[Freesurfer] Group differences of functional connectivity differ in SPM and FSL

Dear users, I writhe in the hope somebody encountered a similar problem. I have individual normalized maps of intrinisc brain networks from a dual regression. This maps are projected back into individual subject space and further into individual surface space. Finally I normalize this maps into

[Freesurfer] Hippocampal sufields in MNI templates

Dear freesurfer users,I was wondering: is there any way to get normalized ROIs for hippocampal subfields in MNI space? Is anything speaking against for example, running freesurfer with subcortical segmentation on an MNI template? cheers and kind regards, Lorenzo Pasquini_

[Freesurfer] Prroblem with segmentation using aparc 2009 labels

Dear Freesurfer users, I used freesurfer to extract the cortical thickness of several regions, which are saved in the aparc.a2009s.stats text file. To create a mask of this regions for further analyzes I used the command line: mri_binarize --i aparc+aseg.mgz --min number --max number -- o testn

[Freesurfer] Hippocampal segmentation: version needed

Dear Freesurfer experts, I used freesurfer v4.3.0 on anatomical data (T1). I am trying to segment hippocampal subfields with the following command:  recon-all -s subjname -hippo-subfields unfortunately I get the following error: ERROR: Flag -hippo-subfields unrecognized I have already the files a

[Freesurfer] hippocampus subfilelds mask

Dear Freesurfer experts, I successfully run a hippocampal subfield segmentation on anatomical data of one subject (resolution 1 mm^3). Now I am building hippocampal subfields masks. I used the FreeView interface to load the mgz volume files of hippocampal subfields. I saved each subfield separa

[Freesurfer] I: hippocampal subfield segmentation

hello carolina to me it took about 5-6 hours. greets,   lorenzo         Da: Carolina Valencia A: Freesurfer Mailing List Inviato: Giovedì 30 Agosto 2012 20:37 Oggetto: [Freesurfer] hippocampal subfield segmentation Hi Freesurfer community,  A quick question,

[Freesurfer] hippocampal segmentation converting mgz to nii

freesurfer:   6851 voxels found in .nii file: 15812 Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards, Lorenzo Pasquini Can. Ph. D., Medical

[Freesurfer] voxel number estimation kvlQuantifyPosteriorProbabilityImages

subfield .mgz images in .nii images. The number of voxels with a probability bigger than 0 in the nii images do not correspond to the estimations extracted with the kvlQuantifyPosteriorProbabilityImages command. Thank you! yours, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology

Re: [Freesurfer] hippocampal segmentation converting mgz to nii

Dear Koen, thank you very much for your help!! by summing the intensities and dividing by 255 I get the same volumes estimated by freesurfer. Thank you again and greets, Lorenzo Pasquini --- Ven 7/12/12, Koen Van Leemput ha scritto: Da: Koen Van Leemput Oggetto: Re: [Freesurfer] hippocampal

[Freesurfer] Vertex space

Dear Freesurfer users, I was wondering if it is possible to transform functional connectivity images (.img format) derived e.g. from an ICA of resting state fMRI data into vertex space reflecting cortical thickness (derived from the Freesurfer pipeline on anatomical data). We have been trying

Re: [Freesurfer] Vertex space

abily distinguish left from right. cheers Bruce On Wed, 3 Sep 2014, lorenzo pasquini wrote: > Dear Freesurfer users, > > I was wondering if it is possible to transform functional connectivity > images (.img format) derived e.g. from an ICA of resting state fMRI data > into ver

[Freesurfer] mincost bb_register

Dear Freesurfer users, I have used the command bb_register to automatically register raw fMRI data on the anatomy. The output looks visually fine, however the mincost file gives me values around 0.5 for my subjects. Is this range acceptable? Does anybody has a hint on how the registration could

[Freesurfer] normalizing activation maps

Dear Freesurfers, I have a question regarding normalization of functional activation maps. Let us assume I have functional activation maps on a vertex space (e.g. mgh files reflecting degree centrality, which do not need previous normalization of functional data). After resampling activation maps

[Freesurfer] problem in building cortex mask

Dear freesurfers, I have a problem in creating  masks of the left and right cerebral cortexes. The message "found 0 values in range" is displayed and an empty mask is created. This is surprising as I am able to build masks of the right and left hippocampi and entorhinal cortexes using the same