[Freesurfer] Error running recon-all

External Email - Use Caution Dear Freesurfer experts, Greetings! In the first minute of recon-all, we are getting following error: mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at slice 0 T1 data type is int16, data type 4 (looked using fslinfo) Looking

Re: [Freesurfer] T1 orientation prior to running recon-all

Hi Abid nope, you shouldn't have to, as long as the header info is correct. Does it come up properly in freeview? That is, does what freeview thinks the orientations are match what they really are? cheers Bruce On Wed, 24 Jul 2019, Abid Qureshi wrote: External Email - Use Caution

[Freesurfer] T1 orientation prior to running recon-all

External Email - Use Caution Dear Freesurfer, Does my T1 MPRAGE need to be in a particular orientation prior to running recon-all? Meaning should I use mri_convert to change to RAS orientation to avoid any L/R confusion with the output measures. For instance, mri_info says the or

Re: [Freesurfer] Multiple overlays onto surface

Hi Zeynab tksurfer has been deprecated for years. Can you use freeview instead? You can do this in freeview by loading one as a "curvature" map and the other as an overlay cheers Bruce On Wed, 24 Jul 2019, Alshelh, Zeynab wrote: Hi Freesurfers, Is it possible to view two overlays on on

Re: [Freesurfer] label to asc

Hi Sam they are not the same. A label is just a list of vertices in the surface (with some possibly voxel coordinates and also with a single value/vertex). It doesn't have to be ever vertex in the surface, and also contains no information about topology (e.g. which vertices are connected by an

Re: [Freesurfer] Mass-Univariate LME - help please!

External Email - Use Caution Dear Kersten, Thank you so much for the quick reply! It was really helpful!! I still have a couple of doubts regarding the visualization of the results if you don't mind. After running the last command *fs_write_Y(sided_pval,mri,'**spval_lh.mgh')*, I

[Freesurfer] Multiple overlays onto surface

Hi Freesurfers, Is it possible to view two overlays on one surface image using TkSurfer? One of the surface overlays is binary while the other isn't. I have been able to load them both onto TkSurfer but I can only view one at a time. Kind regards, Zeynab Alshelh, PhD | Postdoctoral Rese

[Freesurfer] (no subject)

External Email - Use Caution Hello Sebastian, Please download the zip archive from the following link, https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing Then expand and read the README.patch file and follow the instructions.  When you are done, you

Re: [Freesurfer] label to asc

External Email - Use Caution Thanks Bruce. Can I ask you a very basic question? What exactly is the difference between a surface and a label file? I thought the difference was that the label file is just a normal text file containing the vertices that are used to construct a surfac

Re: [Freesurfer] label to asc

Hi Sam the labels are already ascii cheers Bruce On Tue, 23 Jul 2019, Sam W. wrote: External Email - Use Caution Hi, Is it possible to convert a label file like rh.cuneus.label into asc? I tried mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc but g

Re: [Freesurfer] Cluster sizes discrepancy for mri_surfcluster vs mri_segstats

External Email - Use Caution Doug, We are still seeing differences, but I notice that the results from segstats are all whole integers, while the results from surfcluster (Max cluster size) is not. I assume this is because surfcluster is using partial volume. How do we implem

[Freesurfer] WG: Update FreeView on MacOs

Dear all, based on this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051591.htm l Is there any update for this? I have a MacBookPro with MacOs Mojave (10.14.3) and I'm facing the same issue with FreeSurfer 6.0.0 stable. Start FreeView via launch pad is fail