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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu] Sent: Monday, August 29, 2011 11:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 90, Issue 93 Send Freesurfer mailing list submissions to freesurfer@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-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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 (maah...@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 <andersonwink...@hotmail.com> Subject: Re: [Freesurfer] Accuracy of FreeSurfers gray matter segmentation To: freesurfer@nmr.mgh.harvard.edu Message-ID: <blu0-smtp351ac314b26178d2aadb33da1...@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 <legg...@uni-osnabrueck.de> > An: freesurfer@nmr.mgh.harvard.edu <freesurfer@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@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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110828/fc92fefc/attachment-0001.html ------------------------------ Message: 2 Date: Mon, 29 Aug 2011 09:38:26 +0200 From: Lucas Eggert <legg...@uos.de> Subject: Re: [Freesurfer] Accuracy of FreeSurfers gray matter segmentation To: freesurfer@nmr.mgh.harvard.edu Message-ID: <4e5b41f2.4070...@uos.de> Content-Type: text/plain; charset="iso-8859-1" Dear Anderson Winkler, thank you very much for your quick response and your very helpful comments! > > To know if a given structure is gray or white matter you can look in > any reasonable anatomy textbook. That is ture, of course; however, my problem is rather to match labels like "LeftmOg" in the aseg.mgz file to anatomical structures. > 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. That is totally true. Nevertheless, for a comparison between different segmentation methods, if you would like to compare e. g. total gray matter volume, it is important to know, which of the labels should rather be regarded as gray matter and which should be regarded as something else. But as you mention below, a direct comparison between different segmentation methods might not be valid --- Thanks for this important hint! But then, I am a bit suprised, anyway: I am not familiar with the method used by FreeSurfer for (sub)cortical segmentation; but could you, in simple words describe shortly, how FreeSurfer does the segmentation, if not voxel-vise, that is, how does FreeSurfer define a whole structure (see your comment below)? That would be of great help for the upcoming discussion of the results for the evaluation of different segmentation methods. > > 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. With kind regards Lucas Eggert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110829/b412505b/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 4815 bytes Desc: S/MIME Kryptografische Unterschrift Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110829/b412505b/attachment-0001.bin ------------------------------ Message: 3 Date: Mon, 29 Aug 2011 13:26:39 +0300 From: maah...@mappi.helsinki.fi Subject: [Freesurfer] patch present-label missing To: freesurfer@nmr.mgh.harvard.edu Message-ID: <20110829132639.21311mcroj41necf.maah...@webmail.helsinki.fi> Content-Type: text/plain; charset="utf-8" Hi, I did the recon-all using the same case and the same freesurfer edition twice. The second processing I did was missing the label : Medial_wall-rh.label I have the same problem with 20 other cases. I uploaded an image of the first and second attempt here : http://tinyurl.com/3p52zrj You will notice that in the second one, the patches definition is poor around the medial surface of the hemisphere.Is this the problem ?and if so, how can i tackle it ? Can i label the medial patch manually ? Thank you, Mostafa Abdelgawad -------------- next part -------------- A non-text attachment was scrubbed... Name: attachement.JPG Type: image/jpeg Size: 178447 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110829/0608953e/attachment-0001.jpe ------------------------------ Message: 4 Date: Mon, 29 Aug 2011 12:26:30 +0000 From: "Braber, A. den" <a.den.bra...@vu.nl> Subject: Re: [Freesurfer] Paired analysis results into table? To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ed721e106bca02458ec57cc3ee85ce616ca...@pexmb002b.vu.local> Content-Type: text/plain; charset="us-ascii" Hi, I just performed a paired analysis on my twin data. I am interested in the difference in cortical thickness between males and females, and have to run a paired analysis since the males and females in my sample are related (because they are twins). No covariate (such as age) has been included in the mri_glmfit yet, so I only have 1 contrast (mean.mtx = 1, meaning in my case males greater than females). After running the mri_glmfit I viewed my results using ' tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay $SUBJECTS_DIR/ sig.mgh'. Thereafter I corrected my results using FDR-correction, under View->Configure->Overlay->set threshold using FDR, rate 0.05 (so I did not perform a clusterwise correction for multiple comparison). Tksurfer than gives me a really nice overview of the significant results (FDR-corrected) of my paired analysis. I wondered whether there is a tool to export these results into a table (just like it's possible with aparc2table), so I get an overview of, for example, T-statistics, p-value and vertex number, for the observed significant clusters (or vertex with the highest T-value within an observed cluster). Is this possible? I have searched for a command to do this, but unfortunately I couldn't find it. Could you please help me? Thanks in advance. Anouk den Braber -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110829/d81d6bb6/attachment-0001.html ------------------------------ Message: 5 Date: Mon, 29 Aug 2011 08:40:32 -0400 From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] patch present-label missing To: "maah...@mappi.helsinki.fi" <maah...@mappi.helsinki.fi> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <6fb2ad56-fa99-414e-bb54-ccadd3555...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii What version and operating system are you using? On Aug 29, 2011, at 6:26 AM, maah...@mappi.helsinki.fi wrote: > Hi, > > I did the recon-all using the same case and the same freesurfer edition twice. > The second processing I did was missing the label : Medial_wall-rh.label > I have the same problem with 20 other cases. I uploaded an image of the > first and second attempt here : http://tinyurl.com/3p52zrj > You will notice that in the second one, the patches definition is poor > around the medial surface of the hemisphere.Is this the problem ?and if so, > how can i tackle it ? Can i label the medial patch manually ? > > Thank you, > Mostafa Abdelgawad > <attachement.JPG> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 6 Date: Mon, 29 Aug 2011 09:33:53 -0400 From: Anderson Winkler <andersonwink...@hotmail.com> Subject: Re: [Freesurfer] Accuracy of FreeSurfers gray matter segmentation To: freesurfer@nmr.mgh.harvard.edu Message-ID: <blu0-smtp3127f703826b448f07fbb26a1...@phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi Lucas, It seems you are looking at the FreeSurferColorLUT.txt. Not all these labels are in the aseg.mgz file. Try looking at the aseg.stats file, in the subdirectory stats of each directory of your subjects. The labels there are the ones in the aseg.mgz, and have friendly names. For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson On 29/08/11 03:38, Lucas Eggert wrote: > Dear Anderson Winkler, > > thank you very much for your quick response and your very helpful > comments! >> >> To know if a given structure is gray or white matter you can look in >> any reasonable anatomy textbook. > That is ture, of course; however, my problem is rather to match labels > like "LeftmOg" in the aseg.mgz file to anatomical structures. >> 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. > That is totally true. Nevertheless, for a comparison between different > segmentation methods, if you would like to compare e. g. total gray > matter volume, it is important to know, which of the labels should > rather be regarded as gray matter and which should be regarded as > something else. But as you mention below, a direct comparison between > different segmentation methods might not be valid --- Thanks for this > important hint! > > But then, I am a bit suprised, anyway: I am not familiar with the > method used by FreeSurfer for (sub)cortical segmentation; but could > you, in simple words describe shortly, how FreeSurfer does the > segmentation, if not voxel-vise, that is, how does FreeSurfer define a > whole structure (see your comment below)? That would be of great help > for the upcoming discussion of the results for the evaluation of > different segmentation methods. >> >> 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. > > With kind regards > Lucas Eggert > > > _______________________________________________ > Freesurfer mailing list > 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110829/f96a30e4/attachment-0001.html ------------------------------ Message: 7 Date: Mon, 29 Aug 2011 09:45:36 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Accuracy of FreeSurfers gray matter segmentation To: Anderson Winkler <andersonwink...@hotmail.com> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <alpine.lrh.2.00.1108290944530.26...@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Lucas the problem can be one of definitions. For example the FreeSurfer definition of the thalamus extends into the lateral thalamic nuclei that look a lot like wm, whereas others don't necessarily. Thus it's hard to compare apples to apples. cheers Bruce On Mon, 29 Aug 2011, Anderson Winkler wrote: > Hi Lucas, > > It seems you are looking at the FreeSurferColorLUT.txt. Not all these labels > are in the aseg.mgz file. Try looking at the aseg.stats file, in the > subdirectory stats of each directory of your subjects. The labels there are > the ones in the aseg.mgz, and have friendly names. > > For the segmentation, FS still works voxelwise, but it's objective is to > identify each structure as a whole, whereas SPM and FSL/FAST attempt to > classify each voxel as being GM, WM or CSF. > A short description of the method in FS is here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream > You may want also to have a look at this paper: > http://dx.doi.org/10.1016/S0896-6273(02)00569-X > > Hope this helps! > > All the best, > > Anderson > > > On 29/08/11 03:38, Lucas Eggert wrote: > Dear Anderson Winkler, > > thank you very much for your quick response and your very helpful > comments! > > To know if a given structure is gray or white matter you can look > in any reasonable anatomy textbook. > > That is ture, of course; however, my problem is rather to match labels > like? "LeftmOg" in the aseg.mgz file to anatomical structures. > 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. > > That is totally true. Nevertheless, for a comparison between different > segmentation methods, if you would like to compare e. g. total > gray matter volume, it is important to know, which of the labels should > rather be regarded as gray matter and which should be regarded > as something else. But as you mention below, a direct comparison > between different segmentation methods might not be valid --- Thanks > for this important hint! > > But then, I am a bit suprised, anyway: I am not familiar with the > method used by FreeSurfer for (sub)cortical segmentation; but could > you, in simple words describe shortly, how FreeSurfer does the > segmentation, if not voxel-vise, that is, how does FreeSurfer define a > whole structure (see your comment below)? That would be of great help > for the upcoming discussion of the results for the evaluation of > different segmentation methods. > > 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. > > > With kind regards > Lucas Eggert > > > _______________________________________________ > Freesurfer mailing list > 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. > > > > ------------------------------ Message: 8 Date: Mon, 29 Aug 2011 16:18:22 +0200 From: "Tax, C.M.W." <c.m.w....@student.tue.nl> Subject: [Freesurfer] FW: Cortical Flattening To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <c43db61071f7f743b65ee51e9d40c687c631335...@exchange12.campus.tue.nl> Content-Type: text/plain; charset="us-ascii" Dear all, Would it be possible to create a virtual CentOS environment on Ubuntu? Since the computer is used in clinic, it's hard to change. I hope there is some easier solution... Thank you in advance! -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: maandag 29 augustus 2011 15:38 To: Tax, C.M.W. Subject: RE: [Freesurfer] Cortical Flattening Hi Chantal, can you post this to the list so that Nick or Krish (or others) can answer? thanks Bruce On Mon, 29 Aug 2011, Tax, C.M.W. wrote: > Dear Bruce, > > Would it be possible to create a virtual CentOS environment on Ubuntu? Since > the computer is used in clinic, it's hard to change... > > Thank you > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: donderdag 25 augustus 2011 14:41 > To: Tax, C.M.W.; Nick Schmansky; Krish Subramanian > Subject: Re: [Freesurfer] Cortical Flattening > > Nick and Krish: any ideas? > > > > On Aug 25, 2011, at 2:03 AM, "Tax, C.M.W." <c.m.w....@student.tue.nl> wrote: > >> Dear Bruce, >> >> Thank you for your response. I'm working on ubuntu version 10.04 indeed, one >> computer 32b and the other 64b. Is there any way how I could solve this >> problem? >> >> Regards, >> Chantal >> ________________________________________ >> Van: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Verzonden: woensdag 24 augustus 2011 23:23 >> Aan: Tax, C.M.W. >> CC: freesurfer@nmr.mgh.harvard.edu >> Onderwerp: Re: [Freesurfer] Cortical Flattening >> >> Louis just pointed out to me what the thread was about. What operating >> system are you running on? This seems to be a problem in the depths of >> openGL on ubuntu. We haven't seen it on CentOS or red hat. >> >> Bruce >> On Wed, 24 Aug >> 2011, Bruce Fischl wrote: >> >>> Hi Chantal, >>> >>> what went wrong? Sorry, I've lost this thread. >>> >>> cheers >>> Bruce >>> >>> >>> On Wed, 24 Aug 2011, Tax, C.M.W. wrote: >>> >>>> Dear Doug, >>>> >>>> Tank you for your response. The freesurfer wikipage I was following: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch >>>> Do I have to do some additional steps? >>>> >>>> Thank you in advance, >>>> Regards, >>>> Chantal >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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. >> >> >> > > > ------------------------------ Message: 9 Date: Mon, 29 Aug 2011 11:29:35 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] problem with selxavg3 To: Maryam Vaziri Pashkam <mvazir...@gmail.com> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <4e5bb05f.7030...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Maryam, it looks like there is a corrupted file there. Did you run out of space on your disk? If not, have you tried to delete the analysis and rerun? You might also try adding -no-fwhm (I can't remember if 4.5 takes this option). doug Maryam Vaziri Pashkam wrote: > Hi, > > I am encountering a memory allocation error with selxavg3-sess and I > am not sure how to get around it: > > Here is the lines that I am running > mkanalysis-sess -analysis FHPDM_noauto -TR 2 -paradigm allpara.par > -designtype event-related -funcstem fmc -motioncor -runlistfile > FHPDM_runlist.txt -inorm -nconditions 8 -timewindow 20 -TER 2 -polyfit > 2 -mcextreg -noautostimdur -force > > selxavg3-sess -s 110821_xu_FHPDM_02 -df sessdir -analysis FHPDM_noauto > > It is a single subject data with 12 runs, event related design that > each event last for about 4 seconds and the total experiment time is > 328 seconds( at TR=2 is equal to 164 TRs) > > My computer is a MAC with 4 gb of ram. and I am running freesurfer > 4.5. I have ran similar analysis on the same number of runs but much > longer events (12 sec) before and have not had a problem. This is the > first time I am analyzing data for this particular experiment though. > > Here is the error line that I get: > > mri_fwhm(2138) malloc: *** mmap(size=16777216) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIalloc(70, 70, 33): could not allocate 19600 bytes for 49364th slice > > voxelvolume 35.3062 mm3 > Loading mask > /Users/maryam/mri-space/studies/FHPDM/unpackdata/110821_xu_FHPDM_02/bold/FHPDM_noauto/mask.nii > Search region is 60647 voxels = 2141216.616840 mm3 > Polynomial detrending, order = 0 > Detrending > Cannot allocate memory > [dhcp-0170571539-df-00:st > > Can anyone help? > Thanks, > Maryam > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ------------------------------ Message: 10 Date: Mon, 29 Aug 2011 11:34:13 -0400 From: Maryam Vaziri Pashkam <mvazir...@gmail.com> Subject: Re: [Freesurfer] problem with selxavg3 To: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAEEXA4cuqX6HUaCmxnTCa8X_GXuvdD+mHAuAM5p5T=zd3im...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Thanks Doug, I am not running out of space. I did delete the analysis and it did not help. Anyhow, I jsut upgraded my freesurfer to freesurer 5.1 to see if the issue is resolved with the new version. Maryam On Mon, Aug 29, 2011 at 11:29 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Hi Maryam, it looks like there is a corrupted file there. Did you run out > of space on your disk? If not, have you tried to delete the analysis and > rerun? You might also try adding -no-fwhm (I can't remember if 4.5 takes > this option). > doug > > > Maryam Vaziri Pashkam wrote: > >> Hi, >> >> I am encountering a memory allocation error with selxavg3-sess and I am >> not sure how to get around it: >> >> Here is the lines that I am running >> mkanalysis-sess -analysis FHPDM_noauto -TR 2 -paradigm allpara.par >> -designtype event-related -funcstem fmc -motioncor -runlistfile >> FHPDM_runlist.txt -inorm -nconditions 8 -timewindow 20 -TER 2 -polyfit 2 >> -mcextreg -noautostimdur -force >> >> selxavg3-sess -s 110821_xu_FHPDM_02 -df sessdir -analysis FHPDM_noauto >> It is a single subject data with 12 runs, event related design that each >> event last for about 4 seconds and the total experiment time is 328 seconds( >> at TR=2 is equal to 164 TRs) >> >> My computer is a MAC with 4 gb of ram. and I am running freesurfer 4.5. I >> have ran similar analysis on the same number of runs but much longer events >> (12 sec) before and have not had a problem. This is the first time I am >> analyzing data for this particular experiment though. >> Here is the error line that I get: >> >> mri_fwhm(2138) malloc: *** mmap(size=16777216) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> MRIalloc(70, 70, 33): could not allocate 19600 bytes for 49364th slice >> >> voxelvolume 35.3062 mm3 >> Loading mask /Users/maryam/mri-space/**studies/FHPDM/unpackdata/** >> 110821_xu_FHPDM_02/bold/FHPDM_**noauto/mask.nii >> Search region is 60647 voxels = 2141216.616840 mm3 >> Polynomial detrending, order = 0 >> Detrending >> Cannot allocate memory >> [dhcp-0170571539-df-00:st >> >> Can anyone help? >> Thanks, >> Maryam >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 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> > > > > 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>. > 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. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110829/479e924e/attachment-0001.html ------------------------------ Message: 11 Date: Mon, 29 Aug 2011 11:36:28 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] problem with selxavg3 To: Maryam Vaziri Pashkam <mvazir...@gmail.com> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <4e5bb1fc.3020...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed The new version is much different, and you can't run 4.5 analyses on 5.1. It does not run mri_fwhm by default, so that will help. If you want to continue to use 4.5, then try --no-fwhm. doug Maryam Vaziri Pashkam wrote: > Thanks Doug, > > I am not running out of space. I did delete the analysis and it did > not help. Anyhow, I jsut upgraded my freesurfer to freesurer 5.1 to > see if the issue is resolved with the new version. > > Maryam > > On Mon, Aug 29, 2011 at 11:29 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Maryam, it looks like there is a corrupted file there. Did you > run out of space on your disk? If not, have you tried to delete > the analysis and rerun? You might also try adding -no-fwhm (I > can't remember if 4.5 takes this option). > doug > > > Maryam Vaziri Pashkam wrote: > > Hi, > > I am encountering a memory allocation error with selxavg3-sess > and I am not sure how to get around it: > > Here is the lines that I am running > mkanalysis-sess -analysis FHPDM_noauto -TR 2 -paradigm > allpara.par -designtype event-related -funcstem fmc -motioncor > -runlistfile FHPDM_runlist.txt -inorm -nconditions 8 > -timewindow 20 -TER 2 -polyfit 2 -mcextreg -noautostimdur -force > > selxavg3-sess -s 110821_xu_FHPDM_02 -df sessdir -analysis > FHPDM_noauto > It is a single subject data with 12 runs, event related design > that each event last for about 4 seconds and the total > experiment time is 328 seconds( at TR=2 is equal to 164 TRs) > > My computer is a MAC with 4 gb of ram. and I am running > freesurfer 4.5. I have ran similar analysis on the same number > of runs but much longer events (12 sec) before and have not > had a problem. This is the first time I am analyzing data for > this particular experiment though. > Here is the error line that I get: > > mri_fwhm(2138) malloc: *** mmap(size=16777216) failed (error > code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIalloc(70, 70, 33): could not allocate 19600 bytes for > 49364th slice > > voxelvolume 35.3062 mm3 > Loading mask > > /Users/maryam/mri-space/studies/FHPDM/unpackdata/110821_xu_FHPDM_02/bold/FHPDM_noauto/mask.nii > Search region is 60647 voxels = 2141216.616840 mm3 > Polynomial detrending, order = 0 > Detrending > Cannot allocate memory > [dhcp-0170571539-df-00:st > > Can anyone help? > Thanks, > Maryam > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > > > 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 gr...@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 ------------------------------ Message: 12 Date: Mon, 29 Aug 2011 11:38:37 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Correlation cortical thickness and lgi To: dolphin...@aol.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <4e5bb27d.9030...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed If you want to do a vertex-by-vertex analysis, then you can't use QDEC. You'll have to run mri_glmfit manually and use the --pvr option (Per-Vertex Regressor). doug dolphin...@aol.com wrote: > Dear freesurfer experts, > > I have finsihed my lgi analyzes with qdec. > > In the next step I want to make a correlation between lgi and cortical > thickness. Is this possible with qdec and if it is how can I do that? > > Best regards and thanks a lot. > > > Daniel Klein > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 90, Issue 93 ****************************************** _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
