Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

FreeSurfer : About ROI analysis
by Lisa Delalande 10 Apr '17

10 Apr '17

Hello, As a PhD student, I often use Freesurfer software and more precisely QDEC. A great question arises in connection with my last work. After drawing ROIs, I extricated values thanks to a " .levels" and a creation of a "stat" folder for each participant (aparcstat2table). My question is : can I make a correlation between a behavioral score and the value of "average SURFACE" obtained for each participant thanks to the command above-mentioned considering that my ROI has been drawn from clusters detected with a correlational analysis between THICKNESS (and not surface) and a behavioral score on QDEC ? Many thanks in advance for your assistance, and I am looking forward to hearing from you. Marine

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Custom color maps
by Senften, Peter 06 Apr '17

06 Apr '17

Hello, I am wondering if it is possible to create a custom color map that will be visible in freeview using the 3D viewer - not the coronal, axial, or sagital views. I created a copy of the LUT file and then replaced the RGB values the ones I wanted but haven't been able to get it to load at all. In the end I am trying to make pretty 3D pictures to see our regions of interest better for our data. I am open to other ways of doing this. Thanks, Peter

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Help on "mris_anatomical_stats"
by Lim, Lena 06 Apr '17

06 Apr '17

Dear Experts, I ran a group analysis in Qdec for the left volume and found a region of significant group difference. I wanted to extract this ROI. I defined this label and used the "map label to subjects" option in Qdec and ran the following but encountered the following error. Please kindly help... [spjwker@nanlnx2 FSL]1% mris_anatomical_stats -l lh.HCA_vol.label \-b -f PAC07/stats/lh.HCA_vol.stats PAC07 lh limiting computations to label lh.HCA_vol.label. reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz... reading input surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... reading input pial surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial... reading input white surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... Segmentation fault Many thanks, Lena

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Re. display SPM results on inflated surface?
by Schoot, Lotte 06 Apr '17

06 Apr '17

Thanks so much, I appreciate the help. However, I am not sure what I am supposed to do with the output of the recon-all process. Can I simply use the .dat file that is outputted there in MRI_vol2surf? Lotte Date: Wed, 22 Mar 2017 13:01:42 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] display SPM results on inflated surface? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <41134c50-bb0b-792c-c52b-b6850bcecf3c(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" If you have the T1 for the mni152 (which is somewhere in the bowels of the spm distribution), then you just run recon-all on it. I've done this for myself, so you can just download the result (which I have not checked thoroughly) from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz On 3/21/17 1:27 PM, Schoot, Lotte wrote: > Hi Doug and others, > > A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). > My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf? > What would you recommend to get the register.dat file? Is it possible to use bbregister for that? I have tried this, but I don't know whether it is correct: > > bbregister --s fsaverage --mov con_0001.nii --init-spm --reg > register.dat --bold > > > Thanks! > Lotte > > > >If your results are on the MNI152, you can run the mni152 through > >freesurfer, then use mri_vol2surf to map the data to the surface then > >view it with freeview (or tksurfer). You should not confuse this with > >doing the fMRI analysis on the surface. You will not have the > >benefits of surface-based analysis > > > On 02/15/2017 03:37 PM, Schoot, Lotte wrote: > >/Hi all, />//>/I was wondering if you knew of a way to display SPM > >results onto the />/inflated surface in Freesurfer. />//>/I have > >tried using SurfRend but there seem to be problems which might />/be > >due to the fact the results are obtained with SPM12 and SurfRend > >/>/was designed to work with SPM5. />//>/Thanks, />/Lotte > >/>//>//>/_______________________________________________ > >/>/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer / > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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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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Qdec effect sizes, correlation coefficient
by Juan Baldermann 05 Apr '17

05 Apr '17

Dear all, I did a correlation analysis in qdec and now I want to report effect sizes of my significant clustes. How can I extract a correlation coefficient for this type of analyis? Or any other effect size? I saw that i can derive them from the pcc.mgh file, but this somehow didn't work in matlab...does the gamma.mgh file also have effect sizes per cluster? Kind regards Carlos ________________________________ Dr. med. Juan Carlos Baldermann Wissenschaftlicher Mitarbeiter, Assistenzarzt AG Neurobiologie und Neuromodulation psychischer Erkrankungen Klinik für Psychiatrie und Psychotherapie Universitätsklinikum Köln Kerpener Str. 62 D - 50937 Köln Telefon: 0221- 478 86211 Email: juan.baldermann(a)uk-koeln.de __________________________________________________________________________________________________________ VERTRAULICHKEITSHINWEIS: Diese E-Mail und alle anhängenden Dokumente enthalten Informationen, die ausschließlich für die adressierte Person bestimmt sind. Die Informationen können gemäß den einschlägigen Vorschriften vertraulich und/oder von Veröffentlichungen ausgenommen sein. Das Kopieren und die Weitergabe an nicht autorisierte Dritte sind verboten. Falls Sie nicht der Empfänger sind, benachrichtigen Sie uns bitte umgehend. Danke! CONFIDENTIALITY NOTICE : This email and any documents which may accompany it, contains information, which is intended solely for the use of the individual or entity to which it is addressed, and which may contain information that is privileged, confidential, and/or otherwise exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, any disclosure, dissemination, distribution, copying orother use of this communication or its substance are prohibited. If you have received this communication in error, please contact us immediately. Thank you!

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Registration of both the brain and the "surf" files to the same template.
by Paolo 04 Apr '17

04 Apr '17

TO: freesurfer(a)nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same template. AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the same template, so that I can then take slices of brainmask.mgz and the superimposed WM surface accross subjects and compare them, confident that they are well alligned. WHAT I TRIED: used *mri_robust_register *to register all the brainmask.mgz images to a T1_1mm_template. I looked for the respective "surface" template to register the surfaces, and maybe use *mri_surf2surf*, cannot find a "surface" template that corresponds to the "T1" template. *Ideally I would like to use the same .lta transformation BOTH for the T1 image and the surface*. As I understand (?) they have a different mesh-transformation matrix. Best regards, Paolo

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Comparing LME models
by Bronwyn Overs 04 Apr '17

04 Apr '17

Hi Mailing List, If you are comparing two matlab based linear mixed effects models (vertex-wise) with the same number of random effects (e.g. model with random effect for time vs. model with random effect for age at baseline), which segmentation should you use to estimate the parameters for both models? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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ExploreDTI Workshop!
by Szabolcs David 02 Apr '17

02 Apr '17

Thrilled to announce that we are going to hold an ExploreDTI workshop in Utrecht (July 4-6)! More details can be found here: http://www.exploredti.com/workshop. We hope to see you there! Cheers, Szabolcs

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Freesurfer March 2017