[Freesurfer] error in recon-all -autorecon3

Dear FS list, I am trying to finish my first analyses with freesurfer; however, I have some problems when running the last stages of recon-all. In summary what I did: 1) recon-all -autorecon1 (worked well) 2) some minor brain strip editing 3) recon-all -autorecon2 (worked well) 4) some edi

Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32

When I ran this command, " mri_segstats --seg "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in "$hemi".thickness.fsaverage.mgh --sum segstats-"$hemi"_"$roi"_"$subj".txt, this kind of output came out "mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsavera

Re: [Freesurfer] error in recon-all -autorecon3

Dear Paola, I think the problem might be that your operating system ships libtiff.so.4 instead of libtiff.so.3 and that is why mris_volmask.bin cannot find libtiff.so.3. As far as I know you can just create a symbolic link from libtiff.so.3 to libtiff.so.4. In case your libraries are in /usr

[Freesurfer] Space of FreeSurfer Stats

Hi All, Are the volume stats outputted by FreeSurfer in native space or in FreeSurfer's space? According to some older mailing list questions, they are in native space, but I wanted to make sure that this was still the case. Thanks in advance for any help. - Tyler ___

Re: [Freesurfer] Space of FreeSurfer Stats

yes, they are measured in native space. doug bla...@artsci.wustl.edu wrote: > Hi All, > > Are the volume stats outputted by FreeSurfer in native space or in > FreeSurfer's space? According to some older mailing list questions, they > are in native space, but I wanted to make sure that this was st

Re: [Freesurfer] Space of FreeSurfer Stats

Hi Tyler, I'm not sure what you mean by the stats being in a particular space. I had understood it to mean the space that volumes would be measured in. Is that right? If so, then the volumes will be measured in the space of the input, whatever input you supplied. doug ps. I'm copying the frees

Re: [Freesurfer] mri_convert GradFile

Hi Doug, This unsetenv step only works with stable4. In stable5 it still throws the: ERROR: cannot open /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt My mri_convert is called as a subscript of a larger process that I am trying to run, and I need to use a new

Re: [Freesurfer] Space of FreeSurfer Stats

Doug, You understood correctly. Thanks for your help! - Tyler > Hi Tyler, I'm not sure what you mean by the stats being in a particular > space. I had understood it to mean the space that volumes would be > measured in. Is that right? If so, then the volumes will be measured in > the space of th

Re: [Freesurfer] mri_convert GradFile

BTW, you should be able to setenv UNPACK_MGH_DTI 0 to force it to ignore the gradient tables. doug Steven Swinford wrote: > Hi Doug, > > This unsetenv step only works with stable4. In stable5 it still > throws the: > > ERROR: cannot open > /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqp

[Freesurfer] Converting an FSL label to Freesurfer space

Hi everyone, I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to FreeSurfer's fsaverage brain inflated surface. Does anyone know how to do this? Thanks, Massih ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

Re: [Freesurfer] white screen when opening freeview

Do you have a decent graphics card on the box? Also, you may try updating the graphics card driver to the latest. Do you get the same problem with dev build? Ruopeng On 9/28/10 5:06 PM, B.T. Thomas Yeo wrote: Hi, when opening freeview while logged locally on a linux box (at Harvard NCF), w