Re: [Freesurfer] Hippocampal Sub-Field Segmentation -Appropriate Scan Protocol to Use

Hi Joshua, The version of the hippocampal subfield segmentation routines currently in FreeSurfer will only work out of the box on the usual FreeSurfer-resampled 1mm isotropic data. If you are technically skilled, it should be possible to tweak things to make it work on other data (we don't assume

[Freesurfer] color scale interpretation retinotopy eccen maps

Dear freessurfer experts, I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume)

Re: [Freesurfer] Topology correction - segmentation fault

Hi Mehul this is a bug in the topology correction that we haven't been able to track down, mainly because the person who wrote this piece is long gone. If you edit the wm to remove a defect it usually goes away Bruce On Mon, 31 Oct 2011, Mehul Sampat wrote: Hi Folks I am using

Re: [Freesurfer] recon-all error

Yes, I ran it with the -i first, and I got this error: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an

Re: [Freesurfer] Topology correction - segmentation fault

Hi Mehul, Alternatively you can try rerunning the skullstrip step, sometimes this works as well. recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID] -Louis On Tue, 1 Nov 2011, Bruce Fischl wrote: Hi Mehul this is a bug in the topology correction that we haven't been able to track

Re: [Freesurfer] recon-all error

Can you delete them again and re-run? So far, I have not seen anything that recon-all is doing wrong, and I can't debug it until I do! doug Chindhuri Selvadurai wrote: Yes, I ran it with the -i first, and I got this error: ERROR: You are trying to re-run an existing subject with (possibly)

Re: [Freesurfer] color scale interpretation retinotopy eccen maps

Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in

Re: [Freesurfer] Topology correction - segmentation fault

Hi Bruce and Louis, Thank you for the suggestions. I will try them out. Just fyi. For our dataset this error is very rare. So far it occured only in 1 out of 525+ scans processed with FS 5.1. Thank you, Mehul On Tue, Nov 1, 2011 at 6:50 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu

[Freesurfer] VGL error

Hello FreeSurferers, I run tksurfer remotely from a linux machine running CentOS (Boston University) using Virtual GL/TurboVNC. I have been able to do this successfully for years but have recently encountered the following error when calling tksurfer: surfer: tkoInitWindow(RMAUT015) [VGL] ERROR:

Re: [Freesurfer] color scale interpretation retinotopy eccen maps

Hi Doug, I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color red would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find

[Freesurfer] func2roi-sess question

Hi, I've been using func2roi-sess for region of interest analyses and was hoping that someone here could answer what might be a pretty basic question. Does anyone know when in the analysis stream the data from voxels in an ROI are averaged? I can think of two possibilities. The first is that the

Re: [Freesurfer] color scale interpretation retinotopy eccen maps

If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself.

[Freesurfer] surface normals

Dear Sir, Can the surface normals be loaded in matlab? Is there a code for that and what variable should I look at in surf dir? Thank you. HIroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy

Re: [Freesurfer] surface normals

Hi Hiroyuki by default we don't save the surface normals but compute them on the fly. You can however use mris_convert -n surface file normal file name to compute and output the surface normals in an ascii format that should be pretty easy to read into matlab. cheers Bruce On Tue, 1 Nov