Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups

Dear professor Bruce, Thanks for your precious reply. I will try. All the best. 2013-11-26 Rujing Zha 发件人：Bruce Fischl 发送时间：2013-11-25 23:20 主题：Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups 收件人："R

Re: [Freesurfer] Warping to MNI space

Note: you can run each command with --help to get info something like mni152reg --s subject to create the registration file (it will go into $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat then something like mri_label2vol --seg $SUBJECTS_DIR/$subject/mri/aseg.mgz --reg $SUBJECTS_DIR

Re: [Freesurfer] Error in Analyze

Try cutting and pasting that command into a shell. If it fails, send the full terminal output to the list. doug On 11/25/2013 01:02 PM, Christophe de Bezenac wrote: > Hi, > > I am trying to do a group analysis in qdec - one that I was able to run > before. For some reason I now get the follo

Re: [Freesurfer] glm_fit --prune

Oh, I need to give you an updated mri_binarize. Here is one for centos6. If that does not work for you, let me know what your platform is. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize On 11/25/2013 03:38 PM, cel...@nmr.mgh.harvard.edu wrote: > Hi Doug and freesurfe

Re: [Freesurfer] glm_fit --prune

Hi Doug and freesurfer team We just realized that the output framemask created by mri_binarize does not have the same dimension than the input file y.mgh, which is a concatenated file created through mris_preproc. so the dimension of our y.mgh is: 163842 x 1 x 1 x 33 and by running this command (

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

Thanks Doug, I had forgotten that my roadblock was actually in isxconcat_sess, not mri_glmfit. This worked out great. Following this up, how would you recommend calculating the fixed-effects significance of a complex (within subject) contrast with mri_glmfit? For simple contrasts, I have been

[Freesurfer] Error in Analyze

Hi, I am trying to do a group analysis in qdec - one that I was able to run before. For some reason I now get the following error: Error in Analyze: command failed: mri_glmfit --y /Users/chdebezenac/freesurferX/subjects/qdec/Untitled/y.mgh --fsgd /Users/chdebezenac/freesurferX/subjects/qdec/U

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

This is a bit delayed response (my apologies) to an earlier question to the list: The boost library is installed by default on CentOS platforms. If a user gets the libboost error then they are using a different platform which doesn't have boost installed by default. On RedHat systems libboost

Re: [Freesurfer] Warping to MNI space

Hi Douglas, Thanks for the reply. I am very new to Freesurfer and am more used to scripting with AFNI. Would you mind giving me a bit of sample code to get used to what this may look like? Can I script this in a .tcsh file? Also, once I convert the aseg to MNI space, can I simply average or a

[Freesurfer] ECC memory? change in brand of scanners in longitudinal studies?

Hi Thank you for developing this great software. I have two questions: 1) ECC-memory needed or not? - During all the freesurfer-calculations, would there be a validity-benefit of using a Xeon-based system with ECC-memory compared to analysis performed on a similar i7-based system with non-ECC me

Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups

I see. There is really nothing to do but visually inspect them for accuracy. Sorry, you will need to educate yourself a bit on what the anatomy looks like to tell if the boundaries are accurate. It's really not that difficult once you get a bit of experience. Feel free to send us images that yo

Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups

Dear professor Bruce, Thanks for your attention. After recon-all, I get the cortex thickness of all subjects. Then I check the segmentations by tkmedit your_subject_name brainmask.mgz -surfs -aseg. However, my fundamental knowledge is so little that I donot know whether the quality of segmented

Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups

Hi Rujing, sorry, I don't understand. Can you clarify what you are trying to do? Bruce On Mon, 25 Nov 2013, Rujing Zha wrote: Dear freesurfer experts, I met a question about how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 gr

[Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups

Dear freesurfer experts, I met a question about how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups. Thanks. All the best. 2013-11-25 Rujing Zha___ Freesurfer mailing list Freesu

[Freesurfer] curvature and its normalisation

Dear all, Could anyone tell me how to interpret the curvature files that you can create with mris_curvature/mri_make_surfaces? The description on the website tells that the values represent something like: Value in curvature file(*.H) = 1/R, with R being the radius of a sphere tangent to the

Re: [Freesurfer] Hippocampus ROI overlay on orig-image

Hi Theresa you can use mri_mc or mri_tesselate on the aseg.mgz with the hippocampal labels (17 and 53) cheers Bruce On Mon, 25 Nov 2013, "K?be, Theresa" wrote: > Hi guys, > > I did the total brain segmentation by freesurfer. Now I want to overlay in > freeview only the hippocampal ROI on the o

[Freesurfer] Hippocampus ROI overlay on orig-image

Hi guys, I did the total brain segmentation by freesurfer. Now I want to overlay in freeview only the hippocampal ROI on the orig-image. Unfortunately, in the surf-folder is no hippocampus surface. How can I create such a file or are there any other opportunities to see only the segmented hippo