Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

passing a WM lesion mask to recon-all
by Mehul Sampat 04 May '10

04 May '10

Hi Folks, We have some subjects with very large white matter (WM) lesion loads. We noticed that the pial and main are pial surfaces are not affected by WM lesions. However, they seem to be affection by the juxta-cortical WM lesions (which have dark intensity) In the past, my colleagues have manually outlined the lesions and created a binary lesion masks. I was wondering if : 1. I can pass this white matter lesion mask as input to recon-all as an input variable ? essentially the idea is to find a way to make recon-all to consider these as white matter (i am only interested in the cortical thickness measurements and not the WM volume so i think it is okay to do so ) 2. if this is not possible, can i use this white matter lesion mask to edit wm.mgz ? in this option, i could find the locations of the non-zero pixels of the lesion mask and then set the corresponding locations in wm.mgz to 110. Does this sound like a bad idea ? or would you suggest a different way to do this ? thanks Mehul

2 1

contrast correction
by Ilana Hairston 04 May '10

04 May '10

Hi there, We have been doing contrast correction using mri_nu_correct.mni (e.g., mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o FS090620ll/mri/orig/nu2.mgz --n 2). My question is, after subsequent corrections (control points, white matter) do we need to specify nu2.mgz as the target file for secondary recon steps in the command line (e.g., recon-all -autorecon2-cp -autorecon3 -s FS090620ll -i FS090620ll/mri/orig/nu2.mgz -force) thanks ilana

2 4

Combined stats from labels?
by Dankner, Nathan (NIH/NIMH) [F] 04 May '10

04 May '10

Hi all, I have a set of 32 labels that I am attempting to pull average thickness from. I would prefer not to run 32 different asegstats2table commands, so I was wondering if there was any way to consolidate the thickness stats from these labels into one file so I can pull them all out simultaneously. Thanks for your help! Nathan

1 0

missing stats files -posting again
by Rajagopalan, Venkateswaran 04 May '10

04 May '10

Dear All, I am new to freesurfer, in some of our patients stats files lh and rh.curv.stats are missing at the end of recon-all -all. recon-all finished without error in these patients so i am wondering what is the mistake i am doing and where will need these lh and rh.curv stats files. Thanks in advance venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

Thickness values for every voxel
by Ana Catarino 04 May '10

04 May '10

Hello, Does anyone know if there is a way of getting access to the values of thickness for each voxel / point in the mesh? Thank you, Ana Catarino

3 2

"--sfmt curv" flag
by Ritobrato Datta 04 May '10

04 May '10

Hello All, I posted this question yesterday. It probably got lost. So I am posting again. For functional data to be resampled to fsaverage using mri_surf2surf what should be used with " --sfmt " flag ? For the thickness the --sfmt curv is used when running qcache. Thanks Ri

3 2

Talairach failure
by Antoine Leflon 04 May '10

04 May '10

Hi all , I've used data from another Doctor , freesurfer told me the FOV was 330 so I put the flag -cw256 in the command recon-all but the Talairach just failed ... I got this error message . Can someone explain please ? ________________________________________________________________________________ #@# Talairach Failure Detection Tue May 4 12:31:55 IST 2010 /home/cami/freesurfer/subjects/a1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Tue May 4 12:31:55 IST 2010 ________________________________________________________________________________ thanks , Antoine

2 3

Thickness values for every vertex
by Ana Catarino 04 May '10

04 May '10

Hello, Does anyone know if there is a way of getting access to the values of thickness for each vertex in the mesh? Thank you, Ana Catarino

2 1

results
by Antoine Leflon 04 May '10

04 May '10

hello all , I managed to run recon-all fully and I got a table with the following colums : number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index "" structure name the 9th column has no name (the one I've called "") Can Somebody explain or tell me what does this column refers to ? thanks , Antoine

1 0

Submitting Files for Review
by Stefan Du Plessis 04 May '10

04 May '10

Dear All I want to send a file will an example of the segmentation of the Pallidum, as discussed previously, which I want refined in general for my OCD project. Do you generally want only the subject file folder with contents, or the mgz file only? Also when uploading from South Africa, what is the best place for me to upload and how? Also, how do I provide the details again for what I want refined? regards Stefan du Plessis CUBIC South Africa

1 0

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Freesurfer May 2010