RE: [Freesurfer] Comparison of cortical thickness results

Hi Nick, Thank you very much, that worked well. Though the initial command was mri_annotation2label not mris_annot2label in v4.3.0 of FreeSurfer. Regards, Falk -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Tuesday, April 28, 2009 7:08 AM To: Falk Lüse

[Freesurfer] recon-all settings

Hi, I want to use parameters different from default for mri_nu_correct.mni. This command uses nu_correct for which I would like to set the following options: -distance 25 -stop 0.0001 -fwhm 0.1 These settings are more approriate when using 3T T1 data. How can I invoke these in recon-all? Can I

[Freesurfer] is there a command to give resolution information?

Hi, This may be a frivolous question but I was just wondering if anyone knows a quick way to find out resolution of an image file, i.e., if I wanted to look at an older scan and wanted to check its resolution. I couldn't find any information in the wiki, but I may have just missed the correct ar

Re: [Freesurfer] is there a command to give resolution information?

mri_info should do the trick. cheers, Bruce On Tue, 28 Apr 2009 j...@nmr.mgh.harvard.edu wrote: Hi, This may be a frivolous question but I was just wondering if anyone knows a quick way to find out resolution of an image file, i.e., if I wanted to look at an older scan and wanted to check i

[Freesurfer] Label to annot

I have the trouble to convert the BA label to annotation file. The Freesurfer 4.3.0 is on Mac OS 10.5.6. First, I got the BA label: mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/lh.BA1.label --trgsubject 001 --trglabel 001/label/lh.BA1.label --hemi lh --regmethod surface This wo

Re: [Freesurfer] recon-all settings

Ed, Create a file (named whatever you want, say, mri_nu_correct.xopts) containing one line: mri_nu_correct.mni --distance 25 --stop 0.0001 --fwhm 0.1 and then include this at the end of your recon-all command: -expert /mri_nu_correct.xopts and it will append those three flags to the end of the

Re: [Freesurfer] Label to annot

Hi Wayne, why are you trying to convert the label to an annotation? Not sure why it's not working, but I don't know that I've ever used the tksurfer export feature. Bruce On Tue, 28 Apr 2009, Wayne Su wrote: I have the trouble to convert the BA label to annotation file. The Freesurfer 4.3.

Re: [Freesurfer] Label to annot

Hi Bruce, I am wondering whether I can get the white matter volume of the single label by using mri_aparc2aseg -s --labelwm ... But mri_aparc2aseg only works for annotation not the label. Maybe this is not the right way. Any suggestion would be appreciated. Wayne On 28/04/09 11:00 AM, "Bruce F

[Freesurfer] Freesurfer Brain Region Ontology

Hi! I am rather new to the Freesurfer Software, so I'll start with an easy question. Currently I am involved in a SemanticWiki project called ConnetomeWiki, which deals with Brain Regions and their connectivity. This needs to setup a good ontology to start with and I am in the process of merging s

[Freesurfer] Thalamus Segments

Dear Freesurfers, What would be the best approach to sub-segment the subcortical structures (using mri_divide_parcellation) to anatomically relevant sub-segments similar to Thalamus sub-segments in FreeSurferColorLUT.txt (SegID 8001 to 80014). Thank you, Nasim

[Freesurfer] Custom Aseg Atlas Question.

Hi Freesurfer folks- I am in the midst of creating a custom aseg atlas and had a quick question regarding when to use v. discard subjects. I just ran the second iterations of mri_ca_train (when you use all the subjects in subjects.csh and are training from segmented subjects using M3D_ONE) and I

Re: [Freesurfer] Custom Aseg Atlas Question.

Hi Jamie, what do you mean by "bad labels"? Bruce On Tue, 28 Apr 2009, Jamie Hanson wrote: Hi Freesurfer folks- I am in the midst of creating a custom aseg atlas and had a quick question regarding when to use v. discard subjects. I just ran the second iterations of mri_ca_train (when you use

Re: [Freesurfer] Freesurfer Brain Region Ontology

Stephan, At the bottom of this page: http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:QueryAtlas is a link to a spreadsheet that contains the mapping of FreeSurfer segmentation and parcellation names to BIRNLex, NeuroNames, UMLS, and IBVD. The Slicer tool has an ontology mapping functi

Re: [Freesurfer] Custom Aseg Atlas Question.

> Hi Jamie, > what do you mean by "bad labels"? when going through each subject in mri_ca_train, some subjects output the following: ERROR: mri_ca_train: possible bad training data! subject: /study/eemri/data/proc/freesurfer/30_aseg and then after all the subjects are finished in mri_ca_train, it

[Freesurfer] problem downloading freesurfer

I am trying to download FreeSurfer onto a different Linux machine. I am able to download, but when I try to unzip the files, I get this error message: gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I have tried downloading it repe

Re: [Freesurfer] Custom Aseg Atlas Question.

Jamie, There should be some other information in the log informing why the label is 'bad'. There are checks in the mri_ca_train for labels having strange coordinates, mainly there to catch things like a right- hippocampus label in the left hemisphere. So look for those type error messages in the

Re: [Freesurfer] Custom Aseg Atlas Question.

is that all it says? I think we put some checks in to make sure that e.g. the left hippocampus wasn't labeled right. Is there anything like that in the output? On Tue, 28 Apr 2009, Jamie Hanson wrote: Hi Jamie, what do you mean by "bad labels"? when going through each subject in mri_ca_trai

Re: [Freesurfer] problem downloading freesurfer

try: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer- Linux-centos4-stable-pub-v4.3.0-full.tar.gz Nick On Tue, 2009-04-28 at 16:54 -0400, Dana W. Moore wrote: > I am trying to download FreeSurfer onto a different Linux machine. I > am able to download, but when I try

[Freesurfer] skull strip problem

Hi, I am trying to run freesurfer on some SPGR sequences that I have on a few subjects. I managed to import and convert the DICOM files to .mgz with success, but when I ran the skull strip I have a significant amount of skull left in some places and a large chunk of brain missing in other plan

Re: [Freesurfer] skull strip problem

Hi Ben, do the images appear in the right orientation in tkmedit? How did you convert to .mgz? If they are in the correct orientation then feel free to drop an example that isn't working on our website and we'll take a look. cheers, Bruce On Tue, 28 Apr 2009, Wilson, Benjamin wrote: Hi,

Re: [Freesurfer] Thalamus Segments

Hi Nasim, this is an active area of research for us, but we don't have anything ready for use yet. cheers Bruce On Tue, 28 Apr 2009, Nasim Maleki wrote: Dear Freesurfers, What would be the best approach to sub-segment the subcortical structures (using mri_divide_parcellation) to anatomicall

[Freesurfer] longitudinal stream

Hi All, We have recently tracked down a bias in the longitudinal processing stream. We believe we have a fix for the problem, but it will take us a bit of time to get it working and well-tested. We'll keep you posted as to when we will have a new version. Feel free to email me if you have any