[Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the me

Re: [Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

mean of the areal means won't > equal the overall mean. > > cheers > Bruce > > On Sat, 25 Jun 2016, Nabin Koirala wrote: > > Hi freesurfer team, >> I extracted the cortical thickness values using aparcstats2table command >> and >> I got the cortical

Re: [Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

Thank you. Regards, Nabin On Sat, Jun 25, 2016 at 5:36 PM, Bruce Fischl wrote: > the mean across both lh.cortex.label and rh.cortex.label should be pretty > close. If you want it to be exact you should weight by area then normalize > > On Sat, 25 Jun 2016, Nabin Koirala wrote: &g

[Freesurfer] ERROR: QdecGlmDesign::Create: bad factor!

Dear freesurfer team, I was trying to run QDEC with two discrete factors but I got this error and could not quite figure out what is wrong. Your suggestion would be highly appreciated. The table and the error is as shown below: Data table /Applications/freesurfer/subjects/qdec/qdec.table.dat loa

Re: [Freesurfer] ERROR: QdecGlmDesign::Create: bad factor!

The problem is solved. There was an error in table format. Thank you. Regards, Nabin On Wed, Oct 5, 2016 at 6:56 PM, Nabin Koirala wrote: > Dear freesurfer team, > > I was trying to run QDEC with two discrete factors but I got this error > and could not quite figure out what is

[Freesurfer] tksurfer vertex location

Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual. *At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that

[Freesurfer] Fwd: error in long_mri_slopes

Hi all, I am doing longitudinal analysis (recon-all) and while running the long_mri_slopes using the following command, I am getting different errors for each run and its driving me crazy. The command I am running : long_mris_slopes --qdec ./qdec/long.qdec.Sub_7_t0t1.dat --meas thickness --hemi

Re: [Freesurfer] Fwd: error in long_mri_slopes

s trying to run before it prints the > error, try running that command manually from the command line to get more > info on what happens. > > Best, Martin > > > > On 12/17/2015 08:52 AM, Nabin Koirala wrote: > > > Hi all, > > I am doing longitudinal analysis (recon-

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Dear Freesurfer forum, 'I am trying to run qdec analysis for a group of subjects to see if correlation exists but I am getting this error only for this particular set of data but could not figure out what is exactly wrong with it. Your suggestion would be greatly appreciated. Following is the te

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

our covariate > > On 01/30/2016 01:31 PM, Nabin Koirala wrote: > > Dear Freesurfer forum, > > > > 'I am trying to run qdec analysis for a group of subjects to see if > > correlation exists but I am getting this error only for this > > particular set of data bu

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

: > I'm not sure what the difference is. Compute the mean of the 2nd column, > then subtract that number from the values in the 2nd column. > doug > > > On 2/2/16 7:30 AM, Nabin Koirala wrote: > > Thank you for your response . Sorry but for my understanding, should i >

[Freesurfer] Same coordinates for all labels

Dear FS team, I am trying to find the centroid using mri_surfcluster using the following command but I am getting the same coordinate for all labels. I couldn't quiet understand what's wrong. Your suggestion would be really appreciated. NOTE: The coordinates differs for hemisphere. mri_surfclus

Re: [Freesurfer] Same coordinates for all labels

Many thanks Doug. Regards, Nabin On Tue, May 17, 2016 at 7:04 PM, Douglas N Greve wrote: > Set the threshold to be something non-zero (eg, ---thmin .0001) > > On 05/17/2016 10:47 AM, Nabin Koirala wrote: > > Dear FS team, > > > > I am trying to find the cen

Re: [Freesurfer] tksurfer vertex location

Bruce > > > > > On Fri, 20 Jan 2017, Nabin Koirala wrote: > > Dear freesurfer team, >> I was trying to obtain the values at a vertex in tksurfer and this is what >> is written in tksurfer manual. >> >> At first, an empty plot will be displayed in a

Re: [Freesurfer] tksurfer vertex location

that tksurfer is deprecated - we are not developing it anymore. > > > > That said, I thing you can type: > > > > select_vertex_by_vno > > > > at the tcl prompt, where is the number of the vertex you want > > to select > > > >

[Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1

External Email - Use Caution Hi freesurfer community, I am trying to do QDEC with a data for 2 groups but stuck in this error for many hours now. Tried and checked everything I could think of. Also went through the old threads and checked those recommneded but still could not solv

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1

r this group (this requires that you create > your own design matrix). > > On 8/14/18 6:00 AM, Nabin Koirala wrote: > > External Email - Use Caution > Hi freesurfer community, > > I am trying to do QDEC with a data for 2 groups but stuck in this error > for many ho