[Freesurfer] Remove From List

Remove from list amco1...@gmail.com ___ Freesurfer mailing list Freesurfer@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 b

Re: [Freesurfer] FW: Surface Generation Problem Pertaining to FreeSurfer

You can generate a surface from the hippocampus by first running recon-all on an anatomical image, then using mri_mc to tessellate the left and right hippocampi. cheers Bruce On Tue, 22 Feb 2011, Saad Shakeel wrote: > > > > From: saad.ak...@hotmail.com > To: fsregis...@nmr.mgh.harvard.edu; fr

Re: [Freesurfer] overlay sig.mgh onto T1 vol

Try loading it with the surfaces (add -surfs to your tkmedit cmd). It may be on the surface at that location. doug Fernanda Palhano wrote: > Hi Doug, > > Thanks for the command, it worked well. > But, I still have a problem. The overlay seems to be misplaced. > I'm sending a .png with an example

Re: [Freesurfer] mri_glmfit-sim doubt

It should be the case that the clusters in the 2.3 should be clusters in the 1.3, but there p-values will be different. It is possible that a cluster that is sig in the 2.3 is not sig in the 1.3, particularly small clusters like the two you have shown. Small clusters may be very likely at 1.3 u

Re: [Freesurfer] question about weighted regression analysis

I assume that you are comparing maps of Version1:1v0 and Version2:2v0 ? I could imagine it going either way. If the true slope is 0 but the offset is non-0, then Version1 will give you an artificially high slope (and Verion2 will give you the correct slope at 0, and so no activation). Are you c

Re: [Freesurfer] Gammafit parameters

Yes, those are the default (from Dale and Buckner, ``Selective Averaging of Rapidly Presented Individual Trials Using fMRI,'' Human Brain Mapping, pp. 329-340, 1997.) doug Mandy Nagy wrote: > Hi all, > > We are trying to use -gammafit when running the mkanalysis-sess > command. In the FsFast

Re: [Freesurfer] mri_glmfit-sim doubt

This is not my understanding. It is completely dependent on the threshold used, which can be arbitrary. See Supplemental figure 7, page 16 of this document: http://www.jneurosci.org/cgi/data/30/6/2268/DC1/1 This was the motivation for Smith & Nichols' TFCE: http://www.ncbi.nlm.nih.gov/pubmed/1

Re: [Freesurfer] retinotopy manual?

Hi Doug, When you say retinotopy 30, where 30 is the 30 second period. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par Does period mean duration for a cycle or for the whole run? Thanks. Michelle ing Douglas N Greve : > I don't have a form

Re: [Freesurfer] question about weighted regression analysis

You should also look at Version2:1v0. I bet a lot of the areas from Version1:1v0 will also show up. You can also create a Version3 in which you divide your presentations into a low-weight and a high-weight (but set the weight=1). Then create contrasts of low+high and high-low. The low+high shou

Re: [Freesurfer] retinotopy manual?

For a cycle. So for the time it take the wedge to go all the way around or for the ring to start from center and return to center. doug Michelle Umali wrote: > Hi Doug, > When you say retinotopy 30, where 30 is the 30 second period. > > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2

[Freesurfer] Converting an ascii file to a freesurfer volume file

Hello freesurfers, I am trying to convert a partially inflated surface .ply file created in afni to a freesurfer volume so that I can visualize the surfaces via tksurfer. Is there freesurfer command that converts text to volume, in essence the converse of mris_convert? And if not can you sugges

[Freesurfer] recon-all on data with anatomical abnormality or strong artifact

Hi, I run into the following error when running recon-all. ERROR: _FindFacePath: could not find path! in the process: Correcting Topology of defect 2 with euler number -9 (5 loops) computing statistics for defect 2: 1934 vertices location: [ (93,119,57) - average intensity = 85.136 ]...

Re: [Freesurfer] recon-all on data with anatomical abnormality or strong artifact

Hi Eveline can you send us an image? What was your commandline for mris_fix_topology? I think you need to specify -mgz cheers Bruce On Tue, 22 Feb 2011, Eveline Geiser wrote: > Hi, > > I run into the following error when running recon-all. > > ERROR: _FindFacePath: could not find path! > in t

Re: [Freesurfer] installation problem in ubuntu

try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia > Hi Pedro, > > Finally, I could install it with the license file and the environment is > properly set without warnings. > But trying to test it, following the instructi

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Hi all, Just for the record I comment that the problem was solved. It was the name of the sequence, which containted the sting "TR". This messed up the sanity checks mkanalysis-sess. Thank you very much taking a look at it. Best, Pablo On Fri, Feb 18, 2011 at 5:48 PM, Pablo Polosecki < ppolose...