Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

(no subject)
by James Olkin 25 Feb '08

25 Feb '08

Hello, I'm wondering if surfaces need to be smoothed (and if running "recon-all -s SUBJECT -qcache" performs the smoothing) when analyzing data. Thank you. -Ryan McGarry

3 2

qcache flag on recon-all
by Gonzalo Sanchez Benavides 25 Feb '08

25 Feb '08

Dear FS experts, I have a beginner question so sorry if it is obvious for you... Is possible (and a good idea) to include the -qcache flag at the end in the recon-all -s /../ command? or I have to wait until recon-all had finished to run qcache? Many thanks -- Gonzalo Sánchez Benavides

2 1

Vertex-wise thickness correlations
by Juergen Haenggi 22 Feb '08

22 Feb '08

Dear FS experts We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickness of all other vertices in one hemisphere. Therefore my question: Is there any tool in FS yet that is able to do that? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

5 5

talairach striped
by Hoppmann, Fee 22 Feb '08

22 Feb '08

Dear all, I performed reconall -autorecon1 on a set of images derived from to anatomical scans. While checking the talairach transform, I noticed that in many cases, the talairach seemed to have stripes. This usually appears mostly in the sagittal view during the transition from one hemisphere to the other. You don't see this in the volumes, though. Our idea was that this happend due to the fact that the scans are transformed together and not really averaged for the talairach? I assume that this is not a problem for further processing?! I'll send you a screenshot attached. Thanks for any help!

2 1

QDEC
by Juergen Haenggi 22 Feb '08

22 Feb '08

Dear FS experts I tried to open QDEC but the following error occurred: dyld: Library not loaded: /usr/X11R6/lib/libexpat.0.dylib Referenced from: /Applications/freesurfer/lib/KWWidgets/lib/KWWidgets/libKWWidgets.dylib Reason: image not found Trace/BPT trap [Macintosh-3:/usr/X11R6/lib] juergenhaenggi% This library is not there. Where can I find this library? Thanks Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

nu_correct error
by oxro03＠yahoo.com 22 Feb '08

22 Feb '08

Hi, I am trying to run an MPRRAGE scan through the first step of autorecon-all, but get the following error message: Iteration 1 Thu Feb 21 14:57:06 PST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.28541/nu0.mnc ./tmp.mri_nu_correct.mni.28541/nu1.mnc spawn: exec of nu_estimate_np_and_em failed: No such file or directory nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct I have attached the recon-all log file. Does anyone have an idea why this happens? I get the same error from other scans from the same source. Thanks a lot, Thomas --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

2 1

WM mask
by Gallo, Antonio (NIH/NINDS) [F] 21 Feb '08

21 Feb '08

Dear all, We are trying to extract a cerebral white matter mask from the Freesurfer output. We are currently using the aparc+aseg file in order to do this, however we realized that the white matter mask (taken by choosing the voxels with values equal to 2 and 41) doesn't correspond exactly to the white matter we would like to have, which rather would follow the WM boundary obtained with the surface processing. Is there a way to get a more accurate mask that corresponds to these boundaries? Also, is there a description of the file format that the surface files are written in? Thank you, Antonio

3 2

Mac Pro Benchmark
by Dabbs (Kevin) 21 Feb '08

21 Feb '08

Been running Freesurfer on Linux 2.0 GHz machines. I like the results but need to increase through-put for a 500 subject run. Got the money for a Mac Pro with 8 cores and 16 GB ram. Is it likely that I will get an eight times gain in through-put? Just need some kind of benchmark to determine a reasonable schedule for this job. Thanks for any comments; Kevin Dabbs Dept. Neurology Univ. Wisconsin-Madison

2 1

qdec.table.dat & sample.levels for the tutorial data set
by Gallo, Antonio (NIH/NINDS) [F] 20 Feb '08

20 Feb '08

Hi All, I'm trying to follow the FS Tutorial for Qdec/Group Analysis, but I was not able to find the qdec.table.dat and sample.levels for the tutorial data set. Could you please help me with this? Thanks a lot, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5C203B Bethesda, MD, 20892 - USA ph #: 001-301-496.7368 fax #: 001-301-402.0373 ***********************

2 1

Obtaining cortical parcellations
by Dan Dillon 20 Feb '08

20 Feb '08

Dear FreeSurfers, I have several subjects who have fine inflated, white, and pial surfaces, as well as fine curvatures, but no cortical parcellations. Is there a directive I can pass to recon-all to generate the parcellation without having to run autorecon3 all over again? Something like "-autorecon3-parcellation"? I am running version 4.0.1. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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