[Freesurfer] Something wrong with the display image of tksurfer

Hi all, I have a problem about the tksurfer. When I use tksurfer to show the surface of the cortex. The window of the tksurfer is normal, but the image cannot be seen in the front window. And I cannot fix the image, but I click it then the image can display. Is there something wrong when insta

[Freesurfer] -notalairach flag

Hi all, i'm trying to run only the -autorecon1 step of the cortical reconstruction process, but I don't want my data to be transformed into a Talairach template. As I've read on the Freesurfer wiki, I can remove any step of the process using the -no flag, so in my case should be -notalairach

Re: [Freesurfer] -notalairach flag

we don't actually transform the data into tal coords - we just compute the transform for reporting (and a few computational) purposes. cheers, Bruce On Wed, 16 Sep 2009, Fischi Gomez Elda wrote: Hi all, i'm trying to run only the -autorecon1 step of the cortical reconstruction process, but

Re: [Freesurfer] Something wrong with the display image of tksurfer

Try this: http://www.youtube.com/watch?v=9573UYJxlok -- PPJ 2009/9/16 QQ Liu > Hi all, > > I have a problem about the tksurfer. When I use tksurfer to show the > surface of the cortex. The window of the tksurfer is normal, but the image > cannot be seen in the front window. And I cannot fi

[Freesurfer] center of gravity of the aparc.a2005s parcellations

Dear FS experts Sorry for reposting this question. I am looking for the MNI or Tal-coordinates of the center of gravity (COG; "middle-point of a particular parcellation") of the aparc.a2005s parcellations of the FS average brain. I need these coordinates to visualize the results of a graph-theore

[Freesurfer] make_average_subject and qdec problems

Hello all, I am trying to create an average subject from our pediatric brains and run group analyses with qdec. After I ran the make_average_subject command, the terminal exited with no errors. I then open qdec, load our data table, select our common-space subject, select our variables, and hi

Re: [Freesurfer] make_average_subject and qdec problems

Athena, What name did you give the average subject? If one wasnt specified when make_average_subject was run, then the name 'average' is used as the default. Enter that name (average) into the 'Common space subject' text box and press enter. You also probably want to inspect your average subjec

Re: [Freesurfer] Label sizes, min ROI size

Dear Doug, Thank you for your reply! The command results in ERROR: Option --slabel unknown. I could not figure it out from the options descriptions with other option i could use, so i need some help again... Cheers & thank you! Aga On 9/14/09 7:48 PM, "Douglas N Greve" wrote: > > Try somethi

[Freesurfer] Where are all the segmentation names explained?

Hello, Generally speaking the segmentation names are self explanatory like Left-Hippocampus or 5th-Ventricle. There are some segmentation's that I am not sure what they mean like ctx-lh-unknown or ctx-lh-bankssts. Is there any place I can go that would explain these few segmentation names? Is ther

[Freesurfer] segmentation problem

Dear All, I am new to freesurfer and I was wondering if you could give me some advice. I run the freesurfer analysis on the anatomical scan of one subject and I noticed that in output files from wm.asegedit.mgz onwards, large part of the brain (frontal lobes) appears to be missing. I checked th

Re: [Freesurfer] segmentation problem

Can you send us the dataset? On Sep 16, 2009, at 12:18 PM, "Paltoglou, Aspasia E" wrote: > Dear All, > > I am new to freesurfer and I was wondering if you could give me some > advice. > > I run the freesurfer analysis on the anatomical scan of one subject > and I noticed that in output fil

Re: [Freesurfer] displaying retinotopy data with tksurfer and other questions

Ritobrato Datta wrote: > Hello All, > > Many thanks for all the help that you provide to freesurfer users. > > I have a few questions - > > 1. Where do I find ch2better brain ? I want to pipe it through freesurfer all > the way to register to the spherical atlas and plot functional data across

[Freesurfer] longitudinal study

Hi, there, I am going to run the FreeSurfer Longitudinal Stream (FS 4.5) on data from different timepoints. Do we need cross-sectionally process all time points with the default workflow, or just need run the first step of the default workflow. Thanks a lot! Guang ___

Re: [Freesurfer] Label sizes, min ROI size

You probably need a newer version then. Or you can get the size of the ROI from each subject's label (mris_anatomical_stats). That way is probably better anyway. doug Agnieszka Burzynska wrote: > Dear Doug, > Thank you for your reply! > The command results in ERROR: Option --slabel unknown. I c

Re: [Freesurfer] Where are all the segmentation names explained?

These are the same as the cortical (aparc) segmentations. Look in Rahul Desikan and Ron Killiany paper. doug Brain Apprentice wrote: > Hello, > > Generally speaking the segmentation names are self explanatory like > Left-Hippocampus or 5th-Ventricle. There are some segmentation's that > I am not

Re: [Freesurfer] segmentation problem

Check the skull stripping. This can cause the FS-specific talairach alignment to fail. Paltoglou, Aspasia E wrote: > Dear All, > > I am new to freesurfer and I was wondering if you could give me some advice. > > I run the freesurfer analysis on the anatomical scan of one subject and I > noticed

Re: [Freesurfer] longitudinal study

Guang, See this page for details: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing (yes, you will need to process all subjects using the default cross-sectional stream). Nick On Wed, 2009-09-16 at 11:54 -0500, Guang Zeng wrote: > Hi, there, > > I am going to run the FreeSurfer

[Freesurfer] Surface area of subcortical structures

Hello, Is there a way to get the surface area of FreeSurfer subcortical structures? Thanks, Liz Selgrade ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Surface area of subcortical structures

There's not an easy way. You could binarize the structure (mri_binarize), then build a surface around it (mri_tessellate), maybe smooth it (mris_smooth), then compute the surface area (mris_info). This would be a completely untested method though:). Elizabeth Selgrade wrote: > Hello, > > Is the

Re: [Freesurfer] Surface area of subcortical structures

or use mri_extract_label instead of mri_binarize, like this, to get the left hippocampus: mri_extract_label aseg.mgz 17 lh.hippo.mgz mri_tessellate lh.hippo.mgz 128 lh.hippo.unsmoothed mris_smooth lh.hippo.unsmoothed lh.hippo mris_info lh.hippo |& grep total_area this seems to work. '17' is the

[Freesurfer] FW: questions about the surface processing stream

Hi, I have a few questions about the surface processing stream: I compared ?h.orig.nofix, ?h.orig, ?h.sphere and ?h.sphere.reg files. The number of triangles and vertices changes between the first two but after that they're constant. But the numbers are different across subjects. For fsa

Re: [Freesurfer] Surface area of subcortical structures

sure, you could use mri_tessellate to cover it with triangles, then mris_info to get the surface area. You'll need to get the structure index from the FreeSurferColorLUT.txt file to pass to mri_tessellate cheers, Bruce On Wed, 16 Sep 2009, Elizabeth Selgrade wrote: > Hello, > > Is there a wa

Re: [Freesurfer] FW: questions about the surface processing stream

Hi Lars, yes, the size of the faces is initially fixed - we cover the surface of each segmented wm voxel that borders non wm with 2 triangles. This gets changed by both the topology correction and the surface deformation. Note that the fsaverage surface area is less than any individual subject

[Freesurfer] how to extract segmented hippocampus

Hi, there, I'd like to extract the left and right hippocampus from aseg.mgz, so basically what I want is a volume where left hippocampus have value (or label) 17 and right hippocampus have value (or label) 53, all the other place are zero. How can I do it? Using mri_threshold or mri_label2vol?

Re: [Freesurfer] how to extract segmented hippocampus

mri_binarize with --match 17 or --match 53 will do it doug Guang Zeng wrote: > Hi, there, > > I'd like to extract the left and right hippocampus from aseg.mgz, so > basically what I want is a volume where left hippocampus have value > (or label) 17 and right hippocampus have value (or label) 53

Re: [Freesurfer] how to extract segmented hippocampus

mri_extract_label aseg.mgz 17 53 hippo.mgz On Wed, 16 Sep 2009, Guang Zeng wrote: > > Hi, there, > > I'd like to extract the left and right hippocampus from aseg.mgz, so > basically what I want is a volume where left hippocampus have value (or > label) 17 and right hippocampus have value (or la

[Freesurfer] MGZ to DICOM conversion...

Hi: How can I convert an MGZ (or Analyze or NIFTI) file to a DICOM one?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

Re: [Freesurfer] MGZ to DICOM conversion...

sorry, we don't support DICOM writing. On Wed, 16 Sep 2009, Gonzalo Rojas wrote: > Hi: > > How can I convert an MGZ (or Analyze or NIFTI) file to a DICOM one?... > > Sincerely, > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:/

Re: [Freesurfer] how to extract segmented hippocampus

Dear Douglas: And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz with the mri_binarize command ?... Sincerely, Gonzalo Rojas Costa > mri_binarize with --match 17 or --match 53 will do it > > doug > > Guang Zeng wrote: >> Hi, there, >> >> I'd like to extract the lef