Re: [Freesurfer] different fs versions

2012-07-04 Thread Ed Gronenschild
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 som

Re: [Freesurfer] Extraction Longitudinal Stats

2012-07-04 Thread Yolanda Vives
Hi Martin, Thank you for your answer. I am also interested in testing your new scripts, if it is possible. Regards, Yolanda 2012/7/3 Martin Reuter > Hi Yolanda, > > take a look at the longitudinal tutorial: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial > > There is

Re: [Freesurfer] label transformation to MNI space

2012-07-04 Thread Anders Hougaard
Dear Doug, I have problem similar to this: I am trying to convert V1 labels from the Hinds method to volumes and transform them to MNI152 space for use in FSL. I tried using this command: mri_label2vol --label rh.v1.prob.label --reg $FREESURFER_HOME/average/mni152.register.dat --temp MNI152_T1_2m

Re: [Freesurfer] Hippocampal segmentation doubts

2012-07-04 Thread Koen Van Leemput
Hi Gabriel, 1. Using pre-processed data obtained with an older version of FreeSurfer should be OK, as long as you remember that the obtained results might/will be different from the ones you'd get if you had run the whole analysis from scratch. 2. The generic label "hippocampus" is used to denote

[Freesurfer] Hc segmentation: crosssectional stream with v4.5, longitudinal with v5.1

2012-07-04 Thread Wenger, Elisabeth
Dear FreeSurfer experts, we have processed a dataset crossectionally within version 4.5, and then ran the longitudinal stream with v5.1. we are interested in the hippocampus segmentations and now i'm wondering whether i should go back and run the whole analysis from scratch with the newest vers

[Freesurfer] Post-Doctoral position in Computational Morphometry – University of Geneva

2012-07-04 Thread Narly GOLESTANI
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

Re: [Freesurfer] Extraction Longitudinal Stats

2012-07-04 Thread Yolanda Vives
Hi Martin, When I convert my long qdec table to a cross sectional table to analyze for exemple percent change maps, I have some difficulties to identify my independent factor in this case, because I don't have two groups like in the longitudinal study (On-Off). Could you please help me to build th

[Freesurfer] qdec covariate interact with a factor

2012-07-04 Thread Emilia Lentini
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 us

[Freesurfer] Hippocampal segmentation: version needed

2012-07-04 Thread lorenzo pasquini
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 a

Re: [Freesurfer] Extraction Longitudinal Stats

2012-07-04 Thread Martin Reuter
Hi Yolanda, the new files contain some minor bug fixes and mainly some extensions, e.g. additional parameters to compute percent changes with respect to the first time point as estimated from the linear fit. Although I think the old version will work fine, it may be easier to use the newer vers

Re: [Freesurfer] Extraction Longitudinal Stats

2012-07-04 Thread Martin Reuter
Hi Yolanda, you computed the percent change, now I think you want to see if it is different from zero. You don't need groups. qdec should be able to test difference from zero. If you use mri_glmfit there is a flag -osgm (one sample group mean). Cheers, Martin - Original Message -

Re: [Freesurfer] Hippocampal segmentation: version needed

2012-07-04 Thread Koen Van Leemput
Hi Lorenzo, The hippocampal subfield segmentation routines are only available from FreeSurfer 5.1, so you'll need that version to run the code. If all your data is already pre-processed with an older version of FreeSurfer, you might be able to simply run the hippocampal subfield segmentation rout

Re: [Freesurfer] qdec covariate interact with a factor

2012-07-04 Thread Douglas Greve
Yes, you just need to set up qdec with your two groups and one covariate. After you run the analysis, one of the statements should be something like "Does the slope differ between groups XX and XY" . doug On 7/4/12 10:24 AM, Emilia Lentini wrote: Hi. I would like to test the effect of a covar

Re: [Freesurfer] label transformation to MNI space

2012-07-04 Thread Douglas Greve
Where did rh.v1.probl.label come from? The way you call mri_label2vol, it should be in fsaverage space. If it is in an individual space, then the registration is wrong. Try running mni152reg to create a registration from the individual to mni152, then use that reg instead. doug On 7/4/12 5:32