[Freesurfer] Freesurfer dev version not available on the server

External Email - Use Caution Dear Freesurfer Developers I’ve been trying to download the development version but I keep getting an error message. Error: The share does not exist on the server. Please check the share name, and then try again. Any suggestions or alternatives? T

Re: [Freesurfer] Origin of freesusrfer output

also, check out this web page http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 08/05/2018 11:23 AM, Bruce Fischl wrote: > Hi Ritesh > > you can use the vox2ras matrix to compute the RAS coordinates of any > voxel. Just give it column,row,slice,1 indices as the input vector. > > chee

Re: [Freesurfer] Lobe parcellation without cingulate from --lobesStrict

Sorry, I'm not sure I understand. You want the lobes annotation but you want to merge the cingulate with the frontal? After you run the 1st mri_annotation2label, run it again with the lobes as the input annotation and specifying --outdir to break up the annotation into labels. Then run your mer

Re: [Freesurfer] Get error while performing cortical and sub cortical segmentation for PET images

You cannot use PET images as input to FreeSurfer. It must be a T1-weighted MRI. doug On 08/04/2018 03:16 AM, Yubraj Gupta wrote: > > External Email - Use Caution > > Hello Freesurfer Developers, > > I'm attempting to compute RECON-all for PET images, for some image I > am getting the st

Re: [Freesurfer] Lobe parcellation without cingulate from --lobesStrict

External Email - Use Caution Dear Douglas, thank you for your response. Sorry if I've been misunderstood. I want to have the following parcellation of lobes: Frontal • Superior Frontal • Rostral and Caudal Middle Frontal • Pars Opercularis, Pars Triangularis, and Pars Orbitalis •

Re: [Freesurfer] Lobe parcellation without cingulate from --lobesStrict

If you want custom lobes, then the easiest thing to do is to break up the aparc annotation into labels (mri_annotation2label) and then merge each lobe into a single label (mri_mergelabels), then combined the merged labels back into an annotation (mris_label2annot). On 08/06/2018 12:38 PM, Ferna

[Freesurfer] ERROR: dimension mismatch between y and X.

External Email - Use Caution Hello Community! I have an issue while running dt_recon because as can be seen in the output terminal there is some error in matrix dimensions. Renes-MacBook-Air-2:~ andraderenew$ dt_recon --b /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_pr

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution Hello again: I have downloaded this raw data from a database that’s the reason I’m not sure it is T1w but I think what they call ntdi it is. So when I run recon-all from this ntdi.nifti file it gives me a Talairach error. I send you the output termi

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

You should first verify that the input is in fact a T1 of about 1mm resolution and that there are no obvious artifacts. After that, you should check the talairach registration (see the web page it points you to) On 08/06/2018 04:40 PM, Renew Andrade wrote: > External Email - Use Caution

Re: [Freesurfer] ERROR: dimension mismatch between y and X.

It says that in the input (IXI015-HH-1258-DTI-00.nii.gz) has only one frame, which probably means that it is not the right input On 08/06/2018 04:33 PM, Renew Andrade wrote: > > External Email - Use Caution > > Hello Community! > > I have an issue while running dt_recon because as can be

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

and make sure that the direction cosines are correct (that is, the directions that freeview says are in fact the actual anatomical directions) On Mon, 6 Aug 2018, Douglas N. Greve wrote: You should first verify that the input is in fact a T1 of about 1mm resolution and that there are no obviou

[Freesurfer] wm.mgz values

External Email - Use Caution Hello Freesurfers. I was wondering of for the purposes of editing wm.mgz if changing voxel values to anything but 255 and 1 will be useful in anyway. If so I was wondering if you can explain to me what the following values mean and how do I use them.

[Freesurfer] WM segmentation

External Email - Use Caution Hi, I would like to create a mask of the WM for fMRI analysis. I read a previous post in which it was suggested to get the wm segmentation and erode it, since the result will be exclusively WM. My question is why is this so? Why can I assume that gettin

Re: [Freesurfer] WM segmentation

External Email - Use Caution Perhaps erosion was suggested because of partial voluming in your fMRI voxels. Peace, Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ben M mailto:fmri@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nm

Re: [Freesurfer] Origin of freesusrfer output

External Email - Use Caution Hi Doug, I checked the link you suggested. What i understood from this is the origin shift(physical co-ordinate of first voxel) is happening due to the rotation of axis to RAS co-ordinate system. To counter rotation origin shift is done, is that cor