Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 90, Issue 93
by Hasan, Khader M 29 Aug '11

29 Aug '11

I read with interest the comment by Lucas and some excellent responses by Anderson, and possibly others I did not read yet. A. These are my personal views based on experience with T1-weighted, DTI-based, T2-weighted, multi-modal, combined T1-T2-PD-DTI tissue segmentation and lesion methods as we and others published on even across the human lifespan (see list of references below) using FreSurfer and other approaches. Voxel-based approaches could not be compared directly with volume-based results as you obtain from FS or FSL. B. As summarized on the FreSurfer Wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki) FreeSurfer has been validated extensively using postmortem data and one can list scores of human pathologies and hundreds of papers that utlilized FreeSurfer results including child brain development, aging, brain trauma, Schizophrenia, Bipolar disorders, Parkinson, Alzheimer's, multiple sclerosis, Autsim, dyslexia and even the effect of mother's milk on deevelopment. Recently one can also appreciate the use of FreeSurfer in perfusion mapping, Iron mapping (Hasan et al., MRM 2011) and the fusion of quantittaive MRI methods to study the interplay between metrics such as relaxation time and radial diffusivity (Walimini et al., 2011). C. The problem is not in FreeSurfer results as you can always edit what you get or modulate it with experienced-rater masks or known landmarks. For example, thalamus in Fresurfer is a proper, and it is impossible to segment this region on T1-weighted alone into GM and WM. One can use T1-T2 and PD contrasts and hence you will get almost all gray matter zones in the thalmus along with its white matter islands. One can also use DTI along with cortical parcellations to regularize the solutions. For hippocampus, this is complicated and its subfields are highly variable, one may need higher spatial resolution methods, double fluid attenutaion and dedicated atalses. The Diencepahlon or brainstem are complicated as deep gray matter such as substantia nigra and red nucleus are not contrasted on T1-weighted data, so goes the Cerebellum and other regions (e.g. hypothalmus) D. The problem shows up when one tries to compare results, but caution as volume results and methods (x, y) may be related by a scaling or shift (y=a*x+c). No segmentation or parcellation method that uses single modality will be able to segment with 100% accuracy CSF, GM and WM as the very defintion of boundaries is limited by the acquisition paradigm details. For example, total CSF can never be estimated on T1-weighted. Lesions look dark on T1-weighted, so does CSF and GM. If you have iron accumulation you may see it as bright on T1-weighted data which may be confounded as white matter, but the training set and raters may help dtect and remove this from your data. E. From my experience, I am not a big fan of comparing results obtained from packages. I am more concerned with reliability, reproducibility on serial studies of one single package and sensitivity to variables such as Age, Side, Gender, Pathology and Clinical or Cognitive outcome ASSUMING your Scanner is STABLE and the groups being compared are carefully selected and screened (age range matched, comorbids, covariates) F. Clearly in pathologies, plaques, tumors or lesions will confound any method used as hypo or hyper-intesnities will be interpreted differenctly and one has to intervene to overide the results or use other contrasts such as T2-wighted, or FLAIR. G. As far as testing segmentation methods we made some suggestions in a recent Letter (Hasan and Pedraza Neuroimage 2009). I also bring attention for a paper that we published in August 2011 Neuroimage that used FreeSurfer and fused its regional GM and WM results with DTI-derived and Relaxation maps in both GM and WM. We did not find major problems with FreeSurfer volumetry if you carefully inspect the results, we have also tested subsets of the control data as function of age and compared it with known or expected trends using large samples. H. Occasionallly we encountered cases with poor results, but be careful. Failure or poor results may not be fairly blamed on FreeSurfer as some cases had poor SNR, some motion artifcats and we removed them from the analysis. FreeSurfer results are as good as your input data contrast-to-noise, slice thickness and other image acquisition factors that control the contrast (e.g. flip, TE/TR,..). I wont expect magic if the data original contrast and fed to any program does not have sufficient signal and contrast between CSF, GM and WM. I. References 1. http://surfer.nmr.mgh.harvard.edu/fswiki 2. Hasan KM, Frye RE. Diffusion tensor-based regional gray matter tissue segmentation using the international consortium for brain mapping atlases. Hum Brain Mapp. 2011;32(1):107-17. 3. Hasan KM, Walimuni IS, Kramer LA, Frye RE. Human brain atlas-based volumetry and relaxometry: application to healthy development and natural aging. Magn Reson Med. 2010;64(5):1382-9. 4. Hasan KM, Walimuni IS, Kramer LA, Narayana PA. Human brain iron mapping using atlas-based T(2) relaxometry. Magn Reson Med. 2011 (doi: 10.1002/mrm.23054). 5. Hasan KM, Walimuni IS, Abid H, Hahn KR. A review of diffusion tensor magnetic resonance imaging computational methods and software tools. Comput Biol Med. 2011 (doi:10.1016/j.compbiomed.2010.10.008) 6. Hasan KM and Pedraza O. Improving the reliability of manual and automated methods for hippocampal and amygdala volume measurements. Neuroimage. 2009;48(3):497-8. 7. Walimuni IS, Hasan KM. Atlas-based investigation of human brain tissue microstructural spatial heterogeneity and interplay between transverse relaxation time and radial diffusivity. Neuroimage. 2011;57(4):1402-10. 8. Walimuni IS, Abid H, Hasan KM. A computational framework to quantify tissue microstructural integrity using conventional MRI macrostructural volumetry. Comput Biol Med. 2011 (doi:10.1016/j.compbiomed.2010.10.009). Khader M Hasan, PhD Associate Professor of Radiology MSE 168, Tel 713 500 7690 (FAX 713 500 7684) University of Texas Health Science Center at Houston Medical School Diagnostic and Interventional Imaging Magnetic Resonance Imaging Research Division Diffusion Tensor Imaging Lab, Tel 713 500 7683 http://www.uth.tmc.edu/radiology/faculty/khader-m-hasan/index.html ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Monday, August 29, 2011 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 90, Issue 93 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. Re: Accuracy of FreeSurfers gray matter segmentation (Anderson Winkler) 2. Re: Accuracy of FreeSurfers gray matter segmentation (Lucas Eggert) 3. patch present-label missing (maahmed(a)mappi.helsinki.fi) 4. Re: Paired analysis results into table? (Braber, A. den) 5. Re: patch present-label missing (Bruce Fischl) 6. Re: Accuracy of FreeSurfers gray matter segmentation (Anderson Winkler) 7. Re: Accuracy of FreeSurfers gray matter segmentation (Bruce Fischl) 8. FW: Cortical Flattening (Tax, C.M.W.) 9. Re: problem with selxavg3 (Douglas N Greve) 10. Re: problem with selxavg3 (Maryam Vaziri Pashkam) 11. Re: problem with selxavg3 (Douglas N Greve) 12. Re: Correlation cortical thickness and lgi (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Sun, 28 Aug 2011 16:47:18 -0400 From: Anderson Winkler <andersonwinkler(a)hotmail.com> Subject: Re: [Freesurfer] Accuracy of FreeSurfers gray matter segmentation To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <BLU0-SMTP351AC314B26178D2AADB33DA1150(a)phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi Lucas, To know if a given structure is gray or white matter you can look in any reasonable anatomy textbook. In any case, the question itself is somewhat ill-posed, because some of the subcortical structures have heterogeneous tissue composition and can't really be labeled entirely as gray matter, even macroscopically. The most notable examples are perhaps the thalamus and hippocampus, but the same applies to other structures too. Anyway, if you really want to make a hard distinction, you can call then caudate, putamen, pallidum, amygdala, accumbens, hippocampus and thalamus as gray matter. The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra). Importantly, if you are comparing algorithms, you have to be sure they are reporting the same thing. For instance, it's fairly common to run SPM or FSL/FAST segmentation, then sum the GM voxels within a region defined from an atlas. If you do this for, say, caudate or thalamus, you'll get the volume of what the algorithm classified as GM within the structure you selected. FreeSurfer (and, e.g. FSL/FIRST), on the other hand, will segment and report the volume of the structure as a whole, including all what it contains. A direct comparison, thus, is not valid. Hope this helps! All the best, Anderson On 28/08/11 02:53, Lucas Eggert wrote: > Dear List, > > I recently posted the message you see below. > > I currently compare the segmentation results of different > segementation algorithms and FreeSurfer always yields the least > accurate results. Because I still have difficulties to decide which of > the labels in the aseg.mgz files should be considered gray matter, I > have the feeling, the bad results I am getting for FreeSufer might be > caused by not including all relevant gray matter segments. > > So, I would very much appreaciate any help on deciding which of the > labels in the aseg.mgz file belong to gray matter! > > With kind regards > Lucas Eggert > > > -------- Original-Nachricht -------- > Betreff: [Freesurfer] How to determine gray matter in the aseg.mgz > Datum: Tue, 03 May 2011 17:26:55 +0200 > Von: Lucas Eggert <leggert(a)Uni-Osnabrueck.DE> > An: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > > > > Dear Experts, > > I would like to generate a gray matter mask using the aparc+aseg.mgz file. > > Now, my question is whether there exists a file in addition to the > FreeSurferColorLUT.txt > file, which more explicitly, i. e., withouth the abbreviations, explains > the labels, because I > find it hard to decide whether, e. g., "Left-VentralDC", "Line1", > "LeftmOg", or "Left-Interior" > belong to gray matter, or not (to name only a few of those labels I > cannot clearly classify). > > Or is there a easier way to create a gray matter mask? > > Thank you very much in advance! > > Best regards, > Lucas Eggert > > -- > Lucas Eggert, M.Sc. > Institute of Cognitive Science > University of Osnabrueck > Albrechtstrasse 28 > D-49076 Osnabrueck > Germany > > Phone: +49-541-969-44-28 > Website:http://www.cogsci.uni-osnabrueck.de/~leggert/ > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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.

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DTI and FS
by Antonella Kis 29 Aug '11

29 Aug '11

Dear FS experts, I'm interested in doing DTI analysis, using FS. Do I need to have functional data (feat) and then do I need to register the anatomical data on the functional one? My MRI data contains the following folders: 3DAx_T1, Ax_Flair, Ax_T2PD, DTI_15, DTI_30. I am not sure for a DTI /FSL analysis what data should I use. 1).Do I need to use the DTI data (DTI_15, DTI_30) and what steps should I follow in order to run a DTI/FSL data analysis for my subjects versus controls? 2).Do I need to run the dt_recon? In this case my input should be the dicom images from a DTI (DTI_15 or DTI_30) folder? 3) When I need to check the registration where I get the lowb.nii? tkregister2 --mov dti/lowb.nii --reg dti/register.dat \ --surf orig --tag 4) Or, should I use trac-all on the DTI_15 or DTI_30 data? 5) Do I need to run reg-feat2anat to first analyze my data with FEAT (No Smoothing )as in the example posted online: reg-feat2anat –featdir fbert1.feat –subject bert 6) From where fbert1.feat is coming/how was obtained? Sorry for asking so many/silly questions. I will be greatly appreciate any help/directions/suggestions. Antonella

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GLM analysis - covariates
by Jenessa Price 29 Aug '11

29 Aug '11

I'm examining differences in cortical thickness in a sample of drug users and non-users. From the literature, it appears that the 2 covariates I should use for the GLM analysis will be gender and age. Other researchers have examined other possible covariates (like age of first use, # past year uses, IQ, etc.) using correlations between those variables and significant clusters that differed between groups. Is this the best way to go about translating a typical regression model into the Freesurfer statistical package (especially if I'm interested in dose-dependent relationships)? Also, how do you suggest controlling for total brain volume? Other researchers have performed univariate analyses between groups on TBV controlling for age and gender, then examined mean cortical thickness, but I'm not quite sure what the steps are for this. Could someone help me identify the best way to control for TBV (i.e., is there a way to control from the first GLM analysis, or is this a possible covariate to enter in to the analysis)? Thanks! -- Jenessa S. Price, M.A. Graduate Student, Clinical Psychology and Neuropsychology University of Cincinnati Campus Representative, American Psychological Association of Graduate Students (APAGS)

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integrating FSL and Freesurfer
by noam Schneck 29 Aug '11

29 Aug '11

Hi, I am trying to use reg-feat2anat to register my Feat analyses to anatomical images and running into a number of problems. 1) When I check the registration of the mean_func to the anatomical in tkregister2 it looks fine. But when I overlay the fsl statmaps onto the anatomical brain they extend outside of boundaries of the anatomical brain. 2) Also, before using reg-feat2anat. I was trying to do the EPI_2_structural registration in FLIRT with the fsl.mat produced by BBR. When I try this the registered image is rotated 90 degrees from the original image. Why does that happen? 3) I also noticed that if I look at the header information for an image in fslhd and mri_info the orientations are flipped. If the fslhd orientation is RAS it will be LPI in mri_info. Could this be related to what is happening in question (2)? Best, Noam

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use MNI152 normalized images in segmentation
by tony han 29 Aug '11

29 Aug '11

Dear all, I'm just learning Freesurfer and want to import output files of Freesurfer into Carat so that I can generate individual surface. I already have my functional and anatomical images preprocessed (realign, coregister, segment and normalize) in spm5. So the anatomical have been normalized into MNI152 space. Is it ok if I keep these anatomical images normalized in spm5 without using MNI305 during segmentation in Freesurfer ? Or I have to go through all autorecon processing stages? If it's ok, could you tell me specifically how to do this? all the best, Tony

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Fwd: Re: Defining an mrs voxel in the anatomical dataset for partial volume correction
by _andreia_＠sapo.pt 29 Aug '11

29 Aug '11

Hello all! I got no answer on this email, thus I'm posting these questions again, hoe someone can help: Hello! About synthesising a volume using mri_volsynth with direction cosines and RAS from mrs header: In the mrs header I have: - VOI position in the 3 views (sag, cor and tra) which are from the left upper corner of the voxel (these are the RAS coordinates that I need to feed into mri_volsynth, correct?) - position vectors [0] [1] [2] - row and columns vectors (but I think that these are not the ones used to get the direction cosines, is that right?) - VOIRotationInPlane - and I know that my voxel is 3x3x3 cm How do I introduce these infos in mri_volsynth to have a 3x3x3 cube to coregister with the anatomical? Typing mri_volsynth --help I got lots of asked information and I don't know how to feed into it. Also, for defining the geometry the "center" voxel and the first voxel are needed. Shouldn't it be only the RAS of the corner of the voxel? Also, all these infos are in the scanner space, and the anatomical image processed in FS is spacially transformed. What should I use to coregister the synthesized volume to the processed anatomical to get the same transformation in the 3x3x3 volume? Can you give me an example of how this process is done? Thank you very much! Andreia > Hi Doug, > > Ok. Thank you! :) > > Andreia > > Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> Yes, that should work. You will need a registration matrix to give to >> mri_compute_volume_fractions. You can get this from tkregister2: >> >> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat >> >> when you run this, hit the compare button to make sure that the mrs box >> falls on the part of the anatomical you think it should be. Then hit >> "Save" to save the registration. >> >> doug >> >> _andreia_(a)sapo.pt wrote: >>> Hi Doug, >>> >>> This already sheds some light on the issue! I didn't know >>> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have >>> the anatomical and the MRS data acquired in the same session, so I >>> won't need the EPI. If I manage to create the MRS volume using the >>> header info and mri_volsynth I only need to coregister my anatomical >>> with the synthetised volume and then run mri_compute_volume_fractions >>> through the synthesed volume and the identity matrix (?) (since my >>> data are from the same session) to get the % of the different tissue >>> types only inside the voxel. Of course I'll need more advice on this >>> later, but one thing at a time. >>> >>> Thanks! >>> Andreia >>> >>> >>> >>> Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>> >>>> Sorry, I don't know anyone who can help with that. As you note, people >>>> do it, so there must be people around who can extract the relevant >>>> information out of the header. The information you need are the >>>> direction cosines and RAS of the corner of the voxel. You can feed this >>>> into mri_volsynth. >>>> >>>> To register to FS, you'll need to have a whole-brain volume collected >>>> during the same session. If you collected the anatomical analyzed in FS >>>> at the same time, then you don't need another. If you did not, you can >>>> literally use any whole brain acquisition, eg, a single TR of an EPI >>>> (less than 10 sec to acquire). You can then register the EPI to the >>>> anatomical with bbregister. This gives you a "register.dat". You can >>>> then concatenate that with the EPI-MRS registration (I can show you >>>> how). After that, you can run mri_compute_volume_fractions passing it >>>> the synthesized volume and the register.dat (or identity matrix if same >>>> session). >>>> >>>> Another alternative is to collect an actual MRI volume that spans your >>>> MRS volume. You can then substitute that for the synthetic volume. Note >>>> that the actual pixel content of this volume is irrelevant -- it's just >>>> used to get geometry information out of it. This will be the easiest if >>>> you can do it. >>>> >>>> doug >>>> >>>> _andreia_(a)sapo.pt wrote: >>>>> Hi Doug, >>>>> >>>>> Do you know who can help me with this? That's exactly what I think >>>>> that I need to do... The thing is that, unfortunately, I can't find >>>>> anyone who can describe how the creation of an MRI "volume" from the >>>>> MRS voxel is done, although this approach is present in many many >>>>> papers. >>>>> >>>>> About the second part, how do I register the synthetized MRI "volume" >>>>> to the FS anatomical? And how can I get the volumes of only that >>>>> "volume"? >>>>> >>>>> (Hopefully I'll find a way to do the first part...) >>>>> >>>>> Thanks, >>>>> Andreia >>>>> >>>>> >>>>> >>>>> >>>>> Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>>>> >>>>>> Hi Andreia, I've done this before using information in the >>>>>> spectroscopy >>>>>> header, then synthesizing an MRI "volume" with one voxel that >>>>>> covers the >>>>>> size of your spectroscopy voxel, then registering that to the FS >>>>>> anatomical, then computing the partial volume fractions from the >>>>>> anatomical. The hard part is the first step, which I can't really >>>>>> advise >>>>>> you on. >>>>>> >>>>>> doug >>>>>> >>>>>> _andreia_(a)sapo.pt wrote: >>>>>>> Dear list, >>>>>>> >>>>>>> I am performing single-voxel and multivoxel spectroscopy analysis and >>>>>>> I need to do partial volume correction. I found a thread on the list >>>>>>> of someone asking if it possible to achieve this using Freesurfer >>>>>>> (see >>>>>>> below), but there is no answer saying how it is done. My question is >>>>>>> how can I define the voxel (for single-voxel) and the chosen voxels >>>>>>> (for multivoxel) in the anatomical data set to use the >>>>>>> segmentation of >>>>>>> only that defined voxel? I'm using a Siemens TrioTim 3T. All >>>>>>> acquisitions are in the same session. The anatomical dataset is an >>>>>>> average of 2 MPRAGEs which I've already processed using FS, and the >>>>>>> spectra files are .rda. The header of the MRS data has info on >>>>>>> vectors, but I don't know how to use them. >>>>>>> >>>>>>> >>>>>>> >>>>>>> "Re: [Freesurfer] need info for beginner >>>>>>> >>>>>>> Bruce Fischl >>>>>>> Thu, 26 Apr 2007 11:17:01 -0700 >>>>>>> >>>>>>> Hi Pom, >>>>>>> >>>>>>> yes, people here are using it for spectroscopy and for partial volume >>>>>>> correction (also for voxel placement). >>>>>>> >>>>>>> cheers, >>>>>>> Bruce >>>>>>> >>>>>>> On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am about to install FREE SURFER for my Spectroscopy work. >>>>>>> I want to use the software to perform GM/WM segmentation on my >>>>>>> single voxel data sets. >>>>>>> >>>>>>> I am wondering if any one on this mailing list is currently >>>>>>> doing this task. I would like to get comments. >>>>>>> >>>>>>> My study is on a GE 3T scanner. >>>>>>> >>>>>>> thank you, >>>>>>> >>>>>>> Pom" >>>>>>> >>>>>>> >>>>>>> >>>>>>> Any advice, please? >>>>>>> >>>>>>> Thank you! >>>>>>> >>>>>>> Andreia >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Andreia Pereira, MSc student >>>>>>> Visual Neuroscience Laboratory >>>>>>> IBILI-Faculdade de Medicina >>>>>>> Azinhaga de Santa Comba >>>>>>> 3000-354 Coimbra Portugal >>>>>>> Phone +(351) 239480220 >>>>>>> Fax +(351) 239480280 >>>>>>> >>>>>>> ------------------------------------------------------------------------ >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> >>> >> >> -- >> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > > Andreia Pereira, MSc student > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-354 Coimbra Portugal > Phone +(351) 239480220 > Fax +(351) 239480280 -- Andreia Pereira, MSc student Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-354 Coimbra Portugal Phone +(351) 239480220 Fax +(351) 239480280

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ERROR: Option ‐‐hemi unknown for mri_surf2surf
by xian zhang 29 Aug '11

29 Aug '11

Dear Freesurfers: mri_surf2surf  ‐‐hemi  lh  ‐‐s  fsaverage  ‐‐sval  att-lh-thickness.mgh ‐‐fwhm  10  ‐‐tval  att-lh-thickness.10.mgh I got error " command not found" or "ERROR: Option  ‐‐hemi unknown" although I can do mri_surf2surf  ‐‐help with not problem I checked fsaverage, OK but my att-lh-thickness.mgh is not inside the fsaverage folder the result of unix "ls" command is att-lh-thickness.mgh fsaverage Is there a tutorial data so that I can go through group analysis step by step? Thanks!

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Cortical thickness - again
by Ed Gronenschild 29 Aug '11

29 Aug '11

Hi, How do you compute the cortical thickness for each structure as listed in the ?h.aparc.stats file? Is it equal to the thickness at each vertex averaged over all vertices within the structure? Ed

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two questions regarding qdec and conjunction analysis is FS
by Tetiana Dadakova 29 Aug '11

29 Aug '11

Dear FS experts, I have two questions: 1. In qdec.table.dat file I am specifying several continuous factors, e.g factor1 and factor2. For some subjects factor2 is missing, therefore I leave empty space in those cells. When I load a qdec.table.dat into qdec, the whole line of the subject with missing factor2 is omitted. I was wondering if I can make some input into the empty cell, so that qdec recognizes that for this subject the value is missing only for factor2, and the value for factor1 is present. 2. Is it possible to do conjunction analysis in FreeSurfer, I mean looking at common differences in two groups as compared to the third group? Thank you for your time and help, Tanja.

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Accuracy of FreeSurfers gray matter segmentation
by Lucas Eggert 29 Aug '11

29 Aug '11

Dear List, I recently posted the message you see below. I currently compare the segmentation results of different segementation algorithms and FreeSurfer always yields the least accurate results. Because I still have difficulties to decide which of the labels in the aseg.mgz files should be considered gray matter, I have the feeling, the bad results I am getting for FreeSufer might be caused by not including all relevant gray matter segments. So, I would very much appreaciate any help on deciding which of the labels in the aseg.mgz file belong to gray matter! With kind regards Lucas Eggert -------- Original-Nachricht -------- Betreff: [Freesurfer] How to determine gray matter in the aseg.mgz Datum: Tue, 03 May 2011 17:26:55 +0200 Von: Lucas Eggert <leggert(a)Uni-Osnabrueck.DE> An: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Dear Experts, I would like to generate a gray matter mask using the aparc+aseg.mgz file. Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify). Or is there a easier way to create a gray matter mask? Thank you very much in advance! Best regards, Lucas Eggert -- Lucas Eggert, M.Sc. Institute of Cognitive Science University of Osnabrueck Albrechtstrasse 28 D-49076 Osnabrueck Germany Phone: +49-541-969-44-28 Website: http://www.cogsci.uni-osnabrueck.de/~leggert/

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Freesurfer August 2011