[Freesurfer] open *.mgh

Hi, Thank you for your help before. And, I have a problem today. How do I open the file called *.mgh as F.mgh and sig.mgh in the dictionary “qedc”? This problem has been nagging me for some time. Thank you in advance! Feng-Xian - Chang Gung

RE: [Freesurfer] questions about region-wise analysis data

the average subject isn't all that different from group to group since we explicitly normalize out the majority of the differences. Nevertheless, displaying on the average of your study instead of fsaverage gives a better idea of the localization accuracy. The XYZ will be different since they

RE: [Freesurfer] questions about region-wise analysis data

yes, that should work using mri_label2label. What doesn't work? On Mon, 5 Jan 2009, Wang, Xin wrote: an addition question: it is plausible to load multiple sets of ROIs created by different analyses on one subject thickness map after converted all of them back to the individual space. This a

[Freesurfer] Parameter comparison in native vs. template space

I would like to export cortical thickness measures and compare the data across subjects in a vertex-by-vertex fashion. Please could you confirm that similar functions such as mri_glmfit are based on the parameters in template space e.g. lh.thickness.fsaverage.mgh and not on the parameters in nativ

Re: [Freesurfer] open *.mgh

Feng-Xian, In the case of qdec results, those files are associated with the 'fsaverage' surface, specifically, they overlay on that surface. So one option to 'open' the files is to first load an fsaverage surface in tksurfer, and then use the Load->Overlay option to load sig.mgh onto that surface

Re: [Freesurfer] reg-feat2anat failed

Hi Xin, I'm not sure what's going wrong here, I think I need more info. Can you follow the steps in surfer.nmr.mgh.harvard.edu/fswiki/BugReporting? doug Wang, Xin wrote: hello, Freesurfer group, I try to use registration.mat files of FSL/FEAT routines, instead of anat2example_func.bat, to

Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?

You can use feat2surf (or mri_vol2surf directly), this will create something like lh.zstat1.mgh. You can then use lhz1 = MRIread('lh.zstat1.mgh'); doug Yunjie Tong wrote: Hi I was able to view the statistical maps (from FSL) on the subject's surface following the tutorial (FsTutotial/FSL

Re: [Freesurfer] Problem with post-spm registered data

There is no gold standard. Mainly just visualizing it with the surfaces and making sure the surfaces line up with the bright and dark folds in the EPI, as it says in the tutorial. doug Wang, Xin wrote: Sorry for asking same question here again. I asked Dung before holiday about the criteria

[Freesurfer] Poor labeling

Hello, I'm using a home-grown GCA constructed from five acallosal subjects to try to improve the automatic labeling and segmentation of volumes from this population. However, the labeling was quite bad when performed on a representative subject, and the ventricles were only partially fille

Re: [Freesurfer] Poor labeling

Hi Jason, how big are the ventricles? I have some prototype code that seems to work well on huge ventricle subjects. I could try it on your subject data if you want to put it on our website cheers, Bruce On Tue, 6 Jan 2009, Jason S. Minamora wrote: Hello, I'm using a home-grown G

Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?

Thanks Doug, However, I do not know how to interpret the data. For example, my lhz1.vol has dimensions of 1x9022x17. What does that mean? I am looking for the vertex and faces, with which I could display them in Matlab using patch. Do I miss something? Thanks. Best, YJ On Jan 6, 2009,

Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?

you'll only get the vertices. If you multiple those dims together, you'll get the number of vertices in the subject's surface, so just reshape it to 1d doug Yunjie Tong wrote: Thanks Doug, However, I do not know how to interpret the data. For example, my lhz1.vol has dimensions of 1x9022x1

[Freesurfer] Loading Projects Files

Dear Freesurfer Community I have been unable to load any of my saved Project files , and I cannot find any explanation in the tutorial or in the list arcives. I have been saving the project files inside of the qdec/ directory as .qdec. However, when I try to load them, I get an error. I am usi

Re: [Freesurfer] Loading Projects Files

Jennifer, What is the error? Can you send me one of the .qdec files to our file drop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Tue, 2009-01-06 at 12:26 -0800, Bramen, Jennifer E. wrote: > Dear Freesurfer Community > > I have been unable to load any of my saved Pro

Re: [Freesurfer] Parameter comparison in native vs. template space

Christine Ecker wrote: I would like to export cortical thickness measures and compare the data across subjects in a vertex-by-vertex fashion. Please could you confirm that similar functions such as mri_glmfit are based on the parameters in template space e.g. lh.thickness.fsaverage.mgh and no

[Freesurfer] Trouble Creating label

Hello all, I'm creating a label on a volume in tkmedit and as I do it, tkmedit will unexpectedly close and give me the following error message in the terminal window: === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecover

Re: [Freesurfer] Trouble Creating label

Hi Moe Could you copy the output of the command "bugr" which ships with Freesurfer. Just type bugr and send us. Basically, the exact workflow so that we can recreate the problem here. Is it specific to that particular volume? Krish On Jan 6, 2009, at 5:48 PM, Zeidan, Mohamed A. wrote: