Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

comparison between three MRI exams of same patient...
by Gonzalo Rojas 12 Feb '10

12 Feb '10

Hi: I have three MRIs of the same patient taken at different dates/years... I need to compare the hippocampus volume (for example) between the three MRI... I want to compare also the cortical thickness between the three MRI... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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execute a freesurfer command at a specificed time/day...
by Gonzalo Rojas 12 Feb '10

12 Feb '10

Hi: How can I execute a freesurfer command at a specificed time/day ?... Any Ubuntu trick ?... Sincerely, -- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Cortical thickness in controls
by Rajagopalan, Venkateswaran 12 Feb '10

12 Feb '10

Hello All, I would like to clarify the following.I couldn't find the answers i was looking for in the archives so here are my questions; 1) In some of our subjects the WM/GM interface is identified correctly but the pial surface falls short of some voxels which i want to manually edit them inorder to include them. Is there a way to only edit the pial surface if so kindly give directions or direct me the documentation page. 2) I would like to check the cortical thickness values measured in our control subjects with any already published or documented control values inorder to make sure that i am doing right. 3) In some our of subjects WM is not filled completely i.e. in filled.mgz volume there are still some ventricle regions that need to be manually filled, i have done the manual editing it there a way to run rest of the steps from this step i.e inflation smoothing etc. Now i am doing them one by one which is time consuming. Thanks in advance. Regards venkateswaran =================================== 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.

2 1

comparison of values of three MRI exams of same patient...
by Gonzalo Rojas Costa 12 Feb '10

12 Feb '10

Hi: I have three MRIs of the same patient took during different months... I need to compare the hippocampus volume fof the three exams (for example), the cortical thickness, etc... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

1 0

Problems with tksurfer display on laptop
by jentis＠nmr.mgh.harvard.edu 12 Feb '10

12 Feb '10

Hi, I have a laptop equipped with Centos and Freesurfer but I can't get tksurfer to properly display the surface files of either the fsaverage brain or individual subjects. The surfaces are either small portions of cortex or an assemblage of lines/dots. I have attached a few tiff files as examples. Is there something I can do to fix this? I have tried using freeview instead, and the surfaces do display properly, but the program does not seem to allow me to trace label files. Is there another way around this? Does a newer version of freeview include tracing ability? Thanks, Jon

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tksurfer problem and solution
by David Mischel 11 Feb '10

11 Feb '10

We have had similar problems with displays of tksurfer described in http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems. I would like to try freeview, the new solution for display. I don't know anything about freeview and no one here has ever used it. To run tksurfer I set the SUBJECTS_DIR and then use the command tksurfer <subjectCode> lh pial where subjectCode is a directory in the SUBJECTS_DIR. Could someone give me the corresponding command to use with freeview? I appreciate the help. < david David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864

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tksurfer fill holes
by Guang Zeng 11 Feb '10

11 Feb '10

Hi, there, Is there are a command-line version of that 'Fill holes", "Dilate" and "Erode" options in tksurfer. Could I select the size of the kernel for dilation and erosion? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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subject to fsaverage
by Mishkin Derakhshan 11 Feb '10

11 Feb '10

Hi, I am looking for the transformation matrix that takes my input volume (orig.mgh) and maps it into the same space as fsaverage (or the inverse of this transformation if it already exists). I've already run recon-all -all, and -qcache, so I'm pretty sure this information exists somewhere, but after searching through the data, the wiki and the mailing list, I'm embarrassed to say that I still can't find it. If this information hasn't been stored, I imagine mri_surf2surf can calculate it for me. Would this be the best way? thanks, mishkin

3 2

GM exclusion
by johanna feiler 11 Feb '10

11 Feb '10

Dear freesurfer experts, After running the autorecon2 process the pial surface fails to catch up pieces of gm in the medial region. I gained no improvement with setting control points. The problem lasts about twelve slices. As an illustration, I attached a screenshot with three of the problematic slices. How can I solve this problem? Any help would be appreciated! Johanna Feiler ______________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

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question about effect of juxta-cortical lesion
by Mehul Sampat 11 Feb '10

11 Feb '10

Hi Folks, We have a patient with a large juxta-cortical lesion (top right hand side in figure 1) Overall Freesurfer does a great job in defining the white and pial surfaces (figure 2 and 3) (It is actually amazing how well it does in this difficult case.) However, I think that due to the lesion some of the cortical gray matter is not included. Could someone advice what is the recommended procedure in such cases. Should I add control points to correct for this issue ? Also we have 3 MRI exams for this subject (each a year apart) and the lesion is present on every scan and I have the same issue on the other time-points. Thanks Mehul

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