[Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits
External Email - Use Caution Dear FreeSurfer Developers, I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information. We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil. At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated! Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image? Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal Processing - Retaining Manual Edits
External Email - Use Caution Dear FreeSurfer Developers, We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil. At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated! Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image? Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log
External Email - Use Caution Hello FreeSurfer experts, I previously emailed regarding processing longitudinal data in v6.0 using bases with manual edits that had been completed in v5.3. I went ahead and ran recon-all -all on the base of a subject (originally generated in v5.3) in v6.0, but it looks like the header of the recon-all.log still indicates v5.3. Looking at the /stats output, all files indicate v6.0. Below is the head of the log from running recon-all -all on this subject. Is this what you would expect if you ran recon-all -all on a subject_base in v6.0 that was generated in v5.3? If so, is this okay? Recon-all log: setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux c139.keck.waisman.wisc.edu 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 11:12:41 CST 2017 x86_64 x86_64 x86_64 GNU/Linux Thank you! Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0
External Email - Use Caution Hello FreeSurfer experts, We have a large dataset (n=140) that is being processed through the longitudinal pipeline. We have already generated the cross-sectionals and conducted manual edits to the bases in v5.3.0. What is the latest stage (cross, base, long) at which we are able to re-process our data in v6.0, and retain our manual edits, in order to reap the benefits of v6.0? It appears a similar question was asked about whether or not manual edits from an older version are retained and can be ran through recon-all with the newer version (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51197.html), and it appears yes they can. However, since we are using the longitudinal pipeline, we want to confirm the stage at which we can to run recon-all in v6.0. Thank you! Kaley Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Value of ROIs different between FreeSurfer versions?
Hello FreeSurfer Developers, I am extracting ROIs of cross-sectional data using FreeSurfer v6.0. We looked at this data preliminarily about 2 years ago using FreeSurfer v5.3. It looks like there are slight differences in the values of the same subject (see below). Do you know the reason for this difference and whether there is something I should do differently? Subject 2000_1, lh_G_and_S_frontomargin_thickness: v5.3 = 2.416 v6.0 = 2.482 command used: aparcstats2table --hemi lh --subjects $subjectlist --skip --delimiter comma --meas thickness --parc aparc.a2009s --tablefile /PATH/lh_aparc-destrieux-thickness-table.csv Thank you for your time! Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM surface ignoring wm.mgz edits
Hi Bruce, We are using the "voxel-edit" tool and "recon editing" is selected. Thank you, Kaley From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@nmr.mgh.harvard.edu> Sent: Friday, July 7, 2017 11:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 16 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Message: 1 Date: Fri, 7 Jul 2017 10:42:23 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM surface ignoring wm.mgz edits To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1707071041590.9...@door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15" Hi Kaley are you using the "recon edit" tool in freeview? cheers Bruce On Fri, 7 Jul 2017, KALEY E ELLIS wrote: > > Dear?FreeSurfer?Developers, > > > We are attempting to make manual white matter edits to our subjects. The > edits are saving; however, after running with recon-all, the WM surface does > not appear to be taking into account our edits made to wm.mgz. Below is > additional information, and I have attached our recon-all.log. We are only > editing the cross because our dataset is comprised of single timepoints. > > > We are using?FreeSurfer?v5.3 and our operating system is OS X El?Capitan > version 10.11.6. > > Command to open and edit WM:? > > freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f > surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red > surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red > > > Command to submit edits: > > recon-all -autorecon2-wm -autorecon3 -subjid? > > > Recon-all log (see attached) > > > Thank you, > > Kaley?Ellis > > > > Associate Research Specialist > Center for?Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > > -- Message: 2 Date: Fri, 7 Jul 2017 14:51:53 + From: "Boyd, Emma" <ebo...@mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <mwhpr04mb0558426f0d765c043bedcabad1...@mwhpr04mb0558.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260 A FreeSurfer-compliant consistent manual segmentation of ...<https://www.ncbi.nlm.nih.gov/pubmed/25741260> www.ncbi.nlm.nih.gov 1. Front Hum Neurosci. 2015 Feb 18;9:21. doi: 10.3389/fnhum.2015.00021. eCollection 2015. A FreeSurfer-compliant consistent manual segmentation of infant ... Emma From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Das S. <sarbani@soton.ac.uk> Sent: Friday, July 7, 2017 4:58:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas. Sarbani -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: 06 July 2017 21:43 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn It is not only the atlas but the tools that are different. Lilla On Wed, 5 Jul 2017, Das S. wrote: > Dear Lilla, > In that case you mean if I have my own atlas specific to neonates then I can > follow these steps of auto recon. > If you give me little more details will be easy for me to understand the gap. > many thanks > Sarbani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 05 July 2017 22:32 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > We use a similar pipeline but with different atlases and processing > steps for the newborns. > Lilla > > On Wed, 5 Jul 2017, Das S. wrote: > >> >> Thanks for the reply. If you let me know, among the below list of steps of >> current recon-all, currently which is not suitable to perform on neonates >> MRI image, will
Re: [Freesurfer] Freesurfer Digest, Vol 160, Issue 25
. If you believe this e-mail was sent > to you in error and the e-mail contains patient information, > please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error but does not contain patient information, > please contact the sender and properly dispose of the e-mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in > error and the e-mail contains patient information, please contact > the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error but does not contain patient information, please > contact the sender and properly dispose of the e-mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and > the e-mail contains patient information, please contact the Partners > Compliance HelpLine at http://www.partners.org/complianceline . If the > e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170614/77c7e8a9/attachment-0001.html -- Message: 7 Date: Wed, 14 Jun 2017 16:32:38 +0200 From: Douglas Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Brainmask Shifted To: freesurfer@nmr.mgh.harvard.edu Message-ID: <02f67013-f90c-699f-0307-9f1bf9b13...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" what is your freeview command? On 6/14/17 3:51 PM, KALEY E ELLIS wrote: > > Dear FreeSurfer Developers, > > > We are using FreeSurfer v6.0 and our operating system is OS X El > Capitan version 10.11.6. > > > We are going through the manual editing process and are checking the > brainmask by following these instructions: > > http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0 > > We have two subjects who appear to have brainmasks that are shifted up > considerably (see attached image). The recon-all.log file indicates > that it finished without errors: > > > reading volume > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... > reading input surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... > reading input pial surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... > reading input white surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... > INFO: assuming MGZ format for volumes. > > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 277 173970 3.493 0.659 0.107 0.0393 0.4 > ./rh.entorhinal_exvivo.label > > #-- > > Started at Thu Jun 8 10:50:24 CDT 2017 > Ended at Fri Jun 9 00:06:58 CDT 2017 > #@#%# recon-all-run-time-hours 13.276 > recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 > CDT 2017 > > Could you please advise me on how to correct this issue? We have run > all of these subjects the same way, but only two have had this problem. > > > Thank you! > > Kaley > > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging an
[Freesurfer] FreeSurfer v6.0 release
Hello, We are currently setting up our study's structural analyses using FreeSurfer. When will the next version of FreeSurfer (6.0) be released? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FreeSurfer v6.0 release date
Hi FreeSurfer, We are currently setting up our study's structural analyses using FreeSurfer. When will the next version of FreeSurfer (6.0) be released? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Digest, Vol 151, Issue 30
Hi Ruopeng, When I try to open it, this is part of the error message that appears: freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4 libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error: BadValue (integer parameter out of range for operation) 2 Extension:150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension:150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension:150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension:150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension:150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension:150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension:150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension:150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension:150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension:150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension:150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: BadMatch (invalid parameter attributes) 8 Extension:150 (Uknown extension) Minor opcode: 11 (Unknown request) Resource id: 0x6000b8 If I run glxgears, this appears: [edwards@guero ~]$ glxgears libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 28 Current serial number in output stream: 30 [edwards@guero ~]$ Thank you! Kaley Message: 6 Date: Fri, 23 Sep 2016 18:53:45 -0400 From: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freeview display problem To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <732e27d8-179e-4b66-8762-7bf26c1df...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Is there any error message on the terminal? What happens if you run ?glxgears? command? Does it run? Best, Ruopeng > On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS <keedwar...@wisc.edu> wrote: > > Hello FreeSurfer Developers, > > I am attempting to open freeview to view the brainmask on a subject in our > study. Everything looks normal, except there is no image displayed (see > attachment). Could you please let me know how I can fix this? > > Thank you, > Kaley > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > PM.png>___ > Freesurfer mailing list > 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> -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160923/f890bd3a/attachment-0001.html -- Message: 7 Date: Sat, 24 Sep 2016 11:36:46 -0400 From: Satrajit Ghosh <sa...@mit.edu> Subject: [Freesurfer] avoiding FSL when using T2pial To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ca+a4womxc6mvvyglvswthotesocr282mzba-u7jy803kool...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" hi doug, without hacking recon-all is there a way to avoid using FSL when using the T2pial flag? cheers, satra #@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016 bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log Sat Sep 24 08:42:35 UTC 2016 setenv SUBJECTS_DIR /subjects cd /subjects/sub-01/scripts /opt2/freesurfer/bin/bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64 GNU/Linux FREESURFER_HOME /opt
