Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Selxavg3 sets high activation to zero
by Qi Zhu 22 Dec '11

22 Dec '11

Dear Doug, I used selxavg3-sess in freesurfer 5.0 to run a big GLM analysis on a monkey data set containing 147 runs. But When I check the results, I found that in the voxels where the t-values should be very high were turned out to have a value of zero. I checked the brainmask, the ces and the cesvar values, they all look fine. It seems that only the ces values in these voxels are a bit high compared to the nearby normal voxels (e.g. 1.17 (ces)/0.00048(cesvar) compared to 0.74/0.00040 in a nearby normal voxel). And it seems that not only me have this problem (similar problem posted in the mailinglist before. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13789.html) Do you know what the problem would be and how to solve it? Thanks very much for your help. Attached please find an image of the problem. Best, Qi Zhu, PostDoc Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium)

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error when using mri_sur2vol: has many more faces than vertices!
by Minjie Wu 21 Dec '11

21 Dec '11

Dear Surfer, I was trying to project a DTI FA image onto the T1 WM surface (for now), and eventually into the fsaverage as in a recent paper: Phillips OR, Nuechterlein KH, Asarnow RF, Clark KA, Cabeen R, Yang Y, et al. Mapping corticocortical structural integrity in schizophrenia and effects of genetic liability. Biological psychiatry. 2011;70(7):680-9. 1. align the lowb.nii.gz from DTI data to T1.mgz image using bbregister to create the register.dat file. bbregister --s 20808 --mov lowb.nii.gz --reg lowb2orig.dat --dti --init-fsl 2. project FA into surface space mri_vol2surf --mov dtifit_FA.nii.gz --reg lowb2orig.dat --hemi rh --o rh.fa.vol2surf2.w --projfrac 0 --interp nearest --surf white --out_type paint Here is the error message when I tried to check the surface in subject T1 space [Minjie-Wus-Mac-Pro:subjects/20808/dmri] minjiewu% tksurfer 20808 rh fa.vol2surf2.w subject is 20808 hemi is rh surface is fa.vol2surf2.w surfer: current subjects dir: /Volumes/Lion/projects/surface/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Volumes/Lion/projects/surface/subjects/20808/dmri checking for nofix files in 'fa.vol2surf2.w' Reading image info (/Volumes/Lion/projects/surface/subjects/20808) Reading /Volumes/Lion/projects/surface/subjects/20808/mri/orig.mgz surfer: Reading header info from /Volumes/Lion/projects/surface/subjects/20808/mri/orig.mgz nquads=14348288, nvertices=1 ERROR: MRISread: file '/Volumes/Lion/projects/surface/subjects/20808/surf/rh.fa.vol2surf2.w' has many more faces than vertices! Probably trying to use a scalar data file as a surfa Thank you very much for your help. Minjie

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Different versions of FreeSurfer
by Lara Wierenga 21 Dec '11

21 Dec '11

Hi everyone, In our lab we use different versions of FreeSurfer on different computers. Since we share computers with other labs some updates are out of our control. We'd like to edit scans in FreeSurfer V4.5 and V5.1 and thereafter run recon -all in V5.0. Is it important to use the same versions for editing and running recon -all? Kind regards, Lara ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Re: [Freesurfer] Reliability and accuracy of Freesurfer
by Thomas Yeo 20 Dec '11

20 Dec '11

Hi Donald, With regards to longitudinal analysis, I am not as familiar with the issue you are mentioning. Perhaps some other person on the list can comment. With regards to your other comments, I think your reading is correct. However, I should mention that the reported accuracies *really* depends on what structures (cytoarchitectural areas versus functional areas versus macro-anatomical areas) and what accuracy measures (e.g., volume of structures versus overlap of structures, etc.) you are looking at. You probably already know this, but I will elaborate anyhow: The references by Fischl, Hinds, Yeo (from the previous email) are talking about the accuracy of localizing cortical cytoarchitectural and functional areas. Since freesurfer (and most other software packages) uses macro-anatomy (e.g., sulci, gyri, MR intensity) for processing (e.g, alignment of subjects, segmentation) and macro-anatomy does not predict function/cytoarchitecture completely, we expect the accuracy for cytoarchitectural and functional areas to be bounded by the predictive relationship between macro-anatomy and function/cytoarchitecture. In particular, V1 turns out to be very well-predicted by the cortical folds (calcarine), and so when we align sulci/gyri across subjects, there's very small errors in localizing the boundaries of V1. On the other hand, MT turns out to be not as well predicted by the cortical folds, thus the accuracy of MT alignment after freesurfer processing is lower. Conversely, for macroanatomical structures (stuff that is visibly seen in MR) like superior temporal sulcus and the thalamus (in aparc+aseg), we expect the accuracy to be much higher. Even then the accuracy for individual structures may vary. For example, thalamus is more accurately segmented than the amygdala. For individual thalamic nuclei, which are less visible (if not invisible!) in 3T MR, the accuracy is probably much less. You also mentioned that some areas would be larger than the true underlying labels for certain individuals, and some would be smaller. That is certainly the case, but I don't think it is explicitly shown in the papers by Fischl, Hinds, Yeo (although you can probably infer that from other papers listed in the links I sent you). As an extreme example, in one of the experiments in Yeo et al. 2010, "ground truth" functional MT+ for each subject was defined by thresholding the fMRI activation map using a size threshold. Therefore, the way the "ground truth" was set up in that particular experiment, any errors in predicted MT+ is due to errors in predicting MT+ location, rather than size difference. On the other hand, if you look at Figure 3 in Fischl et al, 2002 (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain), there is no obvious systemic differences between volumetric measurement of structures obtained by manual labeling versus automated segmentation in FreeSurfer (circa 2002). --Thomas On Tue, Dec 20, 2011 at 2:05 AM, MCLAREN, Donald <mclaren.donald(a)gmail.com> wrote: > Excellent references. From my reading of these papers, the boundaries of an > individuals subject can shift by up to ~7mm. Meaning that some areas would > be largers than the standard labels and others would be smaller. > > Is my reading of this correct? > > In longitudinal analysis of regional volume measures, do you know of anyway > to correct for the potential correlation induced by the mislabelling of > nodes that go into each regional volume? > > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Postdoctoral Research Fellow, GRECC, Bedford VA > Research Fellow, Department of Neurology, Massachusetts General Hospital and > Harvard Medical School > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at (773) > 406-2464 or email. > > > > On Sat, Dec 17, 2011 at 9:28 PM, Thomas Yeo <ythomas(a)csail.mit.edu> wrote: >> >> There's some reference of test-retest reliability here: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, >> although I doubt it's complete. There's also a section on the wiki of >> paper evaluating freesurfer: >> http://surfer.nmr.mgh.harvard.edu/fswiki/#Articles.evaluations >> >> What I know off hand is that for cytoarchitectonics and some function >> (like MT+ and V1), freesurfer registration accuracy ranges from 2-3mm >> (V1) to 6-12mm (BA44, BA45, MT+). BA2, BA6, etc in between. Here's the >> references: >> >> Fischl et al. 2008 Cortical folding patterns and predicting >> cytoarchitecture >> Hinds et al. 2008 Accurate prediction of V1 location from cortical >> folds in a surface coordinate system >> Yeo et al. 2008 Spherical Demons: Fast Diffeomorphic Landmark-Free >> Surface Registration >> Yeo et al. 2010 Learning Task-Optimal Registration Cost Functions for >> Localizing Cytoarchitecture and Function in the Cerebral Cortex >> >> --Thomas >> >> On Sat, Dec 17, 2011 at 5:49 AM, MCLAREN, Donald >> <mclaren.donald(a)gmail.com> wrote: >> > I've looked through a number of freesurfer papers, but haven't been able >> > to >> > find the answer to what I am looking for and was hoping someone had the >> > references easily available. >> > >> > (1) What is the reliability of regional volumes generated from >> > freesurfer >> > over time? >> > >> > (2) What is the accuracy of labels for these volumes from subject to >> > subject >> > (e.g. how close are the freesurfer labels to cytoarchitecture or >> > manually >> > drawing the labels)? >> > >> > >> > Best Regards, Donald McLaren >> > ================= >> > D.G. McLaren, Ph.D. >> > Postdoctoral Research Fellow, GRECC, Bedford VA >> > Research Fellow, Department of Neurology, Massachusetts General Hospital >> > and >> > Harvard Medical School >> > Office: (773) 406-2464 >> > ===================== >> > This e-mail contains CONFIDENTIAL INFORMATION which may contain >> > PROTECTED >> > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >> > intended only for the use of the individual or entity named above. If >> > the >> > reader of the e-mail is not the intended recipient or the employee or >> > agent >> > responsible for delivering it to the intended recipient, you are hereby >> > notified that you are in possession of confidential and privileged >> > information. Any unauthorized use, disclosure, copying or the taking of >> > any >> > action in reliance on the contents of this information is strictly >> > prohibited and may be unlawful. If you have received this e-mail >> > unintentionally, please immediately notify the sender via telephone at >> > (773) >> > 406-2464 or email. >> > >> > >> > _______________________________________________ >> > 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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Downsampling pial surfaces and mapping output to fsaverage6
by Ecker, Christine 20 Dec '11

20 Dec '11

Dear FreeSurfer Experts, I would like to down-sample the pial surface of individual subjects to have the same number of vertices as fsaverage6. I have done so using: mri_surf2surf --hemi lh --srcsubject 'subjectID' --sval-xyz pial --trgsubject fsaverage6 --trgicoorder 6 --trgsurfval 'outputfilename' This worked well and the pial output surface has 40962 vertices. I now have an overlay vector, which was computed on the down-sampled pial surface, which I would like to map back to fsaverage6 in order to perform a group comparison. Please could you advise on how to do this as all scripts I am aware of (e.g. mris_preproc) use sphere.reg, which has ~150000 vertices. Many thanks, Christine

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recon-all results
by LAOUCHEDI MAKHLOUF 20 Dec '11

20 Dec '11

hi everyone i run recon-all on some datasets using freesurfer version 5.1. Instead of having aparc.a2009s+aseg.mgz at the end of recon-all, i had aparc.a2005s+aseg.mgz. what to do to have the good dataset (2009 instead of 2005) thanks

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Convert aparc to vtk
by Martijn Steenwijk 20 Dec '11

20 Dec '11

Dear all, I would like to convert Freesurfers cortical parcellations to VTK files (just Freesurfers label index on the resulting polydata is fine). Therefore I run mris_convert --annot aparc.annot lh.pial lh.aparc.vtk This results into reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ERROR: unknown file annot file type specified for output: lh.aparc.vtk Does anyone have an idea about how to get this done? Thanks for replies in advance, Best, Martijn

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Converting V1 labels to nifti
by Anders Hougaard 20 Dec '11

20 Dec '11

Dear Freesurfers, I would like to use V1 labels (created with the Hinds method) for a ROI-based analysis on data analyzed with FSL FEAT using FSL featquery. I have not run a full recon-all segmentation, only recon-all -s subjid -label-v1 I need to convert the labels to nifti volumes while registering to MNI standard space. I guess the right command would be something like mri_label2vol --label lh.v1.predict.label --reg register.dat --hemi lh --subject subject --o lh.v1.predict.label Is there a register.dat from the FSL feat directory that I could use for this? Anything else I need to add? Of course, I would like to keep the resulting volume probabilistic. All the best, Anders

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Opportunity for a research associate in MR imaging
by Direktion, Institut f. Schlaganfall- und Demenzforschung 20 Dec '11

20 Dec '11

The Hospital of the University of Munich, Germany, is one of the largest and most capable university hospitals in Germany and Europe. 45 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research (ISD) is a newly founded institution financed from foundation funds. The activity ranges from basic research to clinical trials (www.isd-muc.de) After completion of the construction phase, the Institute for Stroke and Dementia research will employ, around 100 staff members, graduate students, scholars and foreign scholars. The Institute for Stroke and Dementia Research (ISD) is looking at the earliest opportunity for a Research Associate in MR imaging RESPONSIBILITIES: We are looking for a motivated scientist with methodological expertise in MR imaging and good programming skills (e.g. C, C ++, Pearl, Python, Scripting Languages, Matlab). Knowledge in the collection, processing and analysis of functional and structural MR imaging data and an interest in neuro-scientific questions are desired. REQUIREMENTS: University degree. OFFER: Our Institute offers an excellent multidisciplinary environment (medical scientists, neuro-psychologists, biologists, bioinformaticians, epidemiologists) with modern IT infrastructure and defined times on human MR scanners (1.5T and 3T). A new building with its own small-animal-imaging (micro-PET and -MRI) is currently being built (www.isd-muc.de) The tasks include the establishment of new analytical methods for MRI-data, participation in ongoing research projects and developing of own project ideas. Salary is according to TV-L. The position is limited for two years, extension is desired. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can unfortunately not be refunded. For more information, please contact Mr. Frühauf, Tel.: +49 (0)89 7095 7800 (E-Mail: isd(a)med.uni-muenchen.de) HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Markus A. Frühauf, Managing Director ISD Heiglhofstr. 55 81377 Munich | Germany E-Mail: isd(a)med.uni-muenchen.de

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Use bbregister parameters to transform to EPI geometry
by Michael Waskom 20 Dec '11

20 Dec '11

Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care so much about the epi-anat registration, but what I would like to be able to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slice from one of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample the source voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deep enough for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which is different I think from FSFast terminology so apologies for any confusion.

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