[Freesurfer] Postdoc position at the University of Delaware: infant + adolescent fMRI, ANS, EEG
External Email - Use Caution Postdoc with Mary Dozier's Attachment and Biobehavioral Catch-up Lab January 24, 2022 The Attachment and Biobehavioral Catch-Up (ABC) Lab, supervised by Mary Dozier at the University of Delaware (UD), is looking to hire a postdoctoral fellow. The position involves working on one of two randomized clinical trials (RCT) that test the efficacy of an early home visiting intervention (ABC). In one of the RCTs, mothers using opioids and their infants are currently being enrolled. Autonomic nervous system regulation, brain activation (using event related potentials and MRI), cortisol regulation, DNA methylation, attachment, and behavioral regulation are among the variables assessed. The second study assesses adolescents who were first enrolled in an RCT in infancy. All adolescents are scanned at ages 13, 14, and 15, and additional behavioral constructs (inhibitory control, emotion regulation, attachment/affiliation) are assessed. The postdoctoral fellow will be responsible for overseeing research activities. Prior experience with MRI data collection and processing is preferred but not required. This is a full-time benefited position. Salary will follow the NIH postdoc salary scale. Ph.D. required by position start date, preferably in Clinical Psychology, Developmental Psychology, Behavioral Neuroscience, or related field. Strong organizational and interpersonal skills are essential. The position start date is flexible, with a preferred start date in the spring or early summer of 2022. Please send CV and letter of interest to Mary Dozier, mdoz...@udel.edu. More information about the ABC Lab can be found at http://secure-web.cisco.com/1ZTIbTpjH9xQmnw0jjuklLDV1Tav0r5BUlVZbIeqDHOc3ZFl_VChvZTVEJK7n39mc1hzze6SLaMZMZrEtEPS464A_ohLIU_so7MM-YNLh_Dv3ZpIPwi-nlKJkDN3POufH19JO2L1mqm3gJPqZl-3Cxbc38WlcUifD4TBCsaXkrD_UFT85uFzKeGAXQABhSUKMrbMvW1LMDaPhBkBwiECca1ElQcHi-WpNr4JcRgr5bHjo3z9LqRglm8JRoYiSmzVf1Fra8cBgyNZs1P-v82YoDR_kyOvwZwSu7eSnYIv5YmbXJwaattdS_VhN3LeXE0el/http%3A%2F%2Fwww.abcintervention.org%2F -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mko...@udel.edu phone: 646 861 8461 http://secure-web.cisco.com/1ZTIbTpjH9xQmnw0jjuklLDV1Tav0r5BUlVZbIeqDHOc3ZFl_VChvZTVEJK7n39mc1hzze6SLaMZMZrEtEPS464A_ohLIU_so7MM-YNLh_Dv3ZpIPwi-nlKJkDN3POufH19JO2L1mqm3gJPqZl-3Cxbc38WlcUifD4TBCsaXkrD_UFT85uFzKeGAXQABhSUKMrbMvW1LMDaPhBkBwiECca1ElQcHi-WpNr4JcRgr5bHjo3z9LqRglm8JRoYiSmzVf1Fra8cBgyNZs1P-v82YoDR_kyOvwZwSu7eSnYIv5YmbXJwaattdS_VhN3LeXE0el/http%3A%2F%2Fwww.abcintervention.org%2F ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec tutorial video
External Email - Use Caution Hello Freesurfers, I was wondering if anyone has access to a Qdec tutorial, other than the one on the Freesurfer website. The one on the website only covers the basics and it does not have a video component. In case you have a better tutorial available or a video that goes into detail, please send it to me. Thank you, Marta -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mko...@udel.edu phone: 646 861 8461 http://www.abcintervention.org/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in running make_average_subject
External Email - Use Caution Hello Bruce, Doug and Emanuel, I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded the development version and tried that, but neither procedures fixed the problem. In the meantime, my father-in-law took a week and fixed the script and now it runs smoothly and finishes without error. The following code segment of the make_average_subject file needed to be fixed: *Erroneous code segment: * … if($DoSurfaces && $DoVolumes) then set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg) echo $cmd $cmd if($status) exit 1; endif … *New, corrected code segment: * if($DoSurfaces && $DoVolumes) then *#set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)* * set cmd = (recon-all -s $average_subject -nuintensitycor -gcareg -canorm -careg -calabel -cortribbon -aparc2aseg)* echo $cmd $cmd if($status) exit 1; endif … The code that is highlighted with red and a hashtag is what caused the script to exit with errors. The one below that (highlighted with green) is the fixed line of code that finishes without errors. The patched make_average_subject file is also attached. Feel free to use it. Best, Marta (and my father-in-law) On Tue, Jan 22, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > This has been fixed in our development version. I can give you a new > script or you can try this: > cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI! > ln -s orig.mgz norm.mgz > Then re-run make_average_subject > > > > > * > On 12/14/18 1:43 PM, Emanuel Alvaredo wrote: > > > > External Email - Use Caution > > > > Thanks Greve. The output is attached now. > > > > > > Emanuel > > > > > > On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > can you include the full terminal output? > > > > On 12/13/18 7:45 AM, Emanuel Alvaredo wrote: > >> > >> External Email - Use Caution > >> > >> Hello Bruce, thanks for your anwer. Sure. The command is > >> > >> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects > >> Bartley_Recon Baez_Recon Bonilla_Recon* > >> > >> The output is in the attached file > >> > >> Thanks! > >> > >> Emanuel > >> > >> > >> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl > >> mailto:fis...@nmr.mgh.harvard.edu>> > >> wrote: > >> > >> Hi Emanuel, > >> > >> can you include the full command line and output? > >> > >> cheers > >> Bruce > >> On Wed, 12 Dec 2018, > >> Emanuel Alvaredo wrote: > >> > >> > > >> > External Email - Use Caution > >> > > >> > Thanks for your answer Douglas. I replaced the > >> make_average_surface file with the new one but I > >> > have the same message error. > >> > ASeg Vox2RAS: --- > >> > -1.0 0.0 0.0 128.0; > >> > 0.0 0.0 1.0 -128.0; > >> > 0.0 -1.0 0.0 128.0; > >> > 0.0 0.0 0.0 1.0; > >> > mghRead(mri/norm.mgz, -1): could not open file > >> > - > >> > > >> > Labeling Slice > >> > relabeling unlikely voxels in interior of white matter > >> > mri/norm.mgz: could not load norm volume from (null) > >> > > >> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP > >> Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64 > >> > x86_64 GNU/Linux > >> > > >> > Thanks > >> > > >> > Emanuel > >> > > >> > > >> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. > >> mailto:dgr...@mgh.harvard.edu>> wrote: > >> > Sorry, the disk that held that patch failed and we > >> did not have a backup so not > >> > everything was restored. I just put this file there: > >> > > >> > > >> > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface > >> > > >> > Copy it to $FREESURFER_HOME/bin. Let me know how it goes > >> > > >> > > >> > On 12/10/18 12:48 PM, Emanuel Alvaredo wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Thanks Bruce. The following is the command. > >> > > >> > make_average_subject --out avgsubjectPRUEBAESTASIEmac > >> --subjects subject1 > >> > subject2 subject3 > >> > > >> > > >> > And I made a mistake in may last mail. I use the word path > >> instead of patch > >> > > >> > I have found this page with a patch for de issue > >> > > >> > > >> > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html > >> > > >> >
Re: [Freesurfer] Error in running make_average_subject
External Email - Use Caution Hello Bruce, Greve and Emanuel, I have an identical problem. Have you found a solution to this issue? I'm attaching my recon-all.log, as well, in case you need it. Thank you! Marta On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo wrote: > External Email - Use Caution > > Thanks Greve. The output is attached now. > > > Emanuel > > > On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> can you include the full terminal output? >> >> On 12/13/18 7:45 AM, Emanuel Alvaredo wrote: >> >> External Email - Use Caution >> Hello Bruce, thanks for your anwer. Sure. The command is >> >> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects >> Bartley_Recon Baez_Recon Bonilla_Recon* >> >> The output is in the attached file >> >> Thanks! >> >> Emanuel >> >> >> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl >> wrote: >> >>> Hi Emanuel, >>> >>> can you include the full command line and output? >>> >>> cheers >>> Bruce >>> On Wed, 12 Dec 2018, >>> Emanuel Alvaredo wrote: >>> >>> > >>> > External Email - Use Caution >>> > >>> > Thanks for your answer Douglas. I replaced the make_average_surface >>> file with the new one but I >>> > have the same message error. >>> > ASeg Vox2RAS: --- >>> > -1.0 0.0 0.0 128.0; >>> > 0.0 0.0 1.0 -128.0; >>> > 0.0 -1.0 0.0 128.0; >>> > 0.0 0.0 0.0 1.0; >>> > mghRead(mri/norm.mgz, -1): could not open file >>> > - >>> > >>> > Labeling Slice >>> > relabeling unlikely voxels in interior of white matter >>> > mri/norm.mgz: could not load norm volume from (null) >>> > >>> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 >>> 17:16:02 UTC 2018 x86_64 x86_64 >>> > x86_64 GNU/Linux >>> > >>> > Thanks >>> > >>> > Emanuel >>> > >>> > >>> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. < >>> dgr...@mgh.harvard.edu> wrote: >>> > Sorry, the disk that held that patch failed and we did not have >>> a backup so not >>> > everything was restored. I just put this file there: >>> > >>> > >>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface >>> > >>> > Copy it to $FREESURFER_HOME/bin. Let me know how it goes >>> > >>> > >>> > On 12/10/18 12:48 PM, Emanuel Alvaredo wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Thanks Bruce. The following is the command. >>> > >>> > make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects >>> subject1 >>> > subject2 subject3 >>> > >>> > >>> > And I made a mistake in may last mail. I use the word path instead of >>> patch >>> > >>> > I have found this page with a patch for de issue >>> > >>> > >>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html >>> > >>> > But I dont know how to apply the patch. Can you give some information >>> about this? >>> > >>> > >>> > Emanuel >>> > >>> > >>> > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> wrote: >>> > Hi Emanuel >>> > >>> > you need to send us the full command you ran and output of it if >>> you want >>> > us to be able to help you >>> > >>> > cheers >>> > Bruce >>> > On Fri, 7 Dec 2018, Emanuel Alvaredo wrote: >>> > >>> > > >>> > > External Email - Use Caution >>> > > >>> > > Hello!, I am getting the following error using the >>> > command make_average_subject >>> > > >>> > > mri/norm.mgz: could not load norm volume from (null) >>> > > >>> > > I have found this page with a path for de issue >>> > > >>> > > >>> > >>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html >>> > > >>> > > But I dont know how to apply the path. Can you give some >>> information about >>> > this? >>> > > >>> > > Thanks! >>> > > >>> > > >>> > > >>> > > Emanuel >>> > > >>> > >___ >>> > 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 >>> > >>> > >>> > ___ >>> > 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 >> >> >> >> ___ >>
[Freesurfer] nu_correct ERROR (FreeSurfer v6)
External Email - Use Caution Dear FreeSurfer Developers, I have the most recent version of FreeSurfer installed on a MacOS Mojave (10.14) and as I was running recon-all, I received the following error message: "Assertion failed at line 742 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Darwin Martas-MacBook-Pro.local 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 recon-all -s plc0061 exited with ERRORS at Tue Nov 20 22:32:15 EST 2018" I reviewed many threads on the same error message, but none of them were solved. I have the same version of FreeSurfer on two other MacBooks (with older versions of iOS) and both work fine. I ran fixup_mni_paths as it was suggested on multiple threads and nu_correct, as well and I got the following message: "nu_correct nu_correct, version 1.12.0 Usage: nu_correct [-help] [options] in.mnc out.mnc" Any thoughts on what the problem might be and how it could be fixed? Could this be an iOS compatibility issue? Gratefully, Marta -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mko...@udel.edu phone: 646 861 8461 http://www.abcintervention.org/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
