[Freesurfer] qdec and maximum p-value

Hi all. I'm using Qdec to compare two groups of patients, and I'm wondering why the vertex with the highest p-value in the clusters changes when the threshold is changed? When lowering the threshold, the significant area should increase, but intuitively, the vertex corresponding to the area wit

Re: [Freesurfer] Concatenate surfaces

mri_concat, then use the --avgwf option to mri_segstats. doug MCLAREN, Donald wrote: > Is there a way to concatenate surfaces for use with mri_segstats? The > surfaces are already in fsaverage space. > > Best Regards, Donald McLaren > = > D.G. McLaren, Ph.D. > Postdoctoral Researc

[Freesurfer] Concatenate surfaces

Is there a way to concatenate surfaces for use with mri_segstats? The surfaces are already in fsaverage space. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital

[Freesurfer] Error for Patients Abnormal Side Right

Hi Doug, Seems that this will never end... I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left. Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I was running: mri_glmfit

[Freesurfer] Error for Patients Abnormal Side Right

Dear Doug, Seems that this will never end...It is so painful already. I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left. Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I

Re: [Freesurfer] aparc2feat and using Freesurfer Lookup Table

Hi Michelle, we don't currently label V3d automatically. cheers Bruce On Thu, 29 Sep 2011, Michelle Umali wrote: Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For  example, I wanted to use number 433, the Visual_V3d_l.  I tried to

[Freesurfer] Error with Clusters Summary

Hi, Sorry, I am coming up with the same problem. I am running the mri_glmfit_sim on the QDEC results to get the text file with the cortical thickness average and cluster summary but unfortunately I see for one side the --sim is not give me any clusters even if I can see 5 in QDEC after ch

[Freesurfer] aparc2feat and using Freesurfer Lookup Table

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+ aseg.nii.gz -thr 433v uthr 433 \

Re: [Freesurfer] Error with Clusters Summary (ASAP)

The problem is likely that none of your clusters are significant at p<.05 (the default cluster-wise correction). Try changing it with "--cwpvalthresh .99" Antonella Kis wrote: > Dear Doug, > > Sorry, I am coming up with the same problem. I am running the > mri_glmfit_sim on the QDEC results to

[Freesurfer] unpacking error:: "exited abnormally"

Hello, I'm trying to unpack a diffusion run and getting this error, "child process excited abnormally". Anyone encounter this before? Here are the details: [purkinje:pat08_sess2_dti] (nmr-stable3-env) unpacksdcmdir -src /space/archive/181/siemens/TrioTim-35162-20080921-182835-474000 -targ /clus

[Freesurfer] Error with Clusters Summary (ASAP)

Dear Doug, Sorry, I am coming up with the same problem. I am running the mri_glmfit_sim on the QDEC results to get the text file with the cortical thickness average and cluster summary but unfortunately I see for one side the --sim is not give me any clusters even if I can see 5 in QDEC after c

[Freesurfer] problems unpacking diffusion runs

Hello all, I'm trying to unpack some old data and for a couple of sessions it is unpacking the wrong run. I just want to unpack the diffusion run. I give it the correct run number, it see's that number is the diffusion run, but unpacks another run instead. Here is the command I used: [purkinje

Re: [Freesurfer] Bug in freesurfer_read_surf.m & a quick fix

thanks Matti Bruce On Thu, 29 Sep 2011, Matti Stenroos wrote: Hi & sorry for the second post...   ...I made a typo in my fix. Should of course be   If nargout>1,...   Cheers,    Matti   From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] Bug in freesurfer_read_surf.m & a quick fix

Hi & sorry for the second post... ...I made a typo in my fix. Should of course be If nargout>1,... Cheers, Matti From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matti Stenroos Sent: 29 September 2011 15:00 To: freesurfer@

[Freesurfer] Bug in freesurfer_read_surf.m & a quick fix

Hi, In FreeSurfer 4.3.0, the Matlab routine "freesurfer_read_surf.m" crashes, when run with one output argument: function [vertices, faces] = freesurfer_read_surf(fname) The function help says: % Note that reading the faces of a quad file can take a long % time due to their compact storage form

[Freesurfer] missing lh.thickness.fwhm10.fsaverage.mgh in some subjects

Dear All, I was trying to run "mris_preproc" after completing all autorecon steps in some of my subjects folder under "surf" I see "lh.thickness.fwhm10.fsaverage.mgh" whereas in others it is missing. I ran autorecon 1, 2 and 3 the same way in all the subjects so I am wondering what might be th