Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

label transformation to MNI space
by Linda Douw 05 Jul '12

05 Jul '12

Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD.

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Re: [Freesurfer] Hippocampal segmentation doubts
by Gabriel Gonzalez Escamilla 05 Jul '12

05 Jul '12

1 0

qdec covariate interact with a factor
by Emilia Lentini 04 Jul '12

04 Jul '12

Hi. I would like to test the effect of a covariate that interact with a factor. Eg. I have group (XX and XY) as fixed factors, and a ROI thickness (L Fusiform) as covariate. Now I would like to calculate the "correlation LFusiform for XX - correlation LFusiform for XY". Is this possible by using qdec? If so, how should I proceed? Best regards, Emilia

2 1

Hippocampal segmentation: version needed
by lorenzo pasquini 04 Jul '12

04 Jul '12

Dear Freesurfer experts, I used freesurfer v4.3.0 on anatomical data (T1). I am trying to segment hippocampal subfields with the following command: recon-all -s subjname -hippo-subfields unfortunately I get the following error: ERROR: Flag -hippo-subfields unrecognized I have already the files aseg.mgz, nu.mgz, talairach.xfm Does this error occur because I am using an old Freesurfer version? If this is the case which is the optimal version to run hippocampal segmentation? Should I process my whole data again with the newest version? Unfortunately I did not find any convincing answer from the posting list where I had the impression that version 5.1 is facing some problems regarding hippocampal segmentation. Thank you very much and kind regards, Lorenzo Pasquini

2 1

Extraction Longitudinal Stats
by Dídac Vidal 04 Jul '12

04 Jul '12

Hi everybody, I have a question about FS longitudinal post-processing. Currently I obtained some corrected results comparing a Control vs. an Experimental group (pre-post). What i would like to know is if there's a thinning in the control group or a increase in the thickness of the experimental group. I tought in create a label and extract the individual values of both timepoints and then do a t test in order to see if the mean differs to 0. How I can do that?; There is an easier way to do it? Thanks in advance -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

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Post-Doctoral position in Computational Morphometry – University of Geneva
by Narly GOLESTANI 04 Jul '12

04 Jul '12

Post-Doctoral applications are invited at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a starting salary of 68, 964 CHF/year. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch.

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Hippocampal segmentation doubts
by Gabriel Gonzalez Escamilla 04 Jul '12

04 Jul '12

2 1

Re: [Freesurfer] different fs versions
by Ed Gronenschild 04 Jul '12

04 Jul '12

Dear Marise and Laura, As Bruce et al frequently warned users about, you should never mix different versions. The effects have been quantified recently by our group, see http://dx.plos.org/10.1371/journal.pone.0038234 I can add to this that the differences between v5.1.0 and v5.0.0 are somewhat smaller than between v5.0.0 and v4.3.1/v4.5.0. Cheers, Ed On 3 Jul 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 10 > Date: Tue, 3 Jul 2012 14:32:10 +0000 > From: "L. Koenders" <l.koenders(a)amc.uva.nl> > Subject: [Freesurfer] different fs versions > To: "'freesurfer(a)nmr.mgh.harvard.edu'" > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <D03CA44173AD494B8309658B6E1DEFFFEA8609(a)MS-APP-804D.amc.intra> > Content-Type: text/plain; charset="us-ascii" > > Dear Freesurfer people, > > We attended the Freesurfer course in Amsterdam last week, thank you > so much for the information! During the course it was mentioned > that it is a very bad idea to mix Freesurfer versions during the > analysis. However, we did all the preprocessing on an external > server, using version 5.0.0 ('freesurfer-Linux-centos4_x86_64- > stable-pub-v5.0.0') and we are currently doing all of our group- > analysis on a different server, which has version 5.1.0 on it (' > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0'). > > Because both servers are used by a lot of people, it will become > difficult to do an update on either one of these versions. Will > this become a problem, or is there a way to avoid problems while > still using these different versions? > > Thanks in advance for your help! > > Kind regards, > > Marise Machielsen, MD. > Laura Koenders, MSc. > > Laura Koenders > PhD-student > AMC, Academic Psychiatric Centre > Department Early Psychosis > Room: PA3-138 > Meibergdreef 5 > 1105 AZ Amsterdam > +31 (0) 20 8913 609 > +31 (0) 614 285 301 > www.group-project.nl > www.amcpsychiatrie-psychose.nl > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en > de afzender direct te informeren door het bericht te retourneren. > Het Academisch Medisch Centrum is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Amsterdam onder nr. 34362777. De Algemene Inkoop > Voorwaarden van het AMC zijn van toepassing op en maken integraal > onderdeel uit van alle rechtsbetrekkingen, daaronder mede verstaan > alle inkoop opdrachten en overeenkomsten, tussen AMC en derden. > Deze voorwaarden zijn te raadplegen op www.amc.nl en worden op > verzoek toegezonden. > > ________________________________ > > This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the > sender immediately by return e-mail. Academic Medical Center is a > legal person by public law and is registered at the Chamber of > Commerce for Amsterdam under no. 34362777. The AMC General Purchase > Terms constitute an integral part of all legal relations, including > but not limited to all purchase orders and contracts, between the > AMC and third parties. These terms can be downloaded at the website > www.amc.nl and will be sent to you at your request.

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FA (DTI) statistical analysis: 3 covariates
by Jay Morozov 03 Jul '12

03 Jul '12

Dear Freesurfer experts, We are trying to run a statistical analysis for FA in 5 ROIs. We have one group of subjects and our goal is to run regression analysis to find a relation between one behavioral test (episodic memory test) and FA. We are planning to set - the accuracy on episodic memory test as the dependent variable. - age, sex and MMSE (range 21-30) as covariates - FA in each ROI is the predictor We couldn't find an example of 3 covariates on the tutorial website, could you kindly let us know how to run glm analysis for 3 covariates? Thank you Jay Morozov

3 2

axial sheer
by Borzello, Mia 03 Jul '12

03 Jul '12

Hi freesurfers, Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot. Thanks for the help, Mia B.

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Freesurfer July 2012