Freesurfer April 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
78 discussions

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

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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

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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

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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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differences between parcellation and node-by-node
by Goldman, Aaron (NIH/NIMH) [C] 20 Apr '07

20 Apr '07

Hi, I've been looking at thickness data and Freesurfer, and had a question about the process. I initially compared thickness in our two groups on a node-by-node basis using: mris_preproc --fsgd_file file_name --target average --hemi rh --meas thickness --out rh.thickness.mgh mri_surf2surf --hemi rh --s average --sval rh.thickness.mgh --fwhm 10 --tval rh.thick_smooth.mgh mri_glmfit --y rh.thick_smooth.mgh --fsgd file_name doss --glmdir average/glm/rh --surf average rh --C contrast.m with the fsgd file containing inputs like: Input name1 NC-male 31.34 etc. (the number at the end being age) I also tried running GLM on the average label thicknesses in the parcellation stat files to see how similar the results would be. I did this by reading the values in the ThickAvg column into SPSS, and using group and gender as fixed factors with age as a covariate. Doing it this way, several labels came up significant that contained few or no significant nodes doing it the other way. Since this was surprising, I was wondering if there was anything that might be expected to cause this difference. For example, could there somehow be a scaling factor applied to one analysis but not the other? Thanks, -Aaron-

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Coordinate Systems
by Mishkin Derakhshan 20 Apr '07

20 Apr '07

Hi, I am new to FreeSurfer and even after having read the wiki, I have a few questions regarding the coordinate systems. 1. What coordinate system do the final surfaces have. ie. mris_convert rh.pial rh.pial.ascii will list the coordinates in what space? 2. Are the coordinates of T1.mgz and rh.pial for example the same, or does tkmedit compute transforms on the fly so that everything is aligned properly when you view it. 3. What transform (or combination of transforms) will get me from the final surfaces coordinates, to the MNI talairach like space (which I think is called avg305). many thanks, mishkin

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pial surface question
by Turner, Jessica 20 Apr '07

20 Apr '07

Hi there-looking through the archives for pial surface questions I didn't see an answer to this: I've done autorecon1 and autorecon2 on this subject and I was checking the brain mask, wm, etc. There's a tip of temporal lobe lying outside the pial surface (red line), see attached, where the red cross is in both pictures. What are we supposed to do in this case? I can't put control points outside the red line, as I understand it? 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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Freesurfer April 2007