Re: [Freesurfer] Reduction of image size

Hello Bruce, Definitely, I am constructing atlases with these images. Based on the number of available and functioning GPUs in our cluster, I am seemingly able to construct atlases of ~70 images with each image size being 256x256x160 and not of image size 256x256x256. Therefore, I am reslicing

Re: [Freesurfer] Reduction of image size

Hi Sourav Can you explain why you are reslicing? Cheers Bruce > On Feb 8, 2015, at 7:26 PM, SOURAV RANJAN KOLE wrote: > > Thank you, again, Bruce. > > How do I determine the starting coordinates for extraction, so I do not > cutoff relevant info? > > Regards, > > Sourav > > _

Re: [Freesurfer] Reduction of image size

Thank you, again, Bruce. How do I determine the starting coordinates for extraction, so I do not cutoff relevant info? Regards, Sourav From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis

Re: [Freesurfer] Reduction of image size

Hi Sourav mri_extract usage: mri_extract x0 y0 z0 dx dy dz (x0, y0, z0) is the starting coordinate of the rectangle to extract *not* the size. (dx, dy, dz) is the size. Yours should be something like: mri_extract input.mgz 0 0 0 256 256 160 output.mgz or maybe you don't want to start at 0,

[Freesurfer] Insula cytoarchitectonic maps?

Dear Freesurfers, Bit of a long shot...but does anyone know of any insula cytoarchitectonic maps that may be available for use to superimpose MRI studies over? Best wishes, Alex -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] Reduction of image size

Hello Bruce, Thank you for the prompt reply. Although, mri_extract is creating new files but it is giving me the following error- MRIextractInto: bad src location (256, 256, 160). Also, ITK-SNAP cannot read the new image file. Here is what I am doing: 1. Converting from .mgz to .img mri_conve

Re: [Freesurfer] Reduction of image size

mri_extract should do the trick Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: > Dear Freesurfer community, > Please let me know of an elegant way to reduce image size from 256x256x256 > to 256x256x160 and keeping the voxel size the same. The images are currently > in analyze format but I ha

Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

glad to hear it worked out Bruce On Sun, 8 Feb 2015, Liu Y wrote: Hi Douglas and Bruce, Thanks for your suggestions. I found the reason. The mistake begins from the compressing dcm to nii by using dcm2nii. In the first 3 dcm images, two of them have same index, then the dcm2nii could not keep t

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

Thanks. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au Fol

[Freesurfer] Reduction of image size

Dear Freesurfer community, Please let me know of an elegant way to reduce image size from 256x256x256 to 256x256x160 and keeping the voxel size the same. The images are currently in analyze format but I have access to mri_convert and ImageConvert. Thank you. Sourav

Re: [Freesurfer] average values per cluster

But how can i run the appropriate preprocessing and smoothing? The --X flag s not recognised using mris_preproc. I used the same matrix as X in an FSGD file to do this now, it seems to work, but I do not no if it is correct. Furthermore, If I try to run mri_glmfit --sim for the lGI data, I ge

Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

Hi Douglas and Bruce, Thanks for your suggestions. I found the reason. The mistake begins from the compressing dcm to nii by using dcm2nii. In the first 3 dcm images, two of them have same index, then the dcm2nii could not keep the original information of voxel size. I omitted the first 3 dcm imag

Re: [Freesurfer] Differing dimensions between curvature and inflated files

Hi Phil try running recon-all -make all on those subjects. Something was rebuilt but not run to completion I suspect. cheers Bruce On Sun, 8 Feb 2015, Kelly, Philip wrote: Dear FreeSurfer experts,   I am running Spherical Daemon on my reconstructed surfaces as part of the Winkler et al

[Freesurfer] Differing dimensions between curvature and inflated files

Dear FreeSurfer experts, I am running Spherical Daemon on my reconstructed surfaces as part of the Winkler et al (2012) method of analysing surface area. The majority of my subject's surfaces are read perfectly fine, however it exits with error on one particular subject. It seems that the probl