Re: [Freesurfer] recon-all image output

Dear experts, we run this command in a file of MRI 3D .nii : recon-all -force -all -notal-check -i /my_directory_input/my_file.nii -subjid my_directory_output and i get the attached image of output for a single time point, after 40 hours of elaboration. We don't understand why there isn't the

Re: [Freesurfer] recon-all image output

2010/7/23 Michele Placci > Dear experts, we run this command in a file of MRI 3D .nii : > > recon-all -force -all -notal-check -i /my_directory_input/my_file.nii > -subjid my_directory_output > > and i get the attached image of output for a single time point, after 40 > hours of elaboration.

[Freesurfer] segmentation output not in alignment

Dear all I put a T1w image through the recon-all process and it completed without errors, but the segmentation output (aparc.a2009s+aseg) does not line up with the subjects own brain.mgz or orig.mgz. I have had a similar problem with other T1w images that I've used. Any ideas why this might be

[Freesurfer] Description of frontal labels Destrieux 2009

Dear Christophe and team I am writing up something on frontal measures derived from 2009 Destrieux atlas ­ I need to know the anatomical boundaries for frontomarginal, orbital H shaped sulcus, and the three inferior, middle and superior gyrus and sulcus: is there a place where I can find these des

Re: [Freesurfer] segmentation output not in alignment

really? No, we've never seen anything like that. Can you send us a snapshot? What version are you using? On Fri, 23 Jul 2010, Rumana Chowdhury wrote: > Dear all > > I put a T1w image through the recon-all process and it completed without > errors, but the segmentation output (aparc.a2009s+aseg)

Re: [Freesurfer] Description of frontal labels Destrieux 2009

It is my understanding that these are defined based on the Duvernoy atlas. If this is not the case, please let me know. Lena Palaniyappan wrote: > Dear Christophe and team > > I am writing up something on frontal measures derived from 2009 > Destrieux atlas – I need to know the anatomical bounda

Re: [Freesurfer] recon-all image output

Hi Michele, have you gone through trouble shooting steps described on our wiki yet? doug Michele Placci wrote: > > > 2010/7/23 Michele Placci > > > Dear experts, we run this command in a file of MRI 3D .nii : > > recon-all -force -all -notal-check -i

Re: [Freesurfer] recon-all image output

hmm, not sure how you mae this image, but it looks *veyr* noisy. You'll need to try fixing the watershed skull stripping, but the ventricles may be too big in any case. cheers bruce On Fri, 23 Jul 2010, Michele Placci wrote: > 2010/7/23 Michele Placci > >> Dear experts, we run this command

Re: [Freesurfer] segmentation output not in alignment

Hi Rumana, have you gone through the troubleshooting steps that we describe on our wiki? doug Rumana Chowdhury wrote: > Dear all > > I put a T1w image through the recon-all process and it completed without > errors, but the segmentation output (aparc.a2009s+aseg) does not line up > with the su

[Freesurfer] functional ROI analysis for DLPFC

Hi all, I am trying to use func2roi-sess to analyze functional ROI data for the left and right DLPFC, but these are not listed as labels on the FreeSurferColorLUT on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT. Do I need to create my own ROI labels for thes

Re: [Freesurfer] Freesurfer failure with diseased brains

one failed the talairach error detection - did you check it? The other might be a problem Martin fixed. Martin: can you take a look? cheers Bruce On Fri, 23 Jul 2010, H. Reynolds wrote: > Hi Bruce, > > I am using the current stable version of Freesurfer (v4.5.0) and I have > attached two set

Re: [Freesurfer] functional ROI analysis for DLPFC

You have to specify an anatomical constraint that defines DLPFC. What you have done will not have anything to do with the DLPFC, it will average over all voxels with sig > 1.3 regardless of spatial location. The easiest thing to do is to draw a DLPFC label on fsaverage, then map it to each subj

Re: [Freesurfer] Fwd: Plotting functional data on surface

Hi Freesurfers, Thanks for all of the help so far. I just have one more quick follow-up question. Just to remind you I was attempting to plot a functional map on a pial surface in matlab. The solution was to index the functional map so that I just color-coat the pial surface accordingly instead of

Re: [Freesurfer] Fwd: Plotting functional data on surface

use mri_surf2surf to transform it to fsaverage, then go from there. cheers Bruce On Fri, 23 Jul 2010, Corey Keller wrote: > Hi Freesurfers, > > Thanks for all of the help so far. I just have one more quick > follow-up question. Just to remind you I was attempting to plot a > functional map on a

Re: [Freesurfer] Description of frontal labels Destrieux 2009

Hi Antony and Lena they are mainly based on Duvernoy. We just published a paper describing the borders of each parcellation : Neuroimage. 2010 Jun 12. [Epub ahead of print] Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Destrieux C

[Freesurfer] 30 gigabyte recon-all.log file after protocol error

Dear FreeSurfers, I am new to FreeSurfer and just trying to run some simple volumetric analysis and I get a "Protocol error". I went to look at the log file and it is 30 gigabytes in size so something is going awry here... Is there a way to break this error down further to understand what may be

[Freesurfer] error in mri_label2vol

Hi freesurfer programmers, I have a specific question reagrding the output of mri_label2vol. The image is correctly converted, however the analyze header file has an orientation value set to -1. This is invalid as analyze orient fields can only be 0-5, and my next scripts rely on the orient strin

Re: [Freesurfer] error in mri_label2vol

You should stop using analyze and start using nifti! ... it looks like our code always sets the hdr.orient to -1. I don't know why it does this. In general, we mostly expect that if people care about the actual orientation, then they will use the .mat file that we produce with it. So, I guess j