Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

apply fnirt transformation on a surface
by Shani Ben Amitay 02 Sep '13

02 Sep '13

Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani

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Re: [Freesurfer] apply fnirt transformation on a surface
by Bruce Fischl 02 Sep '13

02 Sep '13

A veritable game of telephone! Thanks Jesper. Matt? On Mon, 2 Sep 2013, Jesper Andersson wrote: > Hi guys, > I didn't think we had any tools for doing that, and said so much on the FSL > mailbase. But apparently the WashU people has something that does just that > for you. I think the best person to contact about the details is Matt > Glasser. > > J > > On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> > wrote: > > Hi In Probtrackx, this is done internally. > If you just want to transform the vertex coordinates, then I think > you'll need to play with the FNIRT source code - I've CC'd Jesper who > knows better. > > Cheers, > Saad > > > > On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > you might check on the FSL list. I think I've seen some > traffic indicating that there are some tools for doing > this. I'l cc Saad as he might know > > cheers > Bruce > > > On Mon, 2 Sep 2013, Douglas Greve wrote: > > Hi Shani, I don't think you can apply a FNIRT > transform to a surface. > doug > On 9/2/13 8:20 AM, Shani Ben Amitay wrote: > Dear freesurfer people, > Any idea whether I can apply transformation > that was calculated by fsl > fnirt on the white/pial surfaces calculated > using the freesurfer > stream? > Thanks! > Shani > _______________________________________________ > 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. > > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > > >

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problems with aparcstats2table
by pietro de rossi 02 Sep '13

02 Sep '13

Dear FreeSurfers, I am extracting thickness values through the aparcstats2table command line. Everything works just fine for --hemi lh using the --skip flag. However, when it comes to the right hemisphere I get SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 321, in <module> parc_measure_map = parsed.parse(options.meas) File "/usr/local/freesurfer/bin/fsutils.py", line 194, in parse parcid = strlist[0] IndexError: list index out of range I find it weird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Freesurfer September 2013