Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30082 discussions

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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optimal T1 protocol
by Jason Tourville 20 May '16

20 May '16

Hello freesurfer experts, Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical reconstruction? For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso" protocol which has PAT = 2 and a TA = 6:02. 􀀈􀀎 I'm wondering if a faster option at the same resolution is now available that is recon-approved? For instance, a multi-band option? Thanks for any feedback, Jason

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Cluster Color
by Timothy Hendrickson 20 May '16

20 May '16

Free Surfer Support, I have been using the command line version for group analysis since my data set has too many factors for QDEC. There are a few things that I enjoy about QDEC that I wish I could incorporate into the command line. 1) In QDEC the cluster color is not set arbitrarily, but rather based on significance. Is there any way to have the cluster color be set based on significance at command line? Is there a way to restrict the available colors that the clusters can be set as? Occasionally, cluster colors are a very similar color to the inflated underlay making it difficult to determine the outline of said cluster. 2) In QDEC one is able to visualize a scatter plot for a particular cluster. Is there any way to do this via the command line option? Thank you, -Tim Hendrickson -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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segfault using brainstem module from dev version
by Vincent Beliveau 20 May '16

20 May '16

Hi list (and Eugenio), I've ran the brainstem module from the dev version on some data processed with FS v5.3. The module created some great segmentations of brainstem but when taking a closer look at the log file, there is 2 seg faults which occur when calls to mri_robust_register are made, with the following output (full log attached, see line 319 and 371): /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register: line 3: 36835 Segmentation fault mri_robust_register.bin "$@" /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register --mov imageDump.mgz --dst /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Segmentation fault mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory I'm curious about how is this affecting the overall process, as otherwise everything appears to be working smoothly. Best, Vincent. -- Vincent Beliveau, MSc Neurobiology Research Unit Juliane Maries Vej 28, 3rd floor Rigshospitalet, building 6931 DK-2100 Copenhagen, Denmark phone: +45 3545 6718 e-mail: vincent.beliveau(a)nru.dk

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Question about group analysis
by Josh Gray 20 May '16

20 May '16

Hello, I've got a very basic question related to group analysis. If I want run a correlation of voxels in the cortex with a variable *controlling *for another continous variable, how do I do this. I know how to run them both in a GLM simultaneously by coding the matrix 0 1 1, however, how do I look at the first variable after controlling for the other? Here is an example of my current fsgd input (I want to control for income): GroupDescriptorFile 1 Title MyTitle Class Class1 plus blue CLASS Class2 circle green SomeTag Variables impulsivity income Input subjid1 Main 10 100 Input subjid2 Main 20 200 etc. -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia

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

20 May '16

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 space2. mri_surf2vol to report the label (subj space) to volume (subj space) Thanks. Stefano

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