Re: [Freesurfer] Some questions about fsaverage

Hello, Thanks for your answers :) mri_annotation2label enabled me to convert the ROI of Desikan Atlas as I wanted and the Brodmann were indeed in $FREESURFER_HOME/subjects/fsaverage/label . Have a nice day, Alexandre 2014-12-04 23:01 GMT+01:00 Bruce Fischl : > Hi Alexandre > > I'm not entirel

[Freesurfer] QDEC, Correction for multiple comparisons

Hi ,everyone I have found only two methods(i.e FDR,Monte Carlo simulation) of correcting for multiple comparisons in QDEC .However ,I didn't get any results on my data after correction .Therefore I want to try alphasim corrcetion.So I am wondering if QDEC can achieve it .If so . how can I do it ?

[Freesurfer] unpacking error

Dear Freesurfer expert, I come across an error message when calling 'unpacksdcmdir' to unpack the data that's been pushed to Bourget. I have no trouble navigate to the directory on /cluster/archive and see the files are there, but just could not have the 'unpacksdcmdir' work. Here are the

Re: [Freesurfer] unpacking error

Can you upload one of the dicom files (does not matter which one)? On 12/05/2014 11:00 AM, Fan, Qiuyun wrote: > > Dear Freesurfer expert, > > I come across an error message when calling 'unpacksdcmdir' to unpack > the data that's been pushed to Bourget. I have no trouble navigate to > the direc

Re: [Freesurfer] --pca flag on mri_glmfit

Appreciate the quick reply. I may be re-framing my question a bit here, but I'm curious as to the context in which one would use the PCA analysis. Is it meant primarily for functional data or can it be applied to glmfits for structural data? When I ran this the first time, I got 14 eigenvalues on a

Re: [Freesurfer] --pca flag on mri_glmfit

I did not have a specific application in mind when I wrote it. Part of it was to help look for artifacts (ie, structured noise in the residuals). It will always give you a number of eigenvectors equal to the smaller of the number of "temporal" dimensions or spatial dimensions. For imaging, thi

Re: [Freesurfer] QDEC, Correction for multiple comparisons

No, you can't use alphasim with qdec doug On 12/05/2014 08:47 AM, Xinfa Shi wrote: > Hi ,everyone > > I have found only two methods(i.e FDR,Monte Carlo simulation) of > correcting > for multiple comparisons in QDEC .However ,I didn't get any results on my > data after correction .Therefore I wan

[Freesurfer] Voxel-to-voxel transformation & overlapping voxels

Hello all, I am trying to figure the voxel-to-voxel correspondence between an anatomical image (1mm^3 voxels) and a functional image (2x2x2mm voxels). I registered the functional to the anatomical with bbregister and used the registration matrix to update the geometry info in the header of the

[Freesurfer] Fwd: .label.gii to .label

Dear FreeSurfer Experts, I have some labels in .gii format and I can watch them with freeview (opening one of surf.gii file and loading the label file as an Annotation file ). I used mris_convert --annot and then mri_annotation2label to produce .label files, but derived labels are corrupted. m

[Freesurfer] Dicom from CT

Hi all, I only have experience processing dicom images from MRI. Can Freesurfer handle images from CT as well? Anything to note? Thanks, Will ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] Voxel-to-voxel transformation & overlapping voxels

#1 looks correct (good job!) #2 4.3 means that the center of the anatomical voxel falls 30% of the way between voxels 4 and 5 in the function image (closer to voxel 4). To find out which func voxels a given anatomical voxel falls into, you can compute the func CRS for each corner of the anat v

Re: [Freesurfer] Dicom from CT

What do you mean by "handle"? You cannot run it through the anatomical analysis if that is what you mean. doug On 12/05/2014 03:38 PM, will brown wrote: > Hi all, > > I only have experience processing dicom images from MRI. Can > Freesurfer handle images from CT as well? Anything to note? > > T

Re: [Freesurfer] white matter snr

Hi Lars, I did not have such ideas when I wrote the program. I had intended it only to be a QA measure that one could perhaps send through the same GLM as one would use on the metric of interest (eg, to answer the question as to whether patients had a lower SNR than controls). As a covariate,

Re: [Freesurfer] Voxel-to-voxel transformation & overlapping voxels

Thanks! Just to make sure, do voxel coordinates refer to the centre of the voxel? Like, would [1.5 2.5 3.5] correspond to one corner of [1 2 3]? Jack ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/

[Freesurfer] --reg in mri_vol2surf

Hi Experts, At subject level, I want to convert a functional volume (in a subject's native space) to this subject's native surface. The functional volume has been registered to this subject T1 images in native space. I know "mri_vol2surf' would do the job but unsure how to generate the registrati

Re: [Freesurfer] --reg in mri_vol2surf

Hi Liang try bbregister. cheers Bruce On Fri, 5 Dec 2014, Liang Wang wrote: Hi Experts, At subject level, I want to convert a functional volume (in a subject's native space) to this subject's native surface. The functional volume has been registered to this subject T1 images in native space.

[Freesurfer] Discrete video card: ATI/AMD success stories?

Hi Freesurfers, I am spec'ing a couple of Linux workstations to run Freesurfer, among other software. Complicating matters, our preferred vendor's configurations include ATI/AMD video cards, but the FSWiki recommends nVidia cards. I was wondering if I am likely to run into problems if I go wit