[Freesurfer] problems on matrix design

2015-12-02 Thread nellie
Hi Freesurfer Experts,I have tried to alter wiki example FSGD table into my analyses these days, according to your advice, but there are still some problems. Supposed there are 6 groups (maleclass1, maleclass2, maleclass3, femaleclass1, femaleclass2, femaleclass3) and 2 Variables (age, education

Re: [Freesurfer] Freesurfer Regions

2015-12-02 Thread Bruce Fischl
Hi Ananth we have regions in the LUT table (like the thalamic nuclei) that we don't segment yet. Sorry Bruce On Mon, 30 Nov 2015, Ananth Narayanan wrote: > Hello freesurfer users, > > I am a new user of freesurfer. We are using FS to define ROIs for out PET > analysis. I looked at the FS colo

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

2015-12-02 Thread Bruce Fischl
Hi Annelinde the problem is that your original image only includes about half the cerebellum. We expect a full cerebellum and so the segmentation labels some of the cortex that is superior to cerebellum incorrectly as cerebellu, then removes it from the wm.mgz (since it isn't cerebral cortex).

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

2015-12-02 Thread Annelinde Vandenbroucke
Dear Bruce, Thank you very much for letting me know. Indeed, something went wrong with the slice prescription of that acquisition. I didn't know that would affect segmentation. Our normal acquisition includes the whole brain. Thanks again for to you and your support team! Cheers, Annelinde 2015-

Re: [Freesurfer] Error - extracting percent signal

2015-12-02 Thread Danielle Miller
Hi Doug, Thanks for the response. I used the mri_label2label command: mri_label2label --srclabel --s fsaverage --regmethod vol --paint dmax --trglabel --hemi lh When I input the output from this into mri_segstats as the --seg volume, I get the error: mri_read(): couldn't determine type of file

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

2015-12-02 Thread Bruce Fischl
glad to hear it's not all your subjects! Good luck Bruce On Wed, 2 Dec 2015, Annelinde Vandenbroucke wrote: Dear Bruce, Thank you very much for letting me know. Indeed, something went wrong with the slice prescription of that acquisition. I didn't know that would affect segmentation. Our no

Re: [Freesurfer] Error - extracting percent signal

2015-12-02 Thread Douglas N Greve
Hi Danielle, can you resubmit this email with the previous correspondence? On 12/02/2015 01:14 PM, Danielle Miller wrote: > Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel --s fsaverage --regmethod vol > --paint dmax --trglabel --hemi lh >

Re: [Freesurfer] Error - extracting percent signal

2015-12-02 Thread Danielle Miller
Sure -- should be all here now! The last email contained the following text: "Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel --s fsaverage --regmethod vol > --paint dmax --trglabel --hemi lh > > When I input the output from this into mri_s

Re: [Freesurfer] Error - extracting percent signal

2015-12-02 Thread Douglas Greve
use --slabel, not --seg doug On 12/2/15 3:04 PM, Danielle Miller wrote: Sure -- should be all here now! The last email contained the following text: "Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel --s fsaverage --regmethod vol > --paint d

[Freesurfer] Freesurfer Version mismatch between Subject and Control Stamp in autorecon2 and autorecon3

2015-12-02 Thread Amy L
Hi all, I'm sorry if this is a silly question, but what might cause the version of Freesurfer to be different in the Subject and Current Stamps of the output following autorecon2 and autorecon3? And is this a problem? The relevant lines of output are as follows: INFO: FreeSurfer build stamps do