 132 12.73, -23.67, 126.16 coronal slice 171 14.05, 12.33, 11.61 coronal slice 147 I mention this is not the only subject where I have this problem. Thank you for your help. Octavian On Tue, Apr 4, 2017 at 4:13 PM, David Semanek <seman...@nyspi.columbia.edu> wrote: > Thanks for looking into this. I have uploaded another two subject folders > as dsemanek3.zip, this time from a single time point for the same subject > having been run through the cross stream of recon-all, the one with “test” > appended at the end has had white matter edits on sagittal slices 126-142. > > > > So, I have been able to get the surfaces to change in a single cross run > as demonstrated in this upload. For this test, I did some edits that are > typical on this dataset. Although the surfaces did change to reflect the > edits, in a couple of places the surfaces did not change enough, and still > encompassed space in the wm volume which had the white matter voxels > removed. > > > > For the first pass through these data before I realized there was a > potential problem, I had initially edited the cross folders for the > subjects and then ran the base, expecting the edits to be transferred over, > but they did not seem to be. So I am still left with two issues: 1) > incomplete incorporation of cross edits on the cross folders, 2) so far > being unable to find an intervention point which will change the surfaces > in the long stream, I have edited the base and then ran the long folders > and these were not carried over as demonstrated in my previous uploads. > > > > Thanks again, > > > > 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: *Martin Reuter <mreu...@nmr.mgh.harvard.edu> > *Date: *Tuesday, April 4, 2017 at 11:20 AM > *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > > *Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in > FS 5.3/6 Cross and Long Streams > > > > So the way to debug this is to test if we can replicate the problem of WM > edits not taking effect in a regular cross sectional stream. > > If true this means that there is a bug to the way WM edits are considered > in FS6.0. It is unlikely that we missed that, but can happen. Probably > something else is going on here. > > > > For that it would be good to have a single time point (cross sectional > step) with WM edits send over, so that Andrew can take a look at that. > > > > Best, Martin > > > > > > On 04/04/2017 05:03 PM, David Semanek wrote: > > I used –uselongbasewmedits only as a test to see if I could get some > condition under which the wm edits would be taken into account when the > surfaces were generated. > > > > I did not use that flag for the data I uploaded. The wm edits to base did > not influence the base wm surfaces or the cross wm surfaces. The cross wm > edits (not uploaded) did not influence cross, base, or long wm surfaces. > > > > I’ve found no condition under which wm edits have influenced the white > matter surface in any of my data. > > > > 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: *Martin Reuter <mreu...@nmr.mgh.harvard.edu> > <mreu...@nmr.mgh.harvard.edu> > *Date: *Tuesday, March 28, 2017 at 1:27 PM > *To: *<freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in > FS 5.3/6 Cross and Long Streams > > > > This is how it should work: > > WM edits in the base should affect surfaces in the base, these surfaces > should be used as initialization for the long processing and fix most of > the things there. If not , you need to edit the cross, because WM edits are > copied into long from cross. > > > > Using the -uselongbasewmedits flag is usually not recommended. It copies > WM edits from base to the long and that is only meaningful if there is very > little longitudinal change. > > > > Best, Martin > > > > On 03/23/2017 04:12 PM, David Semanek wrote: > > Thanks for taking another look at our data. > > > > I have uploaded another subject in the archive dsemanek2.zip . For this > subject I have: > > > > 1) run the cross processing stream on both timepoints > > 2) created the base > > 3) edited the wm.mgz on the base > > 4) rerun –base –autorecon2-wm –autorecon3 > > 5) run the long stream to create the long folders for the two time points > > > > It doesn’t look like the white matter edits were factored into any of the > surfaces at any point in the process. NB: some edits have been exaggerated > over protocol for the purpose of testing the software. > > > > These folders were processed on OSX 10.11. I am running the same subject > on Linux and I will let you know if I get a qualitatively different outcome. > > > > 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: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > <ahoo...@mgh.harvard.edu> > *Date: *Monday, March 20, 2017 at 4:54 PM > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > <freesurfer@nmr.mgh.harvard.edu>, David Semanek > <seman...@nyspi.columbia.edu> <seman...@nyspi.columbia.edu> > *Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in > FS 5.3/6 Cross and Long Streams > > > > Hi David, > > > > That is interesting. Sorry to ask you to upload data again, but if you > could upload this subject (with only base wm.mgz edits), I could try to > replicate this and see why no wm changes are showing up in the longs. > > > > best, > > Andrew > > > ------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek > <seman...@nyspi.columbia.edu> <seman...@nyspi.columbia.edu> > *Sent:* Monday, March 20, 2017 1:59 PM > *To:* Hoopes, Andrew; Freesurfer support list > *Subject:* Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in > FS 5.3/6 Cross and Long Streams > > > > Andrew, thanks for your response. I am still not seeing the white matter > edit performance that I am expecting, or that I have seen from using the > cross stream on 5.3 in the past with a different dataset. > > > > I started with a new subject with two timepoints. I ran recon-all on both > for the cross stream with no edits, and then ran the base. I edited the > wm.mgz for the base, then ran “recon-all –autorecon2-wm –autorecon3 –base > xx_base –tp xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change > in the base, but I went ahead and ran the two long runs using “recon-all > –all –long xx_tx xx_base” and although there are minor differences in the > base and time point surfaces, the white matter edits I did on the base were > largely ignored, and none of them were included in the time point long run > wm.mgz files. > > > > I am tempted to try these same analyses using Linux (I am running this on > OSX 10.11 currently), as I experienced a completely different response from > the surface generation modules to my edits in the past when using Linux. > I’m thinking this is a real long shot, but I cannot otherwise figure out > why the software would be behaving so differently from my past experiences. > > > > Any thoughts? Thanks! > > 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: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > <ahoo...@mgh.harvard.edu> > *Date: *Wednesday, March 15, 2017 at 12:47 PM > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > <freesurfer@nmr.mgh.harvard.edu>, David Semanek > <seman...@nyspi.columbia.edu> <seman...@nyspi.columbia.edu> > *Cc: *Bruce Fischl <fis...@nmr.mgh.harvard.edu> > <fis...@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in > FS 5.3/6 Cross and Long Streams > > > > Hi David > > > > Try editing the base wm.mgz first instead of editing the long and cross wm > files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely > rerun the longitudinals. The long surfaces are initialized from the base > surfaces, so this could be why your wm fixes seem to have no effect. > > You can find more info here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#CheatSheet > <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits> > > If editing the base doesn't solve the problem, you can send me > the commands you ran in order and I can look into this further. > > > > best, > > Andrew > > > ------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek > <seman...@nyspi.columbia.edu> <seman...@nyspi.columbia.edu> > *Sent:* Monday, March 13, 2017 11:55 AM > *To:* Bruce Fischl; Freesurfer support list > *Subject:* Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in > FS 5.3/6 Cross and Long Streams > > > > Thanks, I have uploaded the cross and long stream processing from one > subject which requires numerous white matter edits to correct defects in > the white matter surfaces; the file is on the ftp server as dsemanek.zip. > > Both of the cross subject folders, s02_t1 and s02_t2 have had edits done > to both the brainmask as well as the wm files, and autorecon2-wm and > autorecon-3 have been run on them, as well as the long folder for the first > time point, s02_t1.long.s02_base. > > It was in working with the rerun results of s02_t1.long.s02_base that I > noticed the white matter surfaces after being regenerated with the edited > wm.mgz did not reflect any of the edits. The easiest way to see this is to > load the wm.mgz with the white matter surfaces and scroll through the > slices, there are numerous areas where the contours of the white matter > surfaces do not follow the voxels of the wm.mgz volume, mostly near what > should be identified as hyperintense gray matter. I’m fairly certain the > white matter surfaces didn’t change at all after running autorecon2-wm with > the wm.mgz edits. > > Thanks for taking a look at our data. > > 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. > > On 3/12/17, 4:13 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > <fis...@nmr.mgh.harvard.edu> wrote: > > Hi David > > if you upload a subject to our ftp site and give us enough detail to > replicate what you tried we will take a look > > cheers > Bruce > On Fri, 10 Mar 2017, David > Semanek wrote: > > > > > Hello, I have worked quite a bit in the past with fs 5.3 on datasets > which > > required a fair number of manual edits to the white matter volume in > order > > to correct defects in the white matter surface. Typically, these > edits take > > the form of removing voxels in the wm.mgz volume that have been > incorrectly > > identified as white matter, usually near the pial surface caused by > > intensity artifacts resulting from motion. My experience in the past > is that > > generating the white matter surface after edits to the wm.mgz volume > will > > reliably change the geometry of the resulting surfaces. > > > > > > > > However, on my current dataset, 1.5T adolescent brains with > pervasive motion > > artifacts that do not meet the threshold for unusable data, > absolutely no > > intervention I have done on the wm.mgz volume has any impact at all > on the > > generation of the white matter surfaces. I am really very puzzled by > this. > > All of the files that result from wm.mgz reflect the edits, however > the aseg > > does not. > > > > > > > > The resulting white matter surfaces always follow the aseg white > matter > > definitions and never the wm.mgz edits. I feel as if there might be > > something I am missing but this protocol has reliably been used to > do white > > matter edits in the past. I thought it may be an issue with fs 6 or > the long > > stream, but I have tried the same edits in 5.3, 6, long and cross > streams > > and nothing at all has worked. > > > > > > > > Does anyone have any suggestions, or perhaps a hint that I am > overlooking > > something common? > > > > > > > > Thanks, > > > > > > > > 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. > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Freesurfer Info Page - Harvard University > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > mail.nmr.mgh.harvard.edu > > To see the collection of prior postings to the list, visit the Freesurfer > Archives. A searchable archive which of messages PRIOR to March 2004 is at > ... > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. 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