Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

External Email - Use Caution It seems to work. Thanks a lot ! Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France ___ Freesurfer

Re: [Freesurfer] Smooth surface overlay

Hi Heidi, I'm not sure I understand what you are trying to do. Can you elaborate? What do you mean that you do not have statistical info any more? It is unusual to smooth p-values. Probably you should apply smoothing before your analysis On 8/9/2019 2:46 PM, Jacobs, H (NP) wrote:

[Freesurfer] asegstats2table error - measure 63 expected 66

External Email - Use Caution Dear Freesurfer experts, We had just reprocessed our subjects with the -long flag fr the longitudinal processing, and when extracting volumes with asegstats2table I have the following error: WARN: SUBJ229_ses-1.long.SUBJ229_tmpl nmeasures = 63,

Re: [Freesurfer] CORRECTING DEFECT

External Email - Use Caution Bruce, Awesome! I'll try that! Thanks, Brendan -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, August 09, 2019 11:40 AM To: Freesurfer

[Freesurfer] Smooth surface overlay

External Email - Use Caution Hi all, I created an overlay surface map of my analyses (with pvalues in log10) using R. Now I would like to smooth this map to extract clusters and I tried to use: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 3 --sval lh_analyses.mgh --tval

Re: [Freesurfer] CORRECTING DEFECT

Hi Brendan usually defects that are that big don't get corrected properly. I would look at the wm.mgz and the lh.orig.nofix to understand what is causing the large defects and correct them manually cheers Bruce On Fri, 9 Aug 2019, Balken, Brendan wrote: External Email - Use

Re: [Freesurfer] CORRECTING DEFECT

External Email - Use Caution Bruce, Oh okay I understand now. This has been very enlightening! So, you think if I let it keep running it will eventually correct the defects? And then I just need to double check the result to make sure it corrected them properly? When I got the

Re: [Freesurfer] CORRECTING DEFECT

yes, because that is the total # of defects. The 29th or 30th isn't the last one, just what it got stuck on. The #30 should look much bigger though (you'll need to change the overlay thresholds) On Fri, 9 Aug 2019, Balken, Brendan wrote: External Email - Use Caution Bruce, I just

Re: [Freesurfer] CORRECTING DEFECT

External Email - Use Caution Bruce, I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why... Thanks! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] CORRECTING DEFECT

they are an overlay not a surface. Load the surface first then load them as an overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, Balken, Brendan wrote: External Email - Use Caution Bruce, Thanks so much for the quick response! I don't know how to load the defect

Re: [Freesurfer] CORRECTING DEFECT

External Email - Use Caution Bruce, Thanks so much for the quick response! I don't know how to load the defect labels. When I try to load them as a surface, I get an error. I'm doing this in freeview gui. Also, I checked the cerebellum and it's not attached. Thanks, Brendan

Re: [Freesurfer] TRACULA - runlist longer than subject list

External Email - Use Caution Sorry I did not see your reply (having issues getting notifications from the freesurfer list). The error seemed to be an issue with the version I was using, which wasn't reading the subject list correctly. Wanted to make sure I posted a solution. Thank

[Freesurfer] TRACULA - OrientLAS issue for a subject

External Email - Use Caution Hello, I am running TRACULA on my data set and am having issues with one of my subjects. For this subject, I get the following error. INFO: input image orientation is LIS INFO: input image determinant is 18.4229 rdc_new: Undefined variable.

Re: [Freesurfer] CORRECTING DEFECT

Hi Brendan the time to correct goes with the square of the size of the defect (actually the convex hull of the defect) so it can take a very long time for big ones. More importantly, if the defect is that large it may not be corrected in the anatomically desired manner. You should take a look

[Freesurfer] Deconvolution with FSFAST

External Email - Use Caution Hi! I was wondering whether it is possible to do deconvolution of an fMRI time series with FSFAST? Specifically, I would like to get a deconvolved signal from a region of interest to prepare predictors for a PPI analysis. Additional considerations: