Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

surface co-ordinates
by Mishkin Derakhshan 25 Feb '08

25 Feb '08

Hi, 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume? 2. I am making the assumption that the lh.white and the lh.pial will always have the same number of indices and polygons. Can I also make the assumption that the order in which they are printed using mris_convert will be the same. ie. Will the vertex on line 54 of lh.white.ascii correspond to the same vertex on line 54 of lh.pial.ascii? thanks, mishkin

2 3

changing tissue priors
by David Kahn 25 Feb '08

25 Feb '08

Hello, I'm a beginning FS user, and I've been working on segmenting some atypical brains. A colleague has worked out grey/white/csf tissue priors for these subjects and I wanted to insert these into freesurfer before segmentation and parcellation. Does anyone know how freesurfer stores tissue priors and how to change them? Also, I intend upon creating a new cortical parcellation atlas as well (using mris_ca_train and _label). Is swapping out the priors an unnecessary step if I am already prepared to supply the atlas? Thanks for any help, and forgive my relative inexperience with FS. David

2 1

mri_surf2surf
by Daniel Wakeman 25 Feb '08

25 Feb '08

Hi, I have a question (I believe about mri_surf2surf). First, I'll describe my goal: I want to take a surface created with mri_tessellate and modified with mris_smooth and convert it to an isomorphic equally subdivided icosahedron (like mri_watershed creates). e.g. take the lh.smseghead created by mkheadsurf and resample it: mri_surf2surf --srcsubject $SUBJECT --srcsurfval $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --src_type surf --trgsubject ico --trgsurfval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --hemi lh I get the following error: ERROR: could not determine type of /imaging/dw01/simulation/subjects/subject_02/surf/lh.smseghead If this is possible, I want to know how I can correct my command. Cheers, Dan --

2 5

multiple runs and optseq
by Sheeba Arnold 25 Feb '08

25 Feb '08

Hi, We had a question about multiple runs and optseq. If we compute our sequence as one long 12 minute run, then we get a sequence with a VRF around 25. But of course, that's too long and we would want to split it into two. If we calculate a run half as long, then we get a VRF around 10. If we split our long run into two, how would that affect our efficiency? If we calculate the sequence as two short runs, how does the power of the two add up when you analyze them together (after concatenating the two short sessions)? Thanks and Regards, Sheeba

2 1

(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.

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