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><mailto:mreu...@nmr.mgh.harvard.edu> Date: Tuesday, March 28, 2017 at 1:27 PM To: <freesurfer@nmr.mgh.harvard.edu><mailto: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><mailto:ahoo...@mgh.harvard.edu> Date: Monday, March 20, 2017 at 4:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David Semanek <seman...@nyspi.columbia.edu><mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek <seman...@nyspi.columbia.edu><mailto: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><mailto:ahoo...@mgh.harvard.edu> Date: Wednesday, March 15, 2017 at 12:47 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David Semanek <seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu> Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu><mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek <seman...@nyspi.columbia.edu><mailto: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><mailto: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. 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