[Freesurfer] Talairach registration failes

Dear all, I have a problem running Freesurfer on images having a relatively tight FOV. While running talairach_afd, the registration of the template to the image fails. Checking the registration (as explained on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) reveals that the templa

Re: [Freesurfer] volume of different lobes of the brain....

You can run mri_annotation2label with --lobesStrict to get a lobe annotation. If that definition of "lobes" is good for you, then you can run mris_anatomical_stats to get the volume for each lobe. doug Gonzalo Rojas Costa wrote: > Hi: > > How can I get the volume of the different lobes of the

[Freesurfer] QDEC stats table output

Hi, After running QDEC, I would like to  output in a table the average value for the cortical thickness within each clusters. I know this is a dependent variable and I can see the values on the plot but is there a way that I can get this values in a table ? Thanks, Antonella___

Re: [Freesurfer] QDEC stats table output

Will this work (this is from running mri_glmfit-sim --help, which has even more info): csdbase.y.ocn.dat - this is a summary of the input (y) over each cluster. It has a column for each cluster. Each row is a subject. The value is the average of the input (y) in each cluster. This is a simple tex

Re: [Freesurfer] QDEC stats table output

Dear Doug, I got this results while I was running the GLM simulation but I wonder if there is a way to get under QDEC (when I run QDEC from the interface) and I am using the FDR and Monte Carlo simulation. In this case I am not getting any output as in GLM from which I got the csdbase.y.ocn.dat

[Freesurfer] QDEC stats table output

Dear Doug, I got this results while I was running the GLM simulation but I wonder if there is a way to get under QDEC (when I run QDEC from the interface) and I am using the FDR and Monte Carlo simulation. In this case I am not getting any output as in GLM from which I got the csdbase.y.oc

Re: [Freesurfer] QDEC stats table output

You can run mri_glmfit-sim on the QDEC output directory. Or you can run the simulation from within QDEC. Both will give you this output file. doug Antonella Kis wrote: > Dear Doug, > > I got this results while I was running the GLM simulation but I wonder > if there is a way to get under QDEC (w

Re: [Freesurfer] register.dat Matrix Conventions

Clark Fisher wrote: > Hi Doug, > > Thanks for pointing me back to that; I had forgotten how much depth it > goes into! I have 2 remaining questions: > > 1) Why is the tkr vox2ras transform sometimes dramatically different > from the one in the volume header? For instance, in one of the > fun

[Freesurfer] aparc.annot question from August

Hi Everyone, I have not received a response on this question from August -= cold we revisit it please? thanks, Helen [Freesurfer] Saving annotation and stats after expand boundary of region Keefe, Helen L helen-keefe at uiowa.edu

Re: [Freesurfer] register.dat Matrix Conventions

Thanks Sebastian and Doug, that clears everything up. -Clark On Sep 26, 2011, at 11:27 AM, Douglas N Greve wrote: > > > Clark Fisher wrote: >> Hi Doug, >> >> Thanks for pointing me back to that; I had forgotten how much depth it >> goes into! I have 2 remaining questions: >> >> 1) Why is

Re: [Freesurfer] QDEC stats table output

Dear Doug, I don't know if I am doing something wrong but when I run the simulation under QDEC I am not getting the  csdbase.y.ocn.dat file. The only files that I get under after running the  simulation under QDEC are: mc-z.abs.th20.sig.cluster.summary, mc-z.abs.th20.sig.ocn.annot,mc-z.abs.th20

Re: [Freesurfer] Tracula references

Hi Shanqing - You can cite this for now: A Yendiki, P Panneck, A Stevenss, L Zo ̈llei, J Augustinack, R. Wang, D. Salat., S. Ehrlich, T. Behrens, S. Jbabdi, R. Gollub, B, Fischl, Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underl

[Freesurfer] Fw: QDEC stats table output

Dear Doug, I don't know if I am doing something wrong but when I run the simulation under QDEC I am not getting the  csdbase.y.ocn.dat file. The only files that I get under after running the  simulation under QDEC are: mc-z.abs.th20.sig.cluster.summary, mc-z.abs.th20.sig.ocn.annot,mc-z.abs.

Re: [Freesurfer] volume of different lobes of the brain....

Hi Douglas: The solution that you sent me runs only in freesurfer 5... Do you have ay solution for freesurfer 4.5.0 to compute GM+WM volume for each lobule ?... Sincerely, Gonzalo Rojas Costa On Mon, Sep 26, 2011 at 11:01 AM, Douglas N Greve wrote: > You can run mri_annotation2label with

Re: [Freesurfer] volume of different lobes of the brain....

You can use mri_annotation2label to break the labels apart, then use mri_mergelabels to combine the individual labels into lobe labels, then use mris_label2annot to create a lobe annotation, then use mris_anatomical_stats. doug Gonzalo Rojas Costa wrote: > Hi Douglas: > > The solution that y

[Freesurfer] Lateral ventricle volume

Hello all, Quick question, does the Lateral Ventricle volume include the volume of the Inferior Lateral Ventricle (i.e. temporal horn) or do they need to be added together when calculating a total lateral ventricle volume? __

Re: [Freesurfer] Lateral ventricle volume

They are separate labels, so they would need to be added together. cheers, -MH On Mon, 2011-09-26 at 19:21 +, victor del brutto wrote: > Hello all, > > Quick question, does the Lateral Ventricle volume include the volume > of the Inferior Lateral Ventricle (i.e. temporal horn) or do they n

[Freesurfer] using isxconcat for partial correlation coefficient map

Hi, Would you tell me how can I use isxconcat-sess to calculate group averaged "partial correlation coefficient map"? I have already generated pcc.nii files for each individual subject. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___

Re: [Freesurfer] Lateral ventricle volume

they need to be added On Mon, 26 Sep 2011, victor del brutto wrote: Hello all,   Quick question, does the Lateral Ventricle volume include the volume of the Inferior Lateral Ventricle (i.e. temporal horn) or do they need to be added together when calculating a total lateral ventricle volume? _

Re: [Freesurfer] using isxconcat-sess for partial correlation coefficient map

Add "-m pcc" to the command line doug SHAHIN NASR wrote: > Hi, > > Would you tell me how can I use isxconcat-sess to calculate group > averaged "partial correlation coefficient map"? I have already > generated pcc.nii files for each individual subject. > > > -- > Shahin Nasr > > PhD in Cogn

[Freesurfer] thickness_clinical_correlations

Dear All, I am trying to correlate clinical disability measure ALSFRS score with cortical thickness in ALS patients. Attached is the fsgd file. I am not able to run mris_preproc with this fsgd file what am I doing wrong here, also my design matrix contrast is 1 0 am I right. I am interested i

Re: [Freesurfer] thickness_clinical_correlations

what goes wrong when you run mris_preproc? Your contrast will test the significance of the correlation between your ALSFS and thickness. doug Rajagopalan, Venkateswaran wrote: > > Dear All, > > I am trying to correlate clinical disability measure ALSFRS score with > cortical thickness in ALS pat