Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

Mult-Shell Tracula Help
by Kristina Jelinkova 20 May '16

20 May '16

Hello all, I had a question regarding the program Tracula. I have two different DTI sequences that I wish to run (b=900 and b=2000) but am unsure at which step I am suppose to merge the two sequences together. At this point, I have pre-processed each of the sequences separately using trac-all. Should I take each of the separate trac-all output data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick model fit on the new bedpostX output? Also, is there a way to use nii.gz files in the configuration file rather than a dcm list? Thank you in advance for your help!

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trac-all problem
by Zeng, Qi 20 May '16

20 May '16

Hi, I am running dti data with trac-all. I followed the command: trac-all -prep -c /Studies/*/DTI/dmrirc_subject but it exited with error "*Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension." * Before. there is another post about similar problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.… Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but new version wouldn't need this (5.3, a new version?). If so, where can I obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec? Best, Qi

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Re: [Freesurfer] Fwd: trac-all -path error
by Elijah Mak 20 May '16

20 May '16

Dear Anastasia Yendiki, I ran into a hitch while running trac-all -path and came across an identical problem where there was a segmentation fault. I have attached my error and log files. Loading initial proposal SD's from /subject/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt Processing pathway 2 of 18... Initializing MCMC I have also checked the aparc+aseg and aparc+aseg_mask (overlaid on FA; screenshot attached) as you have suggested, but I can't seem to find anything that would have compromised the -path process. What else could have gone wrong? trac-all -path works for other subjects. Thanks for your help. Best Wishes, Elijah

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Re: [Freesurfer] Inquiry a single curve problem for Tracula outputs
by Anastasia Yendiki 20 May '16

20 May '16

Hi Xiaofu - It's hard to tell but it looks like the brain mask (which comes from the structural data) is a bit too large in the temporal lobe, so it's possible that the structural-to-diffusion registration didn't go so well for this subject. You can check on this by overlaying the structural segmentation transformed into diffusion space (from dlabel/diff/aparc+aseg...) onto the FA map. Best, a.y On Sun, 1 May 2016, Xiaofu wrote: > Dear Anastasia or Tracula-group, > I have run Tracula and found there was only one single curve for some tracts. But others went well. I tried setting reinit parameter to 1 and > rerunning > "trac-all -prior" and "trac-all -path" but didn't get improved, e.g., the right UNC was a single curve (see attached). I also checked the two end point > set of right UNC (i.e.,endpt1.pd.nii.gz and endpt2.pd.nii.gz) (see attached) and found those end points were visually not correct when loaded to FA > image. I guess that may be the reason of the single curve problem. Is there anyway to fix this problem? Moreover, do you have any suggestions on the > tract statistics for those single curve tracts. I'd appreciate it if could take a look at it for me. If you need more files for the diagnosis please let > me know. > Looking forward to hearing from you. Thank you very much. > > Best, > Xiaofu > >

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Tracula Pathway reconstruction
by Peggy Skelly 20 May '16

20 May '16

Hi Tracula Experts, How do you determine if a pathway reconstructed well? I've been examining the merged pathways (<subj>/dpath/merged_avg33_mni_bbr.mgz) in freeview, and if the pathway looked too small when viewing with the default threshold, I would reinitialize those pathways. Most of the time, the new pathway would look ok upon re-inspection. A few pathways, however, still appear too small when viewed at the default threshold in Freeview, but at lower thresholds, they begin to look ok. I've encountered 1 pathway that still appears too small in Freeview, but the output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable. On the other hand, its path distribution (path.pd.nii.gz) does not look like a distribution, but a single path -- there are a 38 voxels with values of 4000, and all others are 0. This doesn't seem right. What could cause this to happen? What objective measure can I use to determine if a pathway is reconstructed well enough? Thanks, Peggy

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bvals bvecs Error
by Marissa Pifer 20 May '16

20 May '16

Hi freesurfers, I'm having a problem the bvals and bvecs for one of my subject's DTI data. When I try to run the first step of tracula I get this error message: "Error: data and bvals/bvecs do not contain the same number of entries" I have checked, the bvals and bvecs do contain the same amount of entries (42), and they are in the proper format (bvals one line, bvecs three lines). The entries in the bvals/bvecs matches the number of images within the DTI file as well. Looking online, I saw that this was part of the FAQs on tracula. It suggested making sure the locale settings were correct, which it is (en_US.UTF-8). I've run tracula on every other subject and have not run into this problem, but the same subject had an error with multiple frames when we were processing the T2 images. Could this be related? Any idea about what is going on, or how I can fix it? Thanks in advance, Marissa

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REPOST: TRACULA dev version: Error message
by Elijah Mak 20 May '16

20 May '16

Hi Freesurfer, Sorry about reposting this email from earlier: I can't seem to get the TRACULA in the dev version of FS6 to run. mv -f /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs mv: rename /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs to /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs: No such file or directory The contents of that folder are: dwi_orig.mghdti.bvals dwi_orig.mghdti.bvecs dwi_orig.nii.gz dwi_orig_flip.nii.gz xfms The full error message is enclosed with this email. Thanks! Best Wishes, Elijah

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R: R: Re: R: MASK.label from fsaverage to volume in subject space
by stdp82＠virgilio.it 20 May '16

20 May '16

mri_label2label --srclabel rhrh.label --srcsubject fsaverage --trgsubject SUBJ --trglabel SUBJ_rhrh --regmethod surface --hemi rh does not produce output. Suggestions are very wellcome. Thanks Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 20-mag-2016 19.51 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: R: MASK.label from fsaverage to volume in subject space > >label2label and label2vol are options? > >mri_label2label --srclabel ROI.label --srcsubject fsaverage --trgsubject >Control61 --trglabel prova.label --hemi rh --regmethod surface > >I have tried the command line above ma the mask output is miss registered > > >Stefano > > > >>----Messaggio originale---- >>Da: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>Data: 20-mag-2016 14.38 >>A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh. harvard. >edu> >>Ogg: Re: [Freesurfer] R: MASK.label from fsaverage to volume in subject space >> >>sure, that should work >> >>cheers >>Bruce >>On Fri, 20 May 2016, stdp82(a)virgilio.it wrote: >> >>> Specifically, I have a .label from tksurfer and I would like to report this >>> label on subj orig.nii.gz >>> >>> ----Messaggio originale---- >>> Da: stdp82(a)virgilio.it >>> Data: 20-mag-2016 10.36 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject >>> space >>> >>> Hi list, >>> to trasform a MASK.label (created by tk surfer) from surface to volume >>> is correct to use: >>> >>> 1. mri_surf2surf to register the mask from fsaverage to subj space >>> 2. mri_surf2vol to report the label (subj space) to volume (subj >>> space) >>> >>> Thanks. >>> >>> >>> Stefano >>> >>> >>> >>>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)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(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: R: MASK.label from fsaverage to volume in subject space
by stdp82＠virgilio.it 20 May '16

20 May '16

label2label and label2vol are options? mri_label2label --srclabel ROI.label --srcsubject fsaverage --trgsubject Control61 --trglabel prova.label --hemi rh --regmethod surface I have tried the command line above ma the mask output is miss registered Stefano >----Messaggio originale---- >Da: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Data: 20-mag-2016 14.38 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard. edu> >Ogg: Re: [Freesurfer] R: MASK.label from fsaverage to volume in subject space > >sure, that should work > >cheers >Bruce >On Fri, 20 May 2016, stdp82(a)virgilio.it wrote: > >> Specifically, I have a .label from tksurfer and I would like to report this >> label on subj orig.nii.gz >> >> ----Messaggio originale---- >> Da: stdp82(a)virgilio.it >> Data: 20-mag-2016 10.36 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject >> space >> >> Hi list, >> to trasform a MASK.label (created by tk surfer) from surface to volume >> is correct to use: >> >> 1. mri_surf2surf to register the mask from fsaverage to subj space >> 2. mri_surf2vol to report the label (subj space) to volume (subj >> space) >> >> Thanks. >> >> >> Stefano >> >> >> >>_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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. >

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TWO Postdoctoral Research Associate Positions Opened
by Corbo, Vincent 20 May '16

20 May '16

The Translational Research Center for TBI and Stress Disorders (TRACTS) at VA Boston Healthcare invites applications for two positions as Postdoctoral Research Associate in brain imaging of Veterans. The TRACTS conducts a prospective longitudinal cohort study and has recruited over 500 Veterans from the greater Boston area. The research employs a multimodal approach to examine the effects of prevalent conditions including traumatic brain injury (TBI), posttraumatic stress disorder (PTSD), chronic pain, depression, and other military-related disorders on the health, behavior, and neural function of Veterans. This project is conducted at the Jamaica Plain campus of the VA Boston Healthcare system, and includes behavioral testing, clinical interviews, and neuroimaging. We have an opening for two Postdoctoral Researchers focused on the neuroimaging aspects of the study, which includes magnetic resonance imaging (MRI) of brain structure and function (diffusion tensor imaging, arterial spin labeling, functional connectivity, etc.). We are seeking highly motivated, proactive candidates who are willing to learn new skills and contribute to multiple projects as part of a larger team. We are seeking a postdoctoral research associate for the neuroimaging portion of the TRACTS study, as well as a second postdoctoral research associate for a project that will use MRI and positron emission tomography (PET) of dopamine receptor mapping in individuals from the TRACTS cohort with a history of binge drinking. This project will take place at the Jamaica Plain campus of the VA Boston Healthcare system and at the Athinoula A. Martinos Center for Biomedical Imaging located in Charlestown. Successful candidates of both positions will have major roles in the primary research project including management of the technical/imaging aspects of the study as well as project management/administration, and training and mentorship of research assistants on the project. The researchers will contribute to all aspects of the work including (but not limited to) participant enrollment, characterization, operation of the MRI (and PET) scanners, data management, organization, processing and analysis, manuscript preparation and publications. The researchers will work in close collaboration with clinical neuropsychologists, cognitive neuroscientists, and research assistants, and will likely be involved in multiple projects. There will be significant training and collaboration with the Neuroimaging Research for Veterans (NeRVe) Center, also at VA Boston. Individuals with PhD or equivalent in computer science, biomedical engineering, neuroscience, psychology, or related fields are welcome. Prior experience in brain imaging research and use of neuroimaging software (FSL/Freesurfer/AFNI/SPM) is required. It is additionally expected that individuals will devote time to training to learn new image processing and analysis procedures while in this position. The ideal candidate will have strong computer skill, including expertise in Unix/Linux operating systems, MATLAB, shell scripting, and statistics, and strong prior experience in brain imaging research. The positions also require strong organization, communication, and writing skills. A minimum of a two-year commitment (with opportunity for a longer position) is required, and positions are available beginning immediately. US Citizenship is required. Salary will be consistent with levels in accordance with the Boston VA Medical Center policies for postdoctoral researchers. Compensation includes full staff benefits, including health insurance, and vacation time. Interested candidates should send a cover letter and copy of their CV to Gino Jackson, Administrative Officer, at gino.jackson(a)va.gov . ____________________________ Vincent Corbo, Ph.D. Postdoctoral fellow Translational Research Center for TBI and Stress Disorders (TRACTS) Neuroimaging Research for Veterans (NeRVe) Center Veterans Affairs Boston Healthcare System Boston University School of Medicine

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