[Freesurfer] longitudinal stream: adding a time point

2015-10-08 Thread Adam, Ruth
Dear all, We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points)

[Freesurfer] WM segmentation error longitudinal stream

2015-10-01 Thread Adam, Ruth
Hi all, We have run longitudinal analysis on two time points. The resulting longitudinal WM surface for both time points excludes large parts of the cortex. The cross sectional surfaces and the wm.mgz are correct. The base wm.mgz also seems to be fine, however, the base white and pial surfaces

Re: [Freesurfer] excluding labels

2014-10-14 Thread Adam, Ruth
analysis?On 10/10/2014 03:57 AM, Adam, Ruth wrote:Hi,I would like to exclude areas which were incorrectly segmented andcould not be corrected after editing and re-running recon-all from thecortical thickness measure.Thank you again.Best,ruthiOn 09 Oct 2014, at 19:57, Douglas Greve gr

Re: [Freesurfer] excluding labels

2014-10-10 Thread Adam, Ruth
? On 10/9/14 11:35 AM, Adam, Ruth wrote: Hi all, Would be great is someone can tell me how to exclude user-definedlabels from the analysis. As far as I understand after

[Freesurfer] excluding labels

2014-10-09 Thread Adam, Ruth
Hi all,Would be great is someone can tell me how to exclude user-definedlabels from the analysis.As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the

[Freesurfer] excluding labels from analysis

2014-10-06 Thread Adam, Ruth
Hi all,I would like toexclude user-defined labels from the analysis.As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the new annotation file be

[Freesurfer] create a label file in tkmedit

2014-10-01 Thread Adam, Ruth
Hi all, I am creating a label file using the select voxels tool in TkMedit. However this doesn't work properly with e.g. all saved vertex IDs are set to -1. Example file: #!ascii label ….. , from subject ….. vox2ras=TkReg 19 -1 -40.000 52.000 21.000 110.00 -1 -39.000 52.000