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by Sally Bernardina Seraphin, PhD 11 Jun '09

11 Jun '09

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[FSL] Social event for Iranian Neuroimagers (fwd)
by Bruce Fischl 11 Jun '09

11 Jun '09

FYI ---------- Forwarded message ---------- Date: Thu, 11 Jun 2009 16:27:15 +0100 From: Mojtaba Zarei <mojtaba(a)FMRIB.OX.AC.UK> Reply-To: FSL - FMRIB's Software Library <FSL(a)JISCMAIL.AC.UK> To: FSL(a)JISCMAIL.AC.UK Subject: [FSL] Social event for Iranian Neuroimagers Dear All, I am trying to arrange a social event for Iranian Neuroimagers during HBM in San Francisco. Could anybody who is interested contact me please (with or without suggestion)? Kind regards, Mojtaba Zarei PS: Apologies for using this email list ...

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exporting surface as an image volume
by Mayuresh Korgaonkar 11 Jun '09

11 Jun '09

Dear Freesurfer users and authors, Is it possible to export a surface (eg. ?h.thickness) to an image volume - something which could be read into SPM? I came across mri_surf2vol function, however I am not to familiar with the usage. I understand that a volume registration file is required, what exactly is this file? If anyone can suggest an example usage of mri_surf2vol that will be very helpful. Thanks in advance, Mayuresh Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

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scuba bus error on MacBook
by akram＠nmr.mgh.harvard.edu 10 Jun '09

10 Jun '09

Hello, I remember I had this same issue last summer, and I can't find a record of the solution. I installed freesurfer-Darwin-leopard-i686-stable-pub-v4.3.1 on a MacBook running Mac OS X 10.5.7 with specs: 2.4 GHz Intel Core 2 Duo, 2 GB 667 MHz DDR2 SDRAM. I set my FREESURFER_HOME to /Applications/freesurfer and sourced my SetUpFreeSurfer.csh I type scuba to bring up the scuba gui, but it returns "Bus error" tkmedit/tksurfer/qdec work fine. Is this due to a 32 vs 64 bit issue and is there an easy fix? I suppose we can always VNC in, but I was hoping we could do some work offline. Thanks for the help! Akram

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Re: [Freesurfer] scuba bus error on MacBook
by Nick Schmansky 10 Jun '09

10 Jun '09

its included in the distribution. On Wed, 2009-06-10 at 15:48 -0400, Satrajit Ghosh wrote: > Hi Nick, > > I hadn't heard of freeview. Is there a place we can download it? > > Cheers, > > Satra > > On Wed, Jun 10, 2009 at 3:34 PM, Nick Schmansky > <nicks(a)nmr.mgh.harvard.edu> wrote: > Will Freeview work for you? Support for scuba has ended > because work on > Freeview to replace has been ongoing. > > Nick > > > On Wed, 2009-06-10 at 15:24 -0400, akram(a)nmr.mgh.harvard.edu > wrote: > > Hello, > > I remember I had this same issue last summer, and I can't > find a record of > > the solution. > > I installed freesurfer-Darwin-leopard-i686-stable-pub-v4.3.1 > on a MacBook > > running Mac OS X 10.5.7 with specs: 2.4 GHz Intel Core 2 > Duo, 2 GB 667 MHz > > DDR2 SDRAM. > > > > I set my FREESURFER_HOME to /Applications/freesurfer and > sourced my > > SetUpFreeSurfer.csh > > I type scuba to bring up the scuba gui, but it returns "Bus > error" > > tkmedit/tksurfer/qdec work fine. > > Is this due to a 32 vs 64 bit issue and is there an easy > fix? > > I suppose we can always VNC in, but I was hoping we could do > some work > > offline. > > Thanks for the help! > > Akram > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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rebuild_gca_atlas/mri_ca_train error
by Kevin Scheibel 10 Jun '09

10 Jun '09

I am trying to run rebuild_gca_atlas to create an atlas from my segmented vervet sample. I'm pretty sure I've got everything set up correctly, but am getting an error: ERROR: mri_ca_train: talairach.xfm not found in seg_edited.mgz I'm using vervet (primte) MRIs, so I didn't think a talairach transform for my subjects would be useful. Also, it seems that this script points at seg_edited.mgz as a directory, even though I have it set up in my directory as a file. Kevin Scheibel k.scheibel(a)ucla.edu

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how to to redo the analysis after recon-all
by karlkarl 10 Jun '09

10 Jun '09

Hello, experts: I have finished autorecon1-3 on the data. But now when I am examining the data, some images need skull stripping and white matter editing. So I need to rerun the steps. If I strip the skull after autoreon1 and want to put it to autorecon2, This should be: recon-all �Cs <participants> -autorecon2 And after fixing white matter problem from autorecon2 This should be: recon-all �Cs <participants> -autorecon3 All the old files will be automatically overwritten? What is the most efficient way to redo the analysis after recon-all? Thanks a lot! Karl _________________________________________________________________ Լ��˵��ط��΢��ͼ��msn��ܣ� http://ditu.live.com/?form=TL&swm=1

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Re: Error in Analyze
by Toh Hock Wong 10 Jun '09

10 Jun '09

On 10/06/2009, at 9:51 PM, Toh Hock Wong wrote: > Hi all, > I have reconstructed 12 paediatric subjects aged 4-13 and managed > to load qdec as well as generating stats. The factors are age, > diagnosis, gender and a continuos factor such as lh temporalpole > thickness. When i click analyze, the return is a list of errors as > follow. > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/qdec.fsgd > > labelmask /Applications/freesurfer/subjects/fsaverage/label/ > lh.cortex.label > > maskinv 0 > > glmdir /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness > > DoFFx 0 > > Creating output directory /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness > > Loading y from /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/y.mgh > > Matrix condition is 1e+08 > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > 1.000 0.000 0.000 0.000 3.701 0.000 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 4.554 0.000; > > 1.000 0.000 0.000 0.000 4.044 0.000 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 4.459 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.857 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.537 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.652 0.000; > > 1.000 0.000 0.000 0.000 2.870 0.000 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.736 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.636 0.000; > > 1.000 0.000 0.000 0.000 4.102 0.000 0.000 0.000; > > 1.000 0.000 0.000 0.000 3.755 0.000 0.000 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.816; > > > > > > Error in Analyze: command failed: mri_glmfit --y /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/y.mgh --fsgd / > Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness --surf fsaverage lh --label /Applications/ > freesurfer/subjects/fsaverage/label/lh.cortex.label --C / > Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Avg- > thickness-lh_temporalpole_thickness-Cor.mat --C /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Diff- > nonepileptic-epilepsy-Intercept-thickness.mat --C /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Diff- > nonepileptic-epilepsy-Cor-thickness-lh_temporalpole_thickness.mat -- > C /Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C / > Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > contrasts/lh-Diff-Male-Female-Cor-thickness- > lh_temporalpole_thickness.mat --C /Applications/freesurfer/subjects/ > qdec/lh_temporalpole_thickness/contrasts/lh-X-diagnosis-gender- > Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/contrasts/lh-X-diagnosis-gender-Cor- > thickness-lh_temporalpole_thickness.mat > > What do i need to do from here? > > Do i have to write a fsgd file/contrast etc? Any suggestions will be > most appreciated! > > If i wish to use freesurfer for a paediatric group less than 10 > years old, what errors or difficulties should i be anticipating? > > Thanks! Toh Wong > > > > > >

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using cortical thickness values
by Kai Lutz 09 Jun '09

09 Jun '09

Dear List, in an attempt to divide grey matter segments into an outer and inner layer, I am currently using the vertex coordinates for pial surface (in Matlab>> read_surf('lh.pial') ) and vertex coordinates for white matter surface (MATLAB>>read_surf('lh.white') ). Perhaps naively, I assume, that the order of the two coordinate matrices is identical and calculate the wanted coordinates of a point on a line (say half way) in between the corresponding pial and white matter vertices. What puzzles me is that the distances between corresponding (?) white matter and pial surface vertices are not equal to the cortical thickness values given by >>read_curv('lh.thickness') (GM-WM distances up to 9.3 mm are found, whereas cortical thickness values vary between -0.24 and 5 mm in the data set I am working on) --> To determine a layer, separating outer from inner half of the cortex, would it be a more valid to A: determine vertex normals of pial surface and travel along them by a distance 1/2 the cortical thickness? (Q: which thickness value belongs to which vertex? where do the negative thickness values come from?) or B: determine points half way in between vertex coordinates of corresponding pial and WM vertices? (Q: how can I assure their correspondence?) Is anyone working on / has solved a related problem? Any hint would be greatly appreciated! Cheers, Kai -- Dr. Kai Lutz Neuropsychology Institute for Psychology University of Zurich Binzmühlestrasse 14 /Box 25 CH-8050 Zürich Switzerland _________________________ Diese E-Mail (ggf. nebst Anhang) enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind, oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet. This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. _________________________

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error estimates
by Dana W. Moore 09 Jun '09

09 Jun '09

I was wondering if there is any output in stats that generates an error estimate for the calculated stats for an individual subject? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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