Re: [Freesurfer] A region loss in the ?h.aparc.stats

liang wang wrote: Hi, My freesurfer version is v4.5.0. Using tksurfer, I can find the corpus callosum shown in the ?h.aparc.annot (e.g., .. -annot aparc.annot). Moreover in the FreeSurferColorLUT.txt, this region exists (e.g. #No. 1004 ctx-lh-copuscallosum). However, I am surprised when

[Freesurfer] volume of temporal lobe, frontal lobe, etc...

Hi: How can I automatically compute, the volume of each brain lobe (temporal lobe, occipital lobe, etc) ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile.

Re: [Freesurfer] volume of temporal lobe, frontal lobe, etc...

you can add up the ?h.aparc.stats volumes for the aparc regions that you want to define as the temporal lobe. Alternatively, you could create a label out of those regions and run mris_anatoical_stats on the label doug Gonzalo Rojas wrote: Hi: How can I automatically compute, the volume

Re: [Freesurfer] volume of temporal lobe, frontal lobe, etc...

Hi: There is a tutorial related to the creation of labels ?... Sincerely Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El

Re: [Freesurfer] volume of temporal lobe, frontal lobe, etc...

There's one for drawing labels, but what you will want to do is to use mri_annotation2label to create labels from the ?h.aparc.annot, then use mri_mergelabels to create a single label from the subset that you use to define the temporal lobe. doug Gonzalo Rojas wrote: Hi: There is a

Re: [Freesurfer] Displaying significant difference with a threshold of cluster size

If you can get it past the reviewers. It might be better to report the actual significance of the clusters. doug liang wang wrote: Hello Doug, Thanks for your kind response. I have tried to use mri_glmfit-sim to correct the results. However, no significant differences were observed.

Re: [Freesurfer] A region loss in the ?h.aparc.stats

Hi Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious

Re: [Freesurfer] volume of temporal lobe, frontal lobe, etc...

Dear Doug: But, I need the volume of each lobe including GM and WM... such as the one that we can got from aseg.stats... Sincerely, Gonzalo Rojas Costa Douglas N Greve escribió: There's one for drawing labels, but what you will want to do is to use mri_annotation2label to create

Re: [Freesurfer] volume of temporal lobe, frontal lobe, etc...

Oh, we don't really have anything that will do this specifically, but you can add the volumes of cortex and white matter from the aparc.stats and wmparc.stats for the appropriate structures. doug Gonzalo Rojas Costa wrote: Dear Doug: But, I need the volume of each lobe including GM and

[Freesurfer] creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz

Hi Folks, I would like to create binary masks for any given structure in aseg.mgz and aparc+aseg.mgz. I would then also like to map the masks back to native space. I think, I should use mri_binarize followed by mri_convert as shown in the two examples below: Example 1: a. mri_binarize --i

Re: [Freesurfer] recon-all -all finished without error but didn't produce aseg.mgz files

how much RAM do you have on the machine that it's running on? What was the exit code of the process? On Mon, 12 Jul 2010 aekai...@umich.edu wrote: the recon-all.log does not show anything missing, however it is apparent now that it definitly didn't finish. For most of my subjects it stopped

Re: [Freesurfer] Creating table of segmentation volumes

Hi Liang, this is because of partial volume correction. Use the aseg when they differ cheers, Bruce On Mon, 12 Jul 2010, liang wang wrote: Hi, I was starting to create a table of segmentation volumes corresponding to several given label (--segno 255 i.e., CC_Anterior). However, I found the

[Freesurfer] mc-full duration

Dear FreeSurfer users, I have attempted to run mc-full for 20 iterations on 18 cores to test the time per iteration. The process is taking more than 14 hours. It times out at Poll 4725 job 1 How long does each iteration take for mc-full? We have 8 hemispheres to run, which will total 80,000

Re: [Freesurfer] creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz

Thanks Doug. Using mri_label2vol is a good idea and I will use this approach. Now to create the individual binary masks I just need to use mri_label2vol, followed by mri_binarize: For example: a. mri_label2vol --seg aparc+aseg.mgz --regheader rawavg.mgz --o aparc+aseg-in-rawavg.mgz --temp