Re: [Freesurfer] Fwd: Eccentric lesions

Hi Octavian I wouldn't use control points since it really isn't healthy wm. The only thing you can do is edit the wm.mgz and possibly also the brainmask, but it's so abnormal looking you may not be able to get accurate surfaces. How does the aseg look? If it is ok there may be one other

Re: [Freesurfer] Fwd: Eccentric lesions

so the GM is properly labeled by the aseg there? What about the faint wm? On Tue, 25 Nov 2014, Octavian Lie wrote: Dear Bruce, I am not sure how an ok aseg.mgz would look like for a lesion like that, but it looks like it includes one larger gyrus excluded by the pia, see attached, I would

Re: [Freesurfer] Fwd: Eccentric lesions

It looks like there is only gray matter (int 42), similar to cortical ribbon gray, no white matter in that gyrus in aseg, both in the original recon, and after painting gyral centers in brainmask. Octavian On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie octavian@gmail.com wrote: Dear Bruce,

Re: [Freesurfer] Poor subcortical segmentation

Hi Mihaela if you want to upload a representative subject we will take a look cheers Bruce On Tue, 25 Nov 2014, Mihaela Stefan wrote: Hello Freesurfers, We noticed that our subcortical segmentations have a poor quality (see attachment). Is there a way to improve the segmentation in an

Re: [Freesurfer] Poor subcortical segmentation

Hi Bruce, I uploaded a subject. Thanks! Mihaela On Tue, Nov 25, 2014 at 10:13 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Mihaela if you want to upload a representative subject we will take a look cheers Bruce On Tue, 25 Nov 2014, Mihaela Stefan wrote: Hello Freesurfers,

Re: [Freesurfer] Tracula mri_convert error

Can you send the full terminal output? doug On 11/24/14 10:18 PM, Janosch Linkersdörfer wrote: Hi experts, I wanted to play with Tracula. Strangely, already the first preprocessing step, i.e., conversion to .nii.gz, fails. Apparently, mri_convert (falsely) recognizes my dicom files as MGH

[Freesurfer] TRACULA- DKI?

Dear Tracula Team, Quick question: Is Tracula able to to process diffusion kurtosis data, and yield, let's say, 'mean kurtosis' parameters for specific fiber tracts?cheers,Cat___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer Version

The 64bit Lion version. It should probably be made a little more clear that that version is for 10.7 and higher. Ill fix that. https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke Gentleman Which Version of Freesurfer should I download for use with the OS X Yosemite 10.10.1? Thanks

Re: [Freesurfer] Freesurfer Version

Thanks, Zeke!!! On Tue, Nov 25, 2014 at 10:59 AM, zkauf...@nmr.mgh.harvard.edu wrote: The 64bit Lion version. It should probably be made a little more clear that that version is for 10.7 and higher. Ill fix that. https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke Gentleman

[Freesurfer] Freeview in a VM (Debian)

Hi all, I am running FS in a VM (Debian, wheezy) and I would like to create a 3D reconstruction of the hippocampus in .png. For that, I executed the following code lines: mri_extract_label aseg.mgz 17 lh.nii mri_extract_label aseg.mgz 53 rh.nii freeview -slice 500 500 500 -v

[Freesurfer] Digest mode for mailing list and responding to mails

Hi list, I recently switched to the digest mode for the mailing list. Since then, I don't receive answers to my mails as mails anymore, making it harder to respond to them (or any other mail on the list). Does anybody experience the same issues? How did you solve them? Thanks, Janosch

Re: [Freesurfer] tksurfer curvature and overlay displays

At 11/24/2014 08:23 AM, Bruce Fischl wrote: Hi Graham have you tried freeview? We stopped development on the tktools some time ago. cheers Bruce Hi Bruce, thanks for replying. Yes, I did proceed to try the same task in Freeview (which in general has a nicer UI, to be sure). Some notes: Test

[Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh resultsDirectory 1, 10 gives error line 22: cd: left: No such file or directory

Dear Freesurfer experts, I have processed my subject with recon-all and subfields hippocampal segmentation. . I have tried to use kvlQuantifyHippocampalSubfieldSegmentations.sh on a subset of my subjects. I have these subjects A B C D E fsaverage in a folder. When I try to exclude

Re: [Freesurfer] Poor subcortical segmentation

Hi Bruce, I've heard people saying that FS 5.3 is focusing on better output for cortical thickness and that I should use 5.0 for subcortical segmentation because it's better. Does that make sense? Thanks! Mihaela On Tue, Nov 25, 2014 at 10:43 AM, Mihaela Stefan mikaelastep...@gmail.com wrote:

Re: [Freesurfer] Poor subcortical segmentation

No, I don't think so Bruce On Nov 25, 2014, at 11:05 PM, Mihaela Stefan mikaelastep...@gmail.com wrote: Hi Bruce, I've heard people saying that FS 5.3 is focusing on better output for cortical thickness and that I should use 5.0 for subcortical segmentation because it's better. Does

[Freesurfer] parcellation of group stats maps?

Hi, Is there a way to generate an intersection between a cortical thickness stats map (e.g., sig.mgh) in fsaverage space and native space neuroanatomy using FS parcellations (e.g., lh.apac.anot.)? We would like to plot cortical thickness of the significant clusters for each subject, but separate

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399

[Freesurfer] mri_glmfit-sim

Dear FS experts We would like to force FS's mri_glmfit-sim function of FS 5.3.0 to report all results and not only the significant results. This was the behavior of this function until FS version 4.5.0. Please can you guide as to the relevant lines in the mri_glmfit-sim function and indicate