Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

(no subject)
by hankee 26 Apr '07

26 Apr '07

hi,I have question about the ?h.aparc file in stats directory. Can I use the parahippocample's gray matter volume or other brain structure's gray matter volume to do statistics analysis? For example,select 15 normal people and 15 AD disease patient,using FreeSurfer software to deal with them,when It is done, Can I compare the parahippocample's gray matter volume which located in /stats/lh.aparc file between patient group and normal group? Thank you! hankee，duhanjian(a)sohu.com 2007-04-26

2 1

(no subject)
by hankee 25 Apr '07

25 Apr '07

hi,ereryone I have a question.Can FreeSurfer measure the lateral geniculate nucleus's size? If can, how to implement such function? hankee，duhanjian(a)sohu.com 2007-04-26

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optseq2 questions
by Tamara Cristescu 25 Apr '07

25 Apr '07

Hello list, I am new to optseq2 and I would need some help with it. I have a very long experiment (many stimuli) and on top of that I have a long TR (4s) because I collect 60 coronal slices covering all the brain. My stimuli are quite short 1.5s or 2.5s but according to optseq the stimuli duration should be a multiple of TR. Therefore, the min stim duration I can use is 4s. I thought of modelling stimuli as having a duration of 4sec (1.5 stim and a 2.5 artificial "null" event which is different than the null event optseq estimates). I have a couple of questions: 1 I would like to know whether is better to include psdwin when I estimate a sequence or leave it out and use the TR value instead? 2 Also, would a psdwin of 20s be enough for a 4 sec stimulus? 3 My aim is to get a good sequence estimation with minimum time. I noticed that although I give a certain ntp, optseq estimates a sequence that may run longer. 4 Is the previous version of optseq still available? I only found optseq2 on your website. Thanks a lot for your help. Tamara

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converting register.xfm to register.dat
by s032441＠student.dtu.dk 25 Apr '07

25 Apr '07

Hi >From a separate analysis on pet-data using DOT I have a .xfm regestration file that registers my low resolution data (in .mnc format) to my MRI T1 data (also in .mnc format). Is there any way I can convert this xfm file to the register.dat required by freesurfer to load the analysis result as an overlay? I have read that this command should do the job tkregister2 --mov func.mnc --xfm your.xfm --s yoursubjectname --reg register.dat , but I get the following error message: ERROR: Option --xfm unknown Thanks, Carsten

2 1

Total Cortical Volume, Total Brain Volume and Gyrification Index
by Raznahan, Armin 24 Apr '07

24 Apr '07

Dear FreeSurfers I am new to FreeSurfer, and to this Wiki. I am working in SPSS with measures from FreeSurfer sent to me by a collaborator. It would be great if anyone could help with the following.. 1. When I summate GrayVolume measures for each of the 35 regions in each lobe, the total I get is about 50,000 less than that given under the automatically generated measure "CerebralCortex_Volume" for that lobe. I would be very grateful if someone could shed some light on this for me.. 2. Also - would anyone have advice on which of the three measures ; Brain Mask Volume, Brain Segmentation Volume, and Intracranial Volume performs best as an index of total brain volume when one wants to address this as a covariate in analyses? 3. Finally, I wondered if someone could confirm that the method for calculating Gyrification Index in FreeSurfer is that which appears as formula #2 on the second page of VanEssen's 1997 paper "Structural and functional analyses of human cerebral cortex using a surface-based atlas. J Neurosci. Sep 15;17(18):7079-102". Does this formula produce an index of gyrification that reflects the gyrification of an given area in a manner not influenced by changes in the perimeter of the area in question ie would the GI for a cortical region with an even degree of gyrification "g" and "footprint" area "f" be the same as that which would be generated by the equation if the area were increased to "2f"? All the best Armin Dr Armin Raznahan MBBS(Hons) MRCPCH MRCPsych Clinical Research Worker Institute of Psychiatry Department of Child and Adolescent Psychiatry PO85 16 De Crespigny Park London, SE5 8AF Tel: +44 (0)20 7848 0651 Fax: +44 (0)20 7708 5800 Email: armin.raznahan(a)iop.kcl.ac.uk

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skull stripping mistake
by abel cruz vadell 24 Apr '07

24 Apr '07

Hi everyone I have found some problems in the skull stripping step of my MRI images analysis. The skull was successfully removed but not the whole membrane. I tried to solve that mistake reducing the threshold in the mri watershed algorithm (from 25 to 5) but the problem remain (image 1). The amount of not removed membrane in the volume is high and therefore the manual erasing is very tedious. When I applied the step 2 of the program to segment the brain structures FreeSurfer misclassified some pixels of the membrane as cerebral cortex (image 2). I'm afraid that the cortical thickness can be computed in a wrong way in the nearest areas of the misclassified pixels. Is there any automatic procedure to resolve that problem? Thanks in advance Abel ____________________________________________________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

2 1

color codes for imported data
by Istvan Akos Morocz 23 Apr '07

23 Apr '07

dear freesurfers, could plase anybody advice me how to import with tksurfer correctly SPM5 activation maps so that color coding of the superimposed blobs look satisfying? what i am missing i think is a more complete documentation about tksurfer's run options such as -fthresh -fmid -foffset and -fslope. moreover, i am not sure what files can be imported at all while currently my imported activation maps are of signed int16, range [-127 +127], specified in the SPM5/Analyze header as spm_type=4. any help will be hotly appreciated, thanks, bye, pisti ----- pisti(a)bwh.harvard.edu

2 1

list of control points?
by Turner, Jessica 23 Apr '07

23 Apr '07

Hi folks-I'm doing Freesurfer in a collaborative environment, and I'm looking over someone else's work-Freesurfer loads up the images saying it found some number of control points, but when I skim through the brainmask.mgz images I often don't see them. Is there a way to get a listing of the control points and their coordinates, so I can check the placement of each one? Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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Subgenual surfaces
by Alexander Fornito 23 Apr '07

23 Apr '07

Hi, I've been consistently getting errors in surface reconstruction in the subgenual area of the cingulate - the grey matter gets missed completely, and instead, both the pial and white surfaces run along the grey/white boundary (see attached). The aseg seems to be ok, labelling the region as cerebral cortex (also see attached). I've tried control points and various other fixes but can't seem to adjust it. Any suggestions re: what to do? this happens consistently on just about all my images (they are Phillips 3T). Thanks, Alex

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Pial Surface
by Sharon Ruso 23 Apr '07

23 Apr '07

Dear FreeSurfers. Attached you will find an image of a subject in which I run autorecon1 and autorecon2 on. However, as you can see my pial surface (red line) doesn´t include all the gm, it runs like this from slice 104-133. What should I do? can I get any tips for editing the pial boundaries. Thanks in advance Sharon

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