Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mri_cc and CC thickness option...
by Gonzalo Rojas Costa 16 Dec '11

16 Dec '11

Hi: For example, if I execute the mri_cc command with "-t 2", mri_cc shows me "setting callosum thickness to 5 mm"... Why ?... What exactly specify the -t option ?... Sincerely, Gonzalo Rojas Costa

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run preproc-sess with -nomc
by Thunell Evelina 16 Dec '11

16 Dec '11

Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina

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Estimate Brain Volume Fraction
by Cheryl McCreary 15 Dec '11

15 Dec '11

Hi Freesurfer experts, I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct? I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available. My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well? Thanks for your help. Cheryl -- Cheryl McCreary Seaman Family MR Research Centre Foothills Medical Centre 1403 29th Street NW Calgary, AB T2N 2T9

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ICV and regional brain volumes
by Lugar, Heather 15 Dec '11

15 Dec '11

We are having a difficult time getting the ICV to fit correctly in our sample, but the segmentions and parcellations look accurate. I believe that the ICV is generated from the talairach.xfm early on in the processing stream, but then further processing for segmentations/parcellations is done. So, does the ICV measure affect regional brain volumes in any way, or can we trust the volumetric measures to be accurate even if the ICV is not? Thank you, Heather Lugar

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(no subject)
by Adam Nitenson 15 Dec '11

15 Dec '11

Hi Doug et al, We have been working on a linear regression-type analysis (see attached analysis.info for analysis and slopepar for a sample paradigm file) that involves task-related activation in a working memory test. For each participant, there are four conditions: 1, 3, 5, and 7 items that need to be remembered. The question that we would like to ask is: for each voxel, does the slope of activation (i.e., the slope of the best-fit line as you move from 1 to 3 to 5 to 7 items, as calculated separately for each subject) differ from zero? The second-level analysis would determine if there is a significant difference in activation-related slope between groups. Based on previous discussion, the way we have been doing this is to modify the paradigm file to create the following contrast: Condition 2: activation during working memory, but weighted by condition so the 1 item condition is weighted as 1, the 3 item condition as 3, etc. Condition 0: fixation The contrast is Condition 2 minus Condition 0. However, this method of weighting does not appear to answer the question about slope, but rather focuses on a weighted average. Consider the following scenario, involving 5 subjects (A through E): The SLOPE column is calculated using the slope function of the spreadsheet (i.e., slope of best fit line, using values of 1...3...5...7 for the x-axis, and, say, for subject A, the values of 2...4...6...8 for the y-axis). The WEIGHTED column is calculated in the way that I think FS-FAST is doing it, which is as follows: ((1 * 1 item activ. value) + (3 * 3 item activ. value) + (5 * 5 item activ. value) + (7 * 7 item activ. value))/4 The SLOPE and WEIGHTED values (regardless of their different scale) are not really comparable. For example, for Subject A, the SLOPE value is 1 and the WEIGHTED value is 58, while for Subject E, the SLOPE value is 1.1 and the WEIGHTED value is 28. So when looking at the paradigm file, take the lines 76.57 2 3.4 5 213.42 2 2.29 7 Does this mean that the activation at the first timepoint is accounted for 5-fold and the second timepoint 7-fold? If this is the case then this analysis may not best represent what we are looking for. Is there a way to modify the paradigm file so that the analysis can focus on slope of the best fit line as opposed to the weighted average? Thanks, Josh Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Re: [Freesurfer] Freesurfer Digest, Vol 94, Issue 13
by Maryam Vaziri Pashkam 15 Dec '11

15 Dec '11

Hi, Following up on the preprocessing error: > Can't connect? tcp_connect[connect]: Connection timed out We figured where the problem is. This error came out when freesurfer calls an afni function. Apparently it tries to check which version of afni it is using against the internet to find out the most recent version. Suppressing the afni version check solved the problem. I just added this line to my .bashrc file: export AFNI_VERSION_CHECK=NO Maryam On Mon, Dec 12, 2011 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. preprocessing error (Maryam Vaziri Pashkam) > 2. Re: preprocessing error (Douglas Greve) > 3. convert surface label on to functional image (Zhangyuanchao) > 4. References/materials for interaction analysis in freesurfer > (Bhavani Shankara Bagepally) > 5. Re: dt_recon error (Yuko Yotsumoto) > 6. Re: dt_recon error (Yuko Yotsumoto) > 7. Re: run preproc-sess with -nomc (Thunell Evelina) > 8. Re: mri_ca_register from virtual box (Lorenzo Busti) > 9. Re: mri_ca_register from virtual box (Lorenzo Busti) > 10. Converting thickness maps to vtk (Navid Shiee) > 11. Re: tracula and snow leopard: can't allocate region / memory > error (Anastasia Yendiki) > 12. tracula failed to find header file for -t (Scott Hayes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 11 Dec 2011 14:34:05 -0500 > From: Maryam Vaziri Pashkam <mvaziri.p(a)gmail.com> > Subject: [Freesurfer] preprocessing error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and > matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I > am receiving an error. I connect to the cluster using terminal and SSH > connection in mac. > > the preprocessing is stalled in the middle with this error: > > ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 > Can't connect? tcp_connect[connect]: Connection timed out > ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz > ** Warning: overwriting file 004/fmcpr.mcdat > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > > > It does not stop running and output an error. But rather keeps printing the > last line and does not move forward. Any idea where the problem might be? > > > Thanks, > Maryam >

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nWBV
by Lindsay Ercole 15 Dec '11

15 Dec '11

How might we obtain nWBV from the FS data? What variables could be summed or what variable could be used individually and adjusted to create a nWBV? Does total gray include cerebellar gray, but total white volume does not include cerebellar white? Sincerest thanks! Lindsay

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Extracting area.pial stats
by Robustelli, Briana (NIH/NIMH) [F] 15 Dec '11

15 Dec '11

Dear FreeSurfer team, I have been looking at area.pial differences in two groups using qdec. I would now like to extract stats for each subject at the gyral level (using the Desikan parcellation). I used aparcstats2table with the measure flag set to area. But these numbers seem off. Is this the correct area or am I somehow getting white matter area and it so how do I get the area of the pial surface? Thank you! Briana Robustelli -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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Re: [Freesurfer] multiple overlay - tksurfer
by Douglas N Greve 15 Dec '11

15 Dec '11

Have you tried to change the threshold to see if you see more colors? Don't load it as a segmentation, just look at the overlay. doug vin . wrote: > Thank you so much Doug, > > you are right, it doesn't match exactly, however there is some match. > so, now I am running recon-all T1_1mmMNI.nii, probably it will improve > the registration. > > -extend to previous email - > just to check, I also summed, all binary files. (attached > sum_binarymap.tif : output from tksurfer) > >tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg > register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 > > here sum_binmap : > >mri_binarize --i N.nii --min 0.1 --binval N --o Nb.nii > >fscalc 1b.nii add 2b.nii add 3b.nii ... -o sum_binmap.nii > >mris_seg2annot --seg sum_binmap.nii --hemi lh --s vin --o > lh.seg.annot --ctab vin_colortable.txt > > I just wonder, why I only see one color in sum_binmap overlay. > > > > On Wed, Dec 14, 2011 at 6:01 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > The fsaverage surface does not intersect very well with the MNI > brain (the problem is that the average surface does not have as > deep folds as an individual). You can see what is going on if you > convert your label to fsaverage space with > > tkmedit fsaverage orig.mgz -surfs -fmin 0.5 -overlay 1.nii > -overlay-reg register.dat > > This will show you the surfaces and the label. If the label does > not intersect the surfaces, at all, then there's not much you can > do. If there is some intersection, then you can run mri_vol2surf > with --projfrac-max -.1 1.1 .1 > > doug > > > > On 12/13/11 10:53 PM, vin . wrote: >> #Registration >> >tkregister2 --mov $d/T1.nii.gz --targ >> $d/mri/brain.mgz \ >> --regheader --reg $d/vin_register.dat --noedit >> >> I have cortical-clusters in 1mm MNI space so, I took 1mm MNI >> brain and registered this on the "fsaverage" default subject's >> /mri/brain.mgz" >> >> Find attached register.dat >> >> #checking registration >> > >> tkregister2 --targ $d/mri/brain.mgz \ >> --mov T1.nii.gz --reg vin_register.dat >> >> find attached register.tiff >> >> Regards, >> vin >> >> >> On Wed, Dec 14, 2011 at 4:40 AM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Is your register.dat correct? >> >> >> On 12/13/11 10:33 PM, vin . wrote: >>> Thanx Doug, >>> >>> atleast I see, now something. (see attached "seg.mgh -annot >>> seg.annot.tiff) >>> > tksurfer Sub_ID lh inflated -annot seg.annot -ov >>> lh.seg.mgh -fthresh 0.01 -fmid 0.3 -fslope 1 >>> >>> just to check, I also summed, all binary files. (attached >>> sum_binarymap) >>> >tksurfer Sub_ID lh inflated -ov sum_binmap.nii >>> -overlay-reg register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 >>> >>> also find colortable. >>> >>> Greetings! >>> >>> On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> Try tksurfer Sub_ID lh inflated -annot seg.annot >>> doug >>> >>> >>> On 12/13/11 9:39 PM, vin . wrote: >>>> no, in tksurfer, just inflated lh appears (no >>>> overlay). so, I viewed lh.seg.mgh in freeview and >>>> converted it to .nii and viewed in fslview. >>>> >>>> On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl >>>> <fischl(a)nmr.mgh.harvard.edu >>>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>>> >>>> oh, so you mean you see a line on the surface? >>>> >>>> On Wed, 14 Dec 2011, vin . wrote: >>>> >>>> Thanx Bruce for quick reply. >>>> >>>> you are right, it's surface based file after >>>> mri_vol2surf. yeah, tried with >>>> following command. >>>> >>>> >tksurfer Sub_ID lh inflated -annot >>>> lh.seg.annot -ov lh.seg.mgh -fthresh >>>> 0.01 -fmid 0.3 -fslope 1 >>>> >>>> >>>> On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl >>>> <fischl(a)nmr.mgh.harvard.edu >>>> <mailto:fischl@nmr.mgh.harvard.edu>> >>>> wrote: >>>> Hi Vin >>>> >>>> it looks like your lh.seg.mgh is a >>>> surface-based .mgz not a >>>> volume one. Did you try loading it into >>>> tksurfer? >>>> >>>> cheers >>>> Bruce >>>> >>>> On Wed, 14 Dec 2011, vin . wrote: >>>> >>>> Thank you Doug, >>>> >>>> >tkregister2 --mov $d/T1.nii.gz --targ >>>> $d/mri/brain.mgz \ >>>> --regheader --reg $d/register.dat >>>> --noedit >>>> >>>> after creating register.dat, I >>>> followed the >>>> explained procedure, >>>> Which resulted in "lh.seg.mgh". >>>> can't view this >>>> file. ( appears a line ) >>>> >>>> >mri_info lh.seg.mgh >>>> Volume information for lh.seg.mgh >>>> type: MGH >>>> dimensions: 163842 x 1 x 1 x 17 >>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>> type: FLOAT (3) >>>> fov: 163842.000 >>>> >>>> >mri_info 3b.nii >>>> Volume information for 3b.nii >>>> type: nii >>>> dimensions: 182 x 218 x 182 >>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>> >>>> #binary maps looks okay >>>> >>>> may be I am doing mistake in >>>> registration or >>>> mri_vol2surf ? >>>> >mri_vol2surf --reg register.dat >>>> --mov Nb.nii >>>> --interp nearest --hemi lh --o >>>> lh.Nb.mgh >>>> >>>> Greetings! >>>> >>>> On Tue, Dec 13, 2011 at 5:56 PM, >>>> Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>> wrote: >>>> It's a little involved but >>>> possible. >>>> 1. Binarize Nth cluster to have >>>> a binary value >>>> of N >>>> mri_binarize --i N.nii >>>> --min 0.5 --binval N >>>> --o Nb.nii >>>> 2. Sample Nth cluster to the >>>> surface >>>> mri_vol2surf --reg >>>> register.dat --mov >>>> Nb.nii --interp >>>> nearest --hemi lh lh.Nb.mgh >>>> After doing that will all >>>> clusters, combine >>>> them together with >>>> mri_concat lh.1b.mgh >>>> lh.2b.mgh ... --vote >>>> --o lh.seg.mgh >>>> Now create a surface annotation >>>> mris_seg2annot --seg >>>> lh.seg.mgh --hemi lh --s >>>> subject --o >>>> lh.seg.annot --ctab yourctab >>>> yourctab is a color table like >>>> $FREESURFER_HOME/ >>>> FreeSurferColorLUT.txt. You >>>> >>>> list your regions >>>> and give them the colors you want. >>>> >>>> doug >>>> >>>> vin . wrote: >>>> Hi Doug, >>>> sorry for confusing names. >>>> >>>> - 1.nii is name of the >>>> cluster, which I >>>> want to >>>> overlay. it's a coritical >>>> region, >>>> resulted from >>>> fsl-probtrackx. >>>> I want to have few color >>>> codes in RGB >>>> R G B >>>> 1. 255 0 255 >>>> 2. 116 0 116 >>>> 3. 0 0 255 >>>> ... >>>> >>>> in this way, I would like >>>> to overlay 20 >>>> cortical >>>> regions in different >>>> colours on inflated >>>> brain. >>>> >>>> -fthresh 0.3 here >>>> (1/(10^0.3) == 50.12 % >>>> in freesurfer email >>>> archieve, I found >>>> this. hope >>>> it's correct. >>>> >>>> Thank you >>>> >>>> >>>> >>>> >>>> On Mon, Dec 12, 2011 at 11:11 PM, >>>> Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard. edu >>>> <mailto:greve@nmr.mgh.harvard.edu>>> >>>> wrote: >>>> >>>> Hi Vin, why do you say it's a 50% >>>> threshold? What >>>> is the >>>> 1.nii >>>> data? What colors do you want? >>>> doug >>>> >>>> vin . wrote: >>>> >>>> Dear FreeSurfer list, >>>> Greetings! >>>> >>>> a newbie to freesurfer. >>>> -- would like to overlay >>>> tracking group >>>> results (Sum from >>>> all >>>> subjects)-(from FSL ) in the >>>> inflated lh & >>>> rh. -- >>>> >>>> - it works with one region >>>> (hope it's >>>> correct), with >>>> following command, where, >>>> -fthresh ?? means >>>> it shows 50 % >>>> threshold based on intensity >>>> / only voxels >>>> which are >>>> overlaid >>>> by atleast half of the >>>> subjects ?? >>>> >>>> >tksurfer #Sub_ID lh inflated >>>> -annot >>>> aparc.annot -ov >>>> 1.nii >>>> -ovreg register.dat >>>> -fthresh 0.3 -fmid 0.3 >>>> -fslope 1 >>>> >>>> - How I can overlay multiple >>>> regions, in >>>> specific >>>> colours, >>>> with 50% thr. ? , >>>> Thank you :) >>>> Vin >>>> ----------------------------- - >>>> ------------------------------ >>>> ------------ >>>> >>>> _____________________________ _ >>>> _________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard. >>>> edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:Freesurfer@nmr.mgh. >>>> harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard. >>>> edu/mailman/listinfo/ >>>> freesurfer >>>> >>>> <https://mail.nmr.mgh. >>>> harvard.edu/mailman/listinfo/ freesurfer >>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard. edu >>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>> Phone Number: 617-724-2358 >>>> <tel:617-724-2358> <tel:617-724-2358 >>>> <tel:617-724-2358>> >>>> Fax: >>>> 617-726-7422 <tel:617-726-7422> >>>> <tel:617-726-7422 <tel:617-726-7422>> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/ >>>> <http://surfer.nmr.mgh.harvard.edu/> >>>> fswiki/BugReporting >>>> >>>> <http://surfer.nmr.mgh. >>>> harvard.edu/fswiki/ BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>> FileDrop: >>>> www.nmr.mgh.harvard.edu/ >>>> <http://www.nmr.mgh.harvard.edu/> >>>> facility/filedrop/index.html >>>> >>>> <http://www.nmr.mgh.harvard. >>>> edu/facility/filedrop/index. html >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> >>>> >>>> >>>> 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 >>>> <http://www.partners.org/ >>>> complianceline >>>> <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. >>>> >>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu> >>>> Phone Number: 617-724-2358 >>>> <tel:617-724-2358> Fax: 617-726-7422 >>>> <tel:617-726-7422> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/ >>>> fswiki/BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> FileDrop: >>>> www.nmr.mgh.harvard.edu/ >>>> facility/filedrop/index.html >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> >>>> >>>> >>>> >>>> >>>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@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. >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Post-Doctoral Position in Neuroimaging at UCSD
by Amanda Bischoff-Grethe 14 Dec '11

14 Dec '11

Post-Doctoral Position in Neuroimaging on the role of Reward and Inhibition on Appetite Regulation and Behavior A full-time Post-Doctoral position is available to work with Drs. Walter Kaye, Amanda Bischoff-Grethe, and Martin Paulus, Department of Psychiatry, University of California, San Diego. The post-doctoral fellow will work on several NIMH-funded research projects to investigate how altered reward or inhibition contributes to disturbed appetite regulation and other behaviors in anorexia and bulimia nervosa. Applicants should have experience with fMRI such as data acquisition, processing, and analysis. Moreover, experience working with clinical populations, neuropsychological testing, or programming is desirable. The postdoctoral fellow will be encouraged to develop his or her own research projects that fit within the overall scope of the project. The position will entail immersion in MR image analysis using one or more software tools, including AFNI, FSL, SPM, FreeSurfer, and R. Imaging sessions will take place at UCSD’s Center for Functional MRI, which is equipped with two research-dedicated GE 3T short-bore scanners. Appointment length is up to 5 years and is based upon the NIH salary scale. The position is available immediately, or the summer of 2012, and applications will be accepted until the position is filled. To apply, please send a brief statement of research interest and goals, any selected reprints, CV, and names and addresses of three references. For additional information or to apply, contact: Walter Kaye, MD Professor of Psychiatry Director, UCSD Eating Disorder Research and Treatment Program UCSD Department of Psychiatry 8950 Villa La Jolla Dr. Suite C207 La Jolla, CA 92037 http://eatingdisorders.ucsd.edu wkaye(a)ucsd.edu -- Amanda Bischoff-Grethe Assistant Adjunct Professor UCSD 9500 Gilman Drive MC 0738 La Jolla, CA 92093-0738 Tel: 858-246-0604 Fax: 858-246-0556

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