Freesurfer

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30099 discussions

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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mris_divide_parcellation same divisions between subjects
by Corinna Bauer 10 Apr '14

10 Apr '14

Hello all, I am planning to use mris_divide_parcellation to split the Desikan atlas into smaller ROIs, but will need the new ROIs to be consistent between subjects. Can I achieve this if I register each subject to fsaverage space and then apply the inverse transform to the divided parcellations (which are currently done on the fsaverage brain)? If so, for extracting each label, what would be used for the label number? (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*${subj_dir}/hardi_labels/ctx-rh-insula.nii) Thanks Corinna

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basic high res data question
by Torrisi, Sam (NIH/NIMH) [F] 10 Apr '14

10 Apr '14

Good afternoon gurus- I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 1mm. Now I have basically the same sentiment and question as this thread from ~2 years ago (i’m linking to the middle for simplicity): http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html What’s the very latest on this? Thanks! -Salvatore (Sam) Torrisi Section on the Neurobiology of Fear and Anxiety National Institute of Mental Health

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how to convert fsaverage space mask into other subject original space
by Rujing Zha 10 Apr '14

10 Apr '14

Hi FS experts and others, I try to check my group analysis result by seeing the subjects' original space corresponding area. So I need to know how to convert my mask from fsaverage space into specific subject's space. Thanks All the best. RujingZha

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Re: [Freesurfer] Intermediate stages of cortical inflation
by Xuelong Zhao 10 Apr '14

10 Apr '14

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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Mac OSX installations incomplete? What to do?
by Markus Gschwind 10 Apr '14

10 Apr '14

Dear Freesurfers, As discovered here, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html it seams that some Mac OSX installations suffered from incomplete files. I just veryfied that I had downloaded the complete image and wget says yes: Logging in as anonymous ... Logged in! > ==> SYST ... done. ==> PWD ... done. > ==> TYPE I ... done. ==> CWD (1) /pub/dist/freesurfer/5.3.0 ... done. > ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg ... > 3394499614 > File has already been retrieved. > 2014-04-04 18:24:26 (0.00 B/s) - > 'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved > [3394499614] So this is what I installed recently and it seems that there are some files missing (at least some of the fsl-functions in bin). Doug, you said that you suspected that it could be a problem of the installer script? What should we do (also Eiran) in order to complete the installation? Thanks for you work! Markus

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Advanced Clinical Neuroimaging Course, Brussels, May 30-31, 2014
by Laurent Hermoye 10 Apr '14

10 Apr '14

Advanced Clinical Neuroimaging Course, Brussels, May 30-31, 2014 <http://www.imagilys.com/advanced-clinical-neuroimaging-course-2014/>

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