Freesurfer

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30132 discussions

Re: [Freesurfer] Fwd: recon-all error
by Antonin Skoch 06 Apr '17

06 Apr '17

Dear Patricia, see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html Your working directory probably resides on the filesystem which does not support symbolic links. You probably could workaround this by editing your recon-all and replace line set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) by set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix) Antonin Skoch Hello FreeSurfer Developers, I have installed Freesurfer on Windows using VMware - CentOS 64-bit (the one from FSLuser Linux installation). Everytime I run recon-all, there is an error. The same error occurs when I try to rum mri2mesh command in SIMNIBS toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and logfile attached. Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help. Best, Patricia

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Petsc Error in Freesurfer v6.0
by Michael ONeill 05 Apr '17

05 Apr '17

Hello Freesurfer Developers, I've just installed Freesurfer v6.0 and attempted to run the commands printed below in order to test the installation: freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red Running this resulted in the a PETSC error which i have attached in .txt file. I'm running Ubuntu 16.04 64bit in virtual box on a windows host. I've tried numerous solutions including using the latest dev build of freesurfer v6.0 (as of 23/03/2017), installing the latest version of PETSC and doubling the amount of RAM available to the guest OS from 12GB to 24GB. But unfortunately none of these approaches worked and the issue still persists. I'm very eager to start using Freesurfer v6.0 and this seems to, hopefully, be the last rock in the road. Any help you could offer would be appreciated. Kind Regards, Michael The opinions, conclusions and other information expressed in the above message, or contained within attachments to the above message, are not given or endorsed by Beaumont Hospital unless otherwise indicated by an authorised representative independent of this message. This e-mail message and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. This e-mail has been scanned for viruses. This e-mail and all attachments are confidential and may be privileged. If you have received this e-mail in error, notify the sender immediately. Do not use, disseminate, store or copy it in any way.

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MR Research Coordinator Position Open at Stanford
by Maria Catalina Camacho 05 Apr '17

05 Apr '17

Hello fellow neuroimagers! I'm leaving my current position at Dr. Ian Gotlib's Mood and Anxiety Disorders Lab (soon to be renamed the Stanford Neurodevelopment, Affect, and Psychopathology Lab or SNAP lab), leaving a vacancy on what we call our "Scan Team" that we'd like to fill in the next few months. This position involves coordinating and running the MRI brain scan sessions for several studies spanning development. I've attached a more detailed description of the position, but this is an incredible paid opportunity to do research at Stanford. It is perfect for current undergraduate seniors considering applying to PhDs or recent post-baccs wanting to explore psychopathology, development, affect, and neuroscience research. Please send this along to anyone fitting this description and looking for a research assistant/coordinator job! Questions/application materials should be directed to moodlab.fmri(a)gmail.com<mailto:moodlab.fmri@gmail.com> our website: mood.stanford.edu<http://mood.stanford.edu/> Warmly, Cat -- Maria Catalina Camacho MR Research Coordinator Mood and Anxiety Disorders Laboratory Stanford University catcam1(a)stanford.edu<mailto:catcam1@stanford.edu> (650)721-2399<tel:(650)%20721-2399>

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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams
by Antonin Skoch 05 Apr '17

05 Apr '17

Dear David, I did not see your data, but maybe couple of relevant remarks could be useful: 1. By default the wm.mgz edits are not propagated from cross to the base, but from the cross to long. And surfaces in long are initialized from the base. Therefore the wm.mgz has to be OK both in the cross and in the base. My view and current experience is, that this means that in many cases it is probably necessary to edit wm.mgz both in cross and base. This would explain your observation that the wm.mgz edits in cross are not propagated to the base and the edits in base (but not in cross) are not seen in the long. I implemented a custom script which transfers INTERSECTION of the wm.mgz edits from all cross points to the base. I think that to transfer the intersection of edits is safe approach to prevent to introduce errors in wm.mgz in base due to the false propagation of wm.mgz edits from cross to base in case of significant changes in the anatomy between cross and base. My preliminary testing shows that this approach works well and saves time in wm.mgz editing of large errors which are consistently present in all timepoints. But in case of significant errors, the wm.mgz in the base still needs some additional editing. Therefore I think that there is not any single intervention point in wm.mgz edits. I was discussing the approach of transferring wm.mgz edits with Martin Reuter in the following thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html 2. When there are spots in the cross, where wm.mgz edits do not take an effect, I would suggest to inspect the brain.finalsurfs.mgz to see if there is sufficient contrast of the white/gray matter. In many such cases where I observe my wm.mgz edits do not take an effect, there is local issue with insufficient white/gray matter contrast. The white surface placement is primarily driven by the local gradient of intensity in brain.finalsurfs.mgz, the boundaries/edits of wm.mgz play only supplementary role (as an starting point for gradient search, via ?h.orig, at least in default invocation of mris_make_surfaces, AFAIK). If I have enough clues where the white surface should lie (i.e. from FLAIR) and there is insufficient white/gray matter contrast (typically there are spots in gray matter with spuriously high signal intensity, similar to white matter), I am currently experimenting with workaround, by directly editing gray matter voxels of 001.mgz in problematic spots by setting their values to typical gray matter values to enforce better white surface placement. I decided to place my edits just in the beginning to the recon-all stream (001.mgz) to ensure the edits are not overwritten in case of new recon-all rerun. Maybe other experts could comment on my workaround approach, it would also help me out. Regards, Antonin Skoch I believe what I am seeing in the long stream is the edits not properly taking effect.I uploaded a subject with two timepoints, and only baseline edits to the wm as dsemanek2.zip about a week and a half ago. There doesn’t seem to be any significant changes to the surfaces in the base or either of the long runs. I will redo this subject on my end with some more extreme edits for testing to see if I can “force” something. Thanks again for looking, 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...(a)nmr.mgh.harvard.edu> Date: Wednesday, April 5, 2017 at 2:19 AM To: David Semanek <seman...(a)nyspi.columbia.edu> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>, "Hoopes, Andrew" <ahoo...(a)mgh.harvard.edu> Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams Hi David, so edits are affecting the surfaces in cross, just not as much as you would like. We need to check if there is a problem there. For the longitudinal stream, edits in the base should affect surfaces in the base, which in turn will affect surfaces in the long. In long, surfaces would start from a better starting position. Furthermore, wm edits from cross should be propagated to long, to make sure that surfaces don’t move back to the wrong position. So far the theory. If you don’t see any effect of WM edits (in the base) on surfaces (in the base) then there is a problem. This step should be basically identical to how we treat edits in cross. Best, Martin On 04 Apr 2017, at 23:13, David Semanek <seman...(a)nyspi.columbia.edu<mailto: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...(a)nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>> Date: Tuesday, April 4, 2017 at 11:20 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)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 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...(a)nmr.mgh.harvard.edu><mailto:mreu...@nmr.mgh.harvard.edu> Date: Tuesday, March 28, 2017 at 1:27 PM To: <freesurfer(a)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...(a)mgh.harvard.edu><mailto:ahoo...@mgh.harvard.edu> Date: Monday, March 20, 2017 at 4:54 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David Semanek <seman...(a)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...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...(a)nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek<seman...(a)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...(a)mgh.harvard.edu><mailto:ahoo...@mgh.harvard.edu> Date: Wednesday, March 15, 2017 at 12:47 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David Semanek <seman...(a)nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu> Cc: Bruce Fischl <fis...(a)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...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...(a)nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek<seman...(a)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...(a)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

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Re: [Freesurfer] mri_watershed seed point
by Antonin Skoch 05 Apr '17

05 Apr '17

Dear Kristen, looking at the source code of mri_watershed, the seed point has to be specified in the format: -s i j k and the option can be specified more than once when you want to add more seed points (30 seed points is maximum). i.e., when you want to input seed points in coordinates 50,60,70, and 80,90,100, the option would be: -s 50 60 70 -s 80 90 100 Regards, Antonin Skoch Hello FreeSurfer Community, I am attempting to use mri_watershed to create BEM surfaces, but for some of my subjects part of the cerebellum is being cut off. Adjusting the threshold was not sufficient, so I attempted to add a seed point in the cerebellum using the following command:mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz ./brainvol The coordinates for the seed point are from the T1.mgz image. I reran mri_watershed and the seed point does not seem to be taken into consideration so I'm thinking that the input format I used may be wrong. Could someone please tell me if I am not using the proper input format? And what format to use if I wish to add multiple seed points? Command output is attached. Thanks in advance! Kristen

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mri_watershed seed point
by Kanoff, Kristen Elise 05 Apr '17

05 Apr '17

Hello FreeSurfer Community, I am attempting to use mri_watershed to create BEM surfaces, but for some of my subjects part of the cerebellum is being cut off. Adjusting the threshold was not sufficient, so I attempted to add a seed point in the cerebellum using the following command: mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz ./brainvol The coordinates for the seed point are from the T1.mgz image. I reran mri_watershed and the seed point does not seem to be taken into consideration so I'm thinking that the input format I used may be wrong. Could someone please tell me if I am not using the proper input format? And what format to use if I wish to add multiple seed points? Command output is attached. Thanks in advance! Kristen Kristen Kanoff Clinical Research Coordinator II Department of Neurology Massachusetts General Hospital Boston, MA Ph: 617-726-3958

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Re: [Freesurfer] ROI seed size
by ERIK JAHNER 05 Apr '17

05 Apr '17

Hi Bruce, Thanks for the quick response. Sorry, I meant 6mm radius (for regions such as fusiform face area and visual word form area). I am using the same seeds that are suggested to be associated with reading in the following study. I am wondering whether any guidelines have been set for determining seed size on surface from comparable volume based studies when that seed is a sphere or cube of voxels. I will be doing something similar using the peak coordinates of the components DMN suggested by Yeo 2011. Koyama, M. S., Kelly, C., Shehzad, Z., Penesetti, D., Castellanos, F. X., & Milham, M. P. (2010). Reading Networks at Rest. Cerebral Cortex, 20(11), 2549–2559. http://doi.org/10.1093/cercor/bhq005 Many thanks Erik Jahner Sent from my iPad > On Apr 5, 2017, at 7:12 AM, 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: Can anyone help with this error - trying to compare 2 > scans in same person (Martin Reuter) > 2. Generate stat file of ROI voxel sizes (Ostrowski, Lauren) > 3. Reminder: 3.5-year Postdoc Position in Social Neuroscience at > Bangor University, UK (Kami Koldewyn) > 4. Re: Custom color maps (dg wakeman) > 5. Re: ROI seed size (Bruce Fischl) > 6. PROGRAM DIRECTOR POSITION IN COGNITIVE NEUROSCIENCE AT NSF: > Application deadline May 11, 2017 (Uri Hasson) > 7. Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 > Cross and Long Streams (David Semanek) > 8. Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 > Cross and Long Streams (Octavian Lie) > 9. Re: Comparing LME models (Bronwyn Overs) > 10. Re: Registration of both the brain and the "surf" files to > the same template. (Douglas Greve) > 11. Re: Volume to Surface mapping looks great for Vols created in > FSL but not SPM (Douglas Greve) > 12. Re: Volume to Surface mapping looks great for Vols created in > FSL but not SPM (Rita Elena Loiotile) > 13. Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 > Cross and Long Streams (Martin Reuter) > 14. Surface Integral Questions (Levman, Jacob) > 15. Re: Volume to Surface mapping looks great for Vols created in > FSL but not SPM (Douglas Greve) > 16. Re: Qdec effect sizes, correlation coefficient (Douglas Greve) > 17. Changing the Orientation of Scan Slices (Images included) > (Jeffrey Crawford) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 4 Apr 2017 18:17:16 +0200 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Can anyone help with this error - trying to > compare 2 scans in same person > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1dec67aa-6ef5-1ea2-4241-b578b5213173(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Brad, > > > the base commands needs a space before -tp > > > recon-all -base 005_IHD_1_base -tp 005_IHD_1 -tp 005_IHD_1_post -all > > > check if the directory 005_IHD_1_base exists. > Also check if this file exits: > /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm > > Best, Martin > >> On 04/04/2017 05:55 PM, Brad Matushewski wrote: >> >> *From:*freesurfer-bounces@nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Brad >> Matushewski >> *Sent:* March 30, 2017 2:38 PM >> *To:* freesurfer(a)nmr.mgh.harvard.edu >> *Subject:* [Freesurfer] Trying to compare 2 scans from same person, 6 >> months apart. >> >> First scan is 005_IHD_1 >> >> Second scan is 005_IHD_1_post >> >> These were in $SUBJECTS / ihd >> >> I moved them into $SUBJECTS >> >> (i.e. no subfolder within $SUBJECTS folder). >> >> I am following this; >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing >> >> FsTutorial/LongProcessing - Free Surfer Wiki >> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing> >> >> surfer.nmr.mgh.harvard.edu >> >> Processing your data consists of three steps: First, run all your data >> independently (we also say cross sectionally) using "recon-all -all" >> (i.e. all time points for ... >> >> I ran a normal recon all on both scans first. >> >> I then ran this command: >> >> recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all >> >> and all seemed well. >> >> I then tried to run this command. >> >> recon-all -long <tpNid> <templateID> -all >> >> This is how I entered the command: >> >> recon-all -long 005_IHD_1 005_IHD_1_base -all >> >> It resulted in errors...here is the last bit of the error log: >> >> Applying LTAtransformInterp (resample_type 5) >> MRItoBSpline degree 3 >> writing to >> /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/rawavg.mgz... >> >> mri_add_xform_to_header -c >> /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.xfm >> /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz >> /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz >> >> INFO: extension is mgz >> #-------------------------------------------- >> #@# Talairach Thu Mar 30 14:31:07 EDT 2017 >> /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri >> >> cp >> /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm >> /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.auto.xfm >> >> >> cp: cannot stat >> '/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm': >> No such file or directory >> Linux bjmatush-System-Product-Name 4.4.0-51-generic #72~14.04.1-Ubuntu >> SMP Thu Nov 24 19:22:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 005_IHD_1.long.005_IHD_1_base exited with ERRORS at Thu >> Mar 30 14:31:07 EDT 2017 >> >> What went wrong? >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Changing the Orientation of Scan Slices (Images included)
by Jeffrey Crawford 05 Apr '17

05 Apr '17

Hello everyone! I have two types of scans of the same participant. One was an Axial scan (Image 1) and the other is a Cortical Scan (Image 2), both with the same dimensions (256 by 256 by 124). As you can see, the orientation of the axial scan has the coronal in the top left, the sagittal in the top right, and the axial below. The coronal scan has the axial in the top left, the sagittal in the top right (in an odd orientation) and the cortical on the bottom. Is it possible in Freesurfer to convert the cortical scan, so that it presents itself in the same order and orientation as the axial scan? I realize that this would mean that the converted cortical scan would have different dimensions, but I think that is just fine for my purposes. I would much appreciate any and all opinions, Jeff

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Generate stat file of ROI voxel sizes
by Ostrowski, Lauren 05 Apr '17

05 Apr '17

Hello experts, We are looking to generate a stat file containing the number of voxels in a series of ROIs. We have a collection of about 300 different user-defined cortical ROI nifti volumes (not from aseg) and need to retrieve the number of voxels in each ROI for further analysis, but so far haven't been able to come up with an algorithm to do so. Any help is much appreciated! Thank you, Lauren Ostrowski

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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams
by David Semanek 05 Apr '17

05 Apr '17

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" <AHOOPES(a)mgh.harvard.edu> Date: Monday, March 20, 2017 at 4:54 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, David Semanek <SemanekD(a)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-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of David Semanek <SemanekD(a)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" <AHOOPES(a)mgh.harvard.edu> Date: Wednesday, March 15, 2017 at 12:47 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, David Semanek <SemanekD(a)nyspi.columbia.edu> Cc: Bruce Fischl <fischl(a)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-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of David Semanek <SemanekD(a)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" <fischl(a)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(a)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. 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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