Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Tumor Segmentation in FreeSurfer
by Mohammed Goryawala 11 Apr '14

11 Apr '14

Hello FreeSurfer Experts, On review of stats file in FreeSurfer a tumor volume is reported. How is tumor segmentation achieved by FreeSurfer? Thank you Mohammed Goryawala, PhD

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Subcutaneous fat and intensity normalisation
by N. Medic 11 Apr '14

11 Apr '14

Dear FreeSurfers, I have a question concerning pctsurfcon and subcutaneous fat. The first step in the Freesurfer processing pipeline is intensity normalisation, which assumes that high intensity signal is due to white matter and uses this as a reference point. However this happens prior to skull stripping and therefore slices contain subcutaneous fat, which also has a high signal intensity. When processing images from obese subjects might the large amount of subcutaneous fat affect intensity normalisation thereby affecting measures like pctsurfcon further down the line? Or does freesurfer distinguish between subcutaneous fat and white matter? Thanks Nenad

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Re: [Freesurfer] Intermediate stages of cortical inflation
by Bruce Fischl 11 Apr '14

11 Apr '14

yes, many of our binaries take the -w <n> flag to write out a snapshot of the minimization every nth step, including mris_sphere cheers Bruce On Thu, 10 Apr 2014, Xuelong Zhao wrote: > Is it also possible to track the inflation all the way to the sphere? I was hoping that > I could take snapshots of equi-area intermediate forms as the cortex is unfolded onto > the sphere instead of stopping at the inflated cortex. Thanks. > > > > > Date: Wed, 9 Apr 2014 08:31:46 -0400 > > From: fischl(a)nmr.mgh.harvard.edu > > To: freesurfer(a)nmr.mgh.harvard.edu > > CC: greve(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation > > > > you can use -w 1 to write out every step in the inflation process and > > choose what you want. If you want it to preserve surface area during > > inflation (as opposed to just at the end), also include -scale 1 > > > > cheers > > Bruce > > > > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > > > Hi, > > > > > > I would like to ask whether it is possible to display different levels of > > > cortical inflation? > > > > > > I have been using the command: mris_inflate > > > > > > but the -dist and -n flags do not seem to make that much difference. Also, > > > if I use fsaverage lh.orig as the input file and using the default options > > > for mris_Inflate I don't seem to be able to recover the lh.inflated surface. > > > > > > Are there any alternative commands to control the level of inflation? > > > Thanks. > > > > > > > > > > > > > > _______________________________________________ > > 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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longitudinal template generation with manual registration
by Andreas Werner 10 Apr '14

10 Apr '14

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Vertexwise surface area value?
by sabin khadka 10 Apr '14

10 Apr '14

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject <subject dir> area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin

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Large areas of white matter ignored, even with control points
by Andrea Grant 10 Apr '14

10 Apr '14

Hello, I'm working with T1 weighted scans obtained at 7T and have a problem with a subject. I preprocess the images to deal with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have successfully segmented about 20 scans. I often need to use control points, but they normally work just as I expect. However, I have one subject where large areas of the brain are completely excluded from the segmentation (basically the entire occipital lobe). I added control points and re-ran, to no effect. I'm attaching a screenshot of the brainmask with surfaces, my control points, and the white matter mask. Clearly, the skull stripping wasn't very successful (I adjusted the watershed threshold manually, but at one value I got the current result and at a single integer lower I lost half the brain). I have successfully segmented other subjects with equally poor skull strips, though, so I don't believe this has any bearing on the current issue. Is editing the white matter mask the only way to fix this? If so, do I need to carefully fill in on every slice, or can I just brush in here and there to sort of "goose" the white matter into that region? I can do the slice by slice fix, but if there's a way to avoid the several hours it will take me, I would love to know! Thanks, Andrea ----- Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0260(a)umn.edu umn.edu/~gran0260 <http://umn.edu/%7Egran0260>

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Post-doctoral Research Position at Columbia University
by Jiook Cha 10 Apr '14

10 Apr '14

Post-doctoral Research Position at Columbia University A postdoctoral research position is currently available at Columbia University and the New York State Psychiatric Institute. Candidates must have completed a PhD in clinical, developmental, or cognitive neuroscience, or a related field. Research focuses on translational and developmental neuroimaging. Candidate should be interested in multimodal MRI techniques, attentional and related disorders in children and young adults, and the development of biomarkers of treatment response. Candidates with experience in the following areas are preferred: a) Computer programming skills (e.g., in C/C++, Python, MATLAB) b) Facility in operating of one or more common neuroimaging packages (e.g., AFNI, FSL, or SPM) Applicants should email their CV to Jonathan Posner, MD: jep2111(a)columbia.edu

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select_talairach_point function?
by Celine Louapre 10 Apr '14

10 Apr '14

Hi I am sorry if my question is really basic, but I am choosing the seeds for fsfast resting state connectivity analysis, and I am looking at the different options in the litterature. Seeds are often presented with the talairach coordinates, and I was looking for a way to find the corresponding vertex number on fsaverage surface, so that I can build the corresponding label that I could use for the fcseed-sess command. I found this previous email, and there seem to be a command to do that but I don't know how to launch this command select_talairach_point <xtal> <ytal> <ztal> Thank you very much Celine > -----Message d'origine----- > De : Bruce Fischl [mailto:fischl at nmr.mgh.harvard.edu] > Envoyé : mercredi, 10. février 2010 16:18 > À : Ben Hamida Cammoun Leila Faiza > Cc : freesurfer at nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] ROI based on Talairach coordinate > > Hi Leila, > > you can use the tcl command > > select_talairach_point <xtal> <ytal> <ztal> > > in tksurfer in the tcl window (with the % prompt), then make a label from > that point and dilate it a few times. > > cheers, > Bruce > On Wed, 10 Feb 2010, Ben Hamida > Cammoun Leila > Faiza wrote: > >> Dear Freesurfer users and experts, >> This is my second attempt :( >> I am trying to construct a roi based on some talairach coordinate coming from a paper, but I completely fail to do it with matlab and neither manually with tksurfer. >> My first try was to use the transformation Talairach.xfm with matlab, inverse it and try to recover RAS coordinate, it gives me completely wrong values. >> Second try was to introduce the Tal coordinate directly in Tksurfer, which is not possible I think (correct me if I am wrong), with the version I have the is a bug in tkmedit I guess when introducing Talairach coord (the ideas was to save them and to load the vertex in tksurfer).. the values changes in the edit box.. >> Is there another way?? >> Is it possible with script? Or how to do this by matlab? >> Please don't ignore the request. >> Leila

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Easy automated workflow for separating non-contiguous labels
by Michael Waskom 10 Apr '14

10 Apr '14

Hi Freesurfers, Some of the Freesurfer annotations (specifically the Yeo atlases) have multiple disconnected regions with the same label. What's the best way to separate these annotations (or the labels produced by mri_annotation2label) so that I can get multiple label files where each label has all contiguous vertices? In other words, I want to do something like a clustering procedure, and I'd like to stay on the surface. Can this be done (easily)? Thanks Michael

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caudate and putamen to surface
by gong jinnan 10 Apr '14

10 Apr '14

Dear all, I want to use caudate and putamen as seed in surface to do PROBTRACK in FSL. For doing that, I acquired target surface which in the cortex seed using kris_convert and label2surf script. But I met some problems in extracting caudate and putamen in the surface. At first I used "mdi_extract_label sub1/mri/aseg.auto.noCCseg.mgz 11 /test/L_Caudate.mgz” and it generated L_Caudate.mgz correctly. And then in order to do mri_vol2surf I did bbregister used “bbregister —s sub1 —mov sub1/mri/brain —init-fsl —reg sub1/mri/register.dat”. Then “mdi_vol2surf —src /test/L_Caudate.mgz —srcreg sub1/mri/register.dat —promfrac 0.5 —hemi lh —out /test/L_Caudate2surf.mgz”. Everything looked like went well by the time. But it’s weird when “mri_binarize —i /test/L_Caudate2surf.mgz —min 0.5 —o /test/L_Caudate2surf_bin.mgz” , it showed “Dound 0 values in range” and “Found 0 voxels in final mask”. I checked /test/L_Caudate.mgz and found it was correct. I am wondering is that because of register.dat which I am not very clear how to acquire it correctly? Or is that because lh.white was default used in mri_vol2surf? Could you give me any advises to work around this program? And may be about how to acquire register.dat in this context and how to transform this kind of ROI to surface. Thanks a lot! Sincerely, Jinnan

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