Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

volume to surface
by 赵越 19 Dec '13

19 Dec '13

Hi All, I would like to use "mri_vol2surf" to overlay a volume onto a surface. The synopsis is mri_vol2surf [<options>] --src inputfile --out outpufile --srcreg registrationfile --hemi hemisphere.But I don't know how to generate the registrationfile. Could someone help me with that? Thanks a lot! Yue

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POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE
by Jon Wieser 19 Dec '13

19 Dec '13

POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE. Sponsor: Krista Lisdahl, Ph.D. A Postdoctoral Fellow position at the University of Wisconsin-Milwaukee (UWM), Psychology Department (http://www4.uwm.edu/letsci/psychology/) will be available starting September 2014 (start date is negotiable). Neuroimaging (fMRI, DTI) will be conducted at the Medical College of Wisconsin’s (MCW) world-renowned Center for Imaging Research (http://www.mcw.edu/biophysics/mri/cir.htm) Dr. Krista Lisdahl, a licensed clinical neuropsychologist with specialization in addiction and neuroimaging, will supervise the fellowship. The objective of this NIH-funded research is characterize the effects of marijuana (MJ) use on frontolimbic brain structure, functioning and connectivity in youth by the creation of IDEAA (Imaging Data in Emerging Adults with Addiction), a multi-site consortium comprised of investigators (Drs. Krista Lisdahl, Staci Gruber, Susan Tapert, Francesca Filbey) using common, overlapping neuroimaging and behavioral measures in over 600 MJ-using and healthy control adolescents and emerging adults. Other areas of study within the laboratory include chronic effects of alcohol/binge drinking, MJ, nicotine and ecstasy use on neurocognition; healthy adolescent and emerging adult neurodevelopment; imaging genetics; multi-modal neuroimaging research methods; effects of exercise and body fat on neurocognition; and neuropsychological measurement. Collaborative opportunities and rich didactic experiences at UWM and MCW are available within a wide range of disciplines, especially affective neuroscience, cognitive rehabilitation, clinical neuropsychology, and exercise science. Clinical Experience. Opportunities for supervised clinical neuropsychology work may be arranged at UWM, MCW or the Milwaukee VA for students interested in ABPP-CN certification. However, this is not an official part of the postdoc. Funding: The position will be funded by Dr. Lisdahl’s NIDA grants. Duties will include: processing and analyzing MRI data; completing neuropsychological assessments; managing research assistants; manuscript and grant preparation. Travel funding to conferences will be available. Requirements include: Ph.D. in psychology, neuroscience or related discipline with strong interest in developing research career in addiction neuroscience or adolescent neurodevelopment. Experience with fMRI/DTI-related research methods (e-prime programming; AFNI, Freesurfer, FSL processing; fcMRI analysis methods) are preferred. Position is available for 1 year with the option of extending up to 3 years, depending upon performance and mutual interest. To apply please send cover letter, CV, statement of research interests and goals, and 3 letters of reference to Dr. Krista Lisdahl (krista.medina(a)gmail.com) Applications due July 2014, but will be reviewed on a rolling basis. UWM and Dr. Lisdahl strongly value diversity and are committed to equal opportunity in employment.

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Does this registration need to be fixed?
by sujith vijayan 19 Dec '13

19 Dec '13

Hi All, I am wondering whether the talairach registration for one of my subjects needs to be fixed. It looks a little off to me, but I am not sure from reading the instructions on https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview whether the degree of difference I am seeing is to be expected or not. I've attached a screen shot. Thanks, Sujith [image: Inline image 1]

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2 post-docs in cognitive neuroscience of memory (fMRI and neuropsychology)
by Chris Bird 19 Dec '13

19 Dec '13

Two post-doc positions in cognitive neuroscience of episodic memory Sussex is sunny. Memory is interesting. 2014 is looming. Time for a new job? Two 3-year positions are available to work with Chris Bird on a European Research Council funded project (TRANSMEM) at the University of Sussex in Brighton, UK. One of the post-docs will carry out fMRI investigations of episodic memory using video clips and virtual reality as memoranda. The other will combine fMRI and neuropsychology to investigate memory loss in Alzheimer's disease. Closing date for applications is 16th of January, so get applying! For more details see: http://www.jobs.ac.uk/job/AHV248/post-doctoral-research-fellows-cognitive-n… http://www.sussex.ac.uk/psychology/memory/index

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visualizing lh.gender_age.thickness.10.mgh after mris_preproc
by Rujing Zha 19 Dec '13

19 Dec '13

Dear all, I read the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and I want to know how to visualize the lh.gender_age.thickness.10.mgh. Thanks. All the best. 2013-12-17 Rujing Zha

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Re: [Freesurfer] New features in TRACULA
by Anastasia Yendiki 19 Dec '13

19 Dec '13

Hi Ruth - It's possible that your scans don't have any slices with excessive intensity drop-out. You can gauge that visually, by checking if there are any slices that are much darker than their neighbors. Any operation that performs interpolation on the image intensity values, and thus smooths the images, will affect estimates of intensity drop-out. To what extent exactly, it's impossible to guess. You can just try running them before the bias field correction and see what happens. a.y PS: Please send all tracula-related emails to the freesurfer list and not to me only. The freesurfer list gets archived so that users can search for answers and we can avoid replication of questions. Thanks! On Wed, 18 Dec 2013, Ruth Carper wrote: > So the images should be prior to bias field correction as well? I ran it on > images post bias field correction (but pre eddy_correct) and your dropout > measures (3rd and 4th values) were 0 and 1 respectively for every brain. > > --Ruth > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Ruth Carper <rcarper_99(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, December 18, 2013 8:06 AM > Subject: Re: [Freesurfer] New features in TRACULA > > > Hi Ruth - If you apply the same mask to all the volumes in the DWI series, > it's not a problem. The important thing is not to have applied any > operation that would change the intensities of the images inside the > brain. So these should NOT be the DWIs after the eddy_correct step, they > should be before it. > > a.y > > On Tue, 17 Dec 2013, Ruth Carper wrote: > > > Thanks! I was able to run that with no problem. But as I read the wiki > > closely I notice that with your TRACULA pipeline dmri_motion is processing > > images that are still skull-on. Any thoughts on whether your algorithms > > would work properly if the skull was removed prior to eddy correction? I > > would think the rotation and translation measures would still be fine, but > I > > don't know how you've automated the 2 measures of signal dropout. My dwi > > file is also skull removed. > > > > --Ruth > > > >___________________________________________________________________________ > _ > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > To: Ruth Carper <rcarper_99(a)yahoo.com> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Sent: Tuesday, December 17, 2013 1:28 PM > > Subject: Re: [Freesurfer] New features in TRACULA > > > > > > Hi Ruth - If you download the update and unzip it, you'll see an > > executable called dmri_motion. You can run it without any arguments to see > > the help text. > > > > Try something like this: > > dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals > --out > > output.txt > > > > a.y > > > > On Fri, 13 > > Dec 2013, Ruth Carper wrote: > > > > > > > > Thanks. We haven't yet implemented TRACULA but have run eddy_correct on > > all > > > the brains in our existing pipeline and still have the ecc.log files. > Is > > > there a command line that would let us generate your motion measures > > without > > > running TRACULA? > > > > > > --Ruth > > > > > > > > > > >>__________________________________________________________________________ > _ > > _ > > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > > To: Ruth Carper <rcarper_99(a)yahoo.com> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > > Sent: Tuesday, December 10, 2013 8:28 PM > > > Subject: Re: [Freesurfer] New features in TRACULA > > > > > > > > > Hi Ruth - Glad to hear this is useful to you. The rotation and > translation > > > parameters are extracted from the affine registration of each DWI volume > > > to the first volume, which in trac-all is performed by eddy_correct. > > > > > > a.y > > > > > > On Tue, 10 Dec 2013, Ruth Carper wrote: > > > > > > > Hi Anastasia, > > > > We discussed your paper at our lab meeting yesterday so this was > perfect > > > > timing on the release of motion measures in your updated TRACULA. > But > > I > > > > wasn't clear where the numbers are coming from in your new update. Is > > > this > > > > from EDDY? eddy_correct? Some other registration step? > > > > > > > > Thanks, > > > > Ruth > > > > > > > > > > > > > > > > > > > > > > > > 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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unpacksdcmdir: specifies unpacking rules from the command-line ERROR
by Rujing Zha 19 Dec '13

19 Dec '13

Hi Bruce, It generated a 013 subfolder in after running this code "unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz". It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao", and it finished without error. "recon-all -s liujunhao -all" was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 Rujing Zha

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tcsh in groupanalysis
by Rujing Zha 18 Dec '13

18 Dec '13

Hi all, I learned the tutorial in the website "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". At the beginning of the manu, it told me to run command in tcsh. Can I just run commands in bash shell. If so, what is the function of tcsh? Thanks. All the best. 2013-12-18 Rujing Zha

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design matrix and contrast in fsgdf
by Rujing Zha 18 Dec '13

18 Dec '13

Dear all, I want to design a group t-test analysis and correlation analysis for pial thickness. I have read the PPT of freesurfer.groupanalysis, and I wrote a specific design matrix and contrast for my data. However it is the first time that I design matrix in fsgdf by freesurfer. I didnot confirm whether I wrote is correct. I need someone to help me review it. I have two groups, four groups were classified as sex.(Is this necessary or correct?) Here is my design matrix in fsgdf for 2 group t-test: GroupDescriptorFile 1 Title lh_ttest Class con_male Class con_female Class pat_male Class pat_female Variables Age edu Input subjid1 con_male 19 10 Input subjid2 con_male 20 20 Input subjid3 con_male 20 20 Input subjid4 con_male 19 10 Input subjid5 con_female 20 20 Input subjid6 con_female 20 20 Input subjid7 con_female 19 10 Input subjid8 pat_male 20 20 Input subjid9 pat_male 20 20 Input subjid10 pat_male 19 10 Input subjid11 pat_female 20 20 Input subjid12 pat_female 20 20 DefaultVariable Age In this section, I just want to compare the patient group(class 3 and 4) and control group(class 1 and 2) in thickness controling the age and education by ANCOVA. Does this fsgdf implement ANCOVA? Here is my contrast for this: 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 Here is my design matrix in fsgdf for partial regression: GroupDescriptorFile 1 Title lh_regression Class con_male Class con_female Class pat_male Class pat_female Variables Age edu score1 score2 Input subjid1 con_male 19 10 20 30 Input subjid2 con_male 20 20 20 30 Input subjid3 con_male 20 20 20 30 Input subjid4 con_male 19 10 20 30 Input subjid5 con_female 20 20 20 30 Input subjid6 con_female 20 20 20 30 Input subjid7 con_female 19 10 20 30 Input subjid8 pat_male 20 20 20 30 Input subjid9 pat_male 20 20 20 30 Input subjid10 pat_male 19 10 20 30 Input subjid11 pat_female 20 20 20 30 Input subjid12 pat_female 20 20 20 30 DefaultVariable score1 In this section, I want to implement partial regression analysis(i.e. score1 and score2) by controling the age,edu and sex. Here is my contrast for score1: 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 Here is my contrast for score2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 Any reply will be highly appreciated. Thanks. All the best. 2013-12-17 Rujing Zha

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Generating list of subjects: a tcsh scripting problem
by Emad Ahmadi 18 Dec '13

18 Dec '13

Hello, I am having a tcsh scripting problem for generating a text file containing the list of subjects, and I would appreciate any help. I've explained my problem here: http://stackoverflow.com/q/20617206/2769441 All the best, Emad

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