Re: [Freesurfer] Talairach_afd error (Bruce Fischl)

Hi Bruce, Thanks for the reply. The talairach.xfm file generated by the palarellizing machine is empty; it looks as follows: Talairach.xfm file: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = However, the talaraich.xfm file generated by the non-paralellizing

[Freesurfer] comparison of 4 groups: mri_glmfit or Qdec?

Dear Experts, we want to compare data (thickness) of 4 groups (3 morbid groups and 1 controll group). Both, Qdec and mri_glmfit, will do the same analyses. But we are not sure, if the usage of Qdec is statistically correct in our case. Because in Qdec we can only compare 2 of the 4 groups. But

[Freesurfer] FreeSurfer pve correction tool

Dear FreeSurfer Experts, Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6? Many thanks in advance, Best, Mohamed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] : FOLLOW-UP question: remove label from aseg

On 10/25/15, 3:29 AM, "Jacobs H (NP)" wrote: >Hi. > >Just one another related question: now that I was able to combine left and >right hippocampal subfields with the aparc-aseg correctly, I noticed that >the left and right hippocampal subfields have the same

Re: [Freesurfer] Error with Group Analysis using Qdec

Thanks a lot. 2015-10-26 10:35 GMT+08:00 Douglas Greve : > can you send your qdec.table.dat? > > > On 10/25/15 9:42 PM, haidong wang wrote: > > Yes,'con_chenchen' exists in $SUBJECTS_DIR,/media/work/FC_DATA/ckd-T1. > > 2015-10-21 11:15 GMT+08:00 Douglas Greve

Re: [Freesurfer] FreeSurfer pve correction tool

oh, then I'll leave it for Doug Bruce On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote: > Hi Bruce, > > Yes, for PET analysis. > > Best, > > Mohamed > > On 26/10/15 14:45, Bruce Fischl wrote: >> Hi Mohamed >> >> do you mean for PET analysis or for the recent paper that Rebecca Shafee >> wrote on

[Freesurfer] Extract single time frame

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify

Re: [Freesurfer] FreeSurfer pve correction tool

Hi Bruce, Yes, for PET analysis. Best, Mohamed On 26/10/15 14:45, Bruce Fischl wrote: > Hi Mohamed > > do you mean for PET analysis or for the recent paper that Rebecca Shafee > wrote on e.g. tissue intensity properties? > > cheers > Bruce > > > > On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:

Re: [Freesurfer] Head circumference

As a rough approximation, you can fit a sphere to the inner skull surface (created, e.g., by the watershed) as we did in some of the TMS modeling stuff (see, appendix of): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790855/ and then scale the result with an approximation of a brain-to-skin

Re: [Freesurfer] FreeSurfer pve correction tool

no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.ba...@ulg.ac.be wrote: > Dear FreeSurfer Experts, > > Are there any documentation comes out for the pve correction tool implemented > in the FreeSurfer V6? > > Many thanks in advance, > > Best, > > Mohamed >

Re: [Freesurfer] FreeSurfer pve correction tool

Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)? Best, Mohamed On 26/10/15 13:27, Bruce Fischl wrote: > no, sorry, we haven't had time to document it > On Mon, 26 Oct 2015, > m.ba...@ulg.ac.be

Re: [Freesurfer] Head circumference

Hi John, There is nothing, which I can think of. What do you want the head circumference for (perhaps we can get you a different measure, which will help)? hth d On Sat, Oct 24, 2015 at 2:22 PM, John Anderson wrote: > Dear FS experts, > I want to inquire if there is

Re: [Freesurfer] FreeSurfer pve correction tool

Hi Mohamed do you mean for PET analysis or for the recent paper that Rebecca Shafee wrote on e.g. tissue intensity properties? cheers Bruce On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote: > Is it possible to tell what are the implemented methods? and how we can > obtain the corrected 4D

Re: [Freesurfer] Head circumference

you could probably generate a skull model from the BEM surface stuff used in MEG/EEG then find the average radius or something cheers Bruce On Mon, 26 Oct 2015, dgw wrote: > Hi John, > > There is nothing, which I can think of. What do you want the head > circumference for (perhaps we can get

Re: [Freesurfer] Extract single time frame

Hi Eli a couple of different ways would work. The frams are numbered starting at 0 for the first one. So for frame #5 (the 6th one) it would be: mri_convert -nth 5 file.nii file.frame5.nii Alternatively, all of our tools accept the extension # so you could do: mri_convert file.nii#5

Re: [Freesurfer] Extract single time frame

Thank you, I was not aware of the #frame extension! Eli On 10/26/2015 10:26 AM, Bruce Fischl wrote: Hi Eli a couple of different ways would work. The frams are numbered starting at 0 for the first one. So for frame #5 (the 6th one) it would be: mri_convert -nth 5 file.nii file.frame5.nii

Re: [Freesurfer] Funcroi-Table-Sess Error

Hi there, Just following up on this. Any help would much appreciated! Thanks, Keji > On Oct 23, 2015, at 1:46 PM, Morenikeji Adebayo > wrote: > > Hi there, > > I ran the following analysis commands: > > mri_cor2label --c >

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before >it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still