Freesurfer

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30132 discussions

recon-all on version 4.5
by Saad Ramadan 07 Apr '11

07 Apr '11

Dear all, I ran (on an isotropic MPRAGE ): recon-all -subject mysubject -i ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all which ran for few hours and then exited without a successful end as can be seen on log file below. Contents of *recon-all-status.log* are: Wed Apr 6 12:31:55 EDT 2011 #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 #@# Talairach Wed Apr 6 12:35:22 EDT 2011 *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 *#@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 #@# CA Reg Wed Apr 6 15:22:59 EDT 2011 The last few lines of *recon-all.log* produces: 0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=766 Do you have any idea what is going wrong here? Thanks

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LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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the threshold value in qdec window
by 汪贵宏 07 Apr '11

07 Apr '11

Hi all, I used the freesurfer 5.0,there is a question in my reseach,may be not a question! When i view the results of analysis in the qdec window,why did i cannot change the value of the Threshold,such as min(which had been seted with the value of 2) ,in the same way,the max is 5?If i want to change the value of them,how can i do it? thanks a lot wang

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wmparc
by Jose Soares 06 Apr '11

06 Apr '11

Hi all, I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in 5.0 there are volumes (segmentations) that do not appear in the wmparc.stats file (and appear in 4.5 version), for instance the subcortical structures, ventricles, cerebellum. In wmparc V 4.5 I have 1189 rows with structures and in v 5.0 I just have 70. Why is this? Thanks for the help, Jose.

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Freesurfer visuliazation
by Ritobrato Datta 06 Apr '11

06 Apr '11

Hello All, I have two questions. 1. Is there a way to save a vtk format WITH greyscale gyri/sulci outlines ? 2. Is there a way to modify the color spectrum with the viewer? I am trying to get a gradient like attached, but am having extreme trouble obtaining it. Thanks Ri

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retinotopy manual?
by Michelle Umali 05 Apr '11

05 Apr '11

Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. Thanks. Michelle

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Re: [Freesurfer] Interpreting results from Qdec
by Nick Schmansky 05 Apr '11

05 Apr '11

Courtney, if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats. (btw, i'm putting this answer on the list, as others may have better ideas.) n. On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote: > Hi Nick > > Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer. > > A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. > Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance? > > Thanks in advance! > Courtney > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Thursday, December 30, 2010 2:44 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Interpreting results from Qdec > > ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a > plot of the data at that surface vertex will appear. the group will be > apparent from that (say, demented group is thinner than non-demented > group). this data is significance data (log p, so '2' is 0.01), so mean > and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data > of all subjects in the analysis, so you could extract mean and stdev > from that. > > ans. 2. - slide the 'annotation' opacity slider to show the annotation > data (cortical parcellation). the ctrl left click will also put the > region info for that vertex on the lower left of the display. > > see also: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis > > n. > > On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] > wrote: > > Hi, > > > > > > > > I’m currently running analyses in Qdec and have identified areas that > > show significant effects in my contrasts. I have two questions related > > to interpreting these results. > > > > > > > > 1. How can you interpret the effect in each “blob?” (i.e., which > > group has a greater cortical surface area, etc.). Right now, all I > > know is that there is an effect in certain areas. Can you export this > > data to get means and standard errors? > > > > 2. Is there a way to localize where these effects are? E.g., a > > tool that tells you this effect is located in __ area of the brain? > > > > > > > > Thanks in advance > > > > Courtney > > > > > > > > Courtney Gallen > > > > Post-baccalaureate IRTA > > > > Neuroimaging Research Branch > > > > National Institute on Drug Abuse (IRP) > > > > 251 Bayview Blvd > > > > Suite 200 > > > > Baltimore, MD 21224 > > > > Tel: (443) 740-2631 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > >

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2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy
by angelika lingnau 05 Apr '11

05 Apr '11

*2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC, http://www.unitn.it/en/cimec<http://www.unitn.it/en/cimec/11702/angelika-lingnau>), University of Trento, there will soon be an opening for a two-year postdoctoral fellowship to work with Dr. Angelika Lingnau. Our group examines the neural systems involved in action execution and observation. Some recent publications as well as further descriptions of our ongoing research projects can be found under the following link: https://sites.google.com/site/angelikalingnau/. The postdoc will be responsible for the design of several fMRI studies, conducting data analysis and leading the write-up of scientific work. The ideal applicant is highly motivated and creative and is capable of working both independently as well as in a young, dynamic group. The applicant furthermore should have experience with functional magnetic resonance imaging and/ or transcranial magnetic stimulation and a solid background in Cognitive Neuroscience. Programming experience with MATLAB or C is very desirable. The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The University of Trento is ranked first among research universities in Italy. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. Informal inquiries should be sent to Angelika Lingnau ( angelika.lingnau(a)gmail.com)

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Mapping segmentations to SPM Functional Space
by Palzes, Vanessa 05 Apr '11

05 Apr '11

I am wondering if there is a similar function as aseg2feat (which maps the automatic segmentations from Freesurfer to FSL FEAT functional space) for the use in SPM functional analysis. This tool poses to be very useful in creating ROI masks, however, we are using SPM for functional analysis rather than FSL FEAT. Thanks, Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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Convert annotations longitudinally
by Andrew Dumas 05 Apr '11

05 Apr '11

Hi FreeSurfer experts, Is there a way to move annotations from the same subject at one timepoint to another? I've tried doing this using a discrete-valued surface and using seg2annot, but, when I convert surfaces there are vertices between regions whose values are averages of bordering vertices. This ruins the continuity of each individual label with little islands of various values. Is there a mri_annot2annot or equivalent? Thanks! Andrew Dumas

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