[Freesurfer] Fwd: transforms/talairach.xfm ***FAILED***
Dear Freesurfers, I haven't been able to run recon-all in a set of subjects. All them stop at the point of the talairach transform verification. I uploaded one of the files here (5.3MB): http://dl.getdropbox.com/u/74925/20070404.nii.zip For that volume, the transform.xfm file looked indeed odd (m22=7.2??): 1.39488649 0.08332049 0.01164643 3.51684260 -0.14383204 7.20834160 -2.21084833 11.16247082 -0.16614650 1.02134335 1.85208952 -45.74753189 Using flirt (flirt -in 20070404.nii -ref MNI152_T1_1mm -out 20070404trans.nii -omat 20070404trans.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear), the transformation was: 1.05366 -0.050378 0.0606504 4.05766 0.0446432 1.09476 0.1321 -28.652 -0.058117 -0.180136 1.09158 31.7066 0 0 0 1 The voxel size of the volume is 1.17x1.17x1.2, so it shouldn't be a problem of resolution. When I converted the volume to mgz (mri_convert 20070404.nii mri/orig/001.mgz), the orientation was wrong; but changing it using the Volume Tools in tkmedit did not alter the outcome... Finally, I also used the --notal-check switch in recon-all, but then the script failed before completing skull stripping... thank you very much in advance for your help! roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: transforms/talairach.xfm ***FAILED***
Hi Nick and Bruce, thank you for your help. Now everything's working :) first I tried just the -cw256 flag and it didn't work, but then I erased all the old transformation files and volumes created by freesurfer, and everything went fine... and yes, the orientation is correct. thanks again! roberto On Sat, Feb 7, 2009 at 3:37 PM, Bruce Fischl wrote: > Hi Roberto, > > when you bring up the volume does it appear correctly in tkmedit? That is, > is the coronal view really coronal, etc? > > Bruce > On Fri, 6 Feb 2009, roberto toro wrote: > >> Dear Freesurfers, >> >> I haven't been able to run recon-all in a set of subjects. All them >> stop at the point of the talairach transform verification. I uploaded >> one of the files here (5.3MB): >> http://dl.getdropbox.com/u/74925/20070404.nii.zip >> >> For that volume, the transform.xfm file looked indeed odd (m22=7.2??): >> >> 1.39488649 0.08332049 0.01164643 3.51684260 >> -0.14383204 7.20834160 -2.21084833 11.16247082 >> -0.16614650 1.02134335 1.85208952 -45.74753189 >> >> Using flirt (flirt -in 20070404.nii -ref MNI152_T1_1mm -out >> 20070404trans.nii -omat 20070404trans.mat -bins 256 -cost corratio >> -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp >> trilinear), the transformation was: >> >> 1.05366 -0.050378 0.0606504 4.05766 >> 0.0446432 1.09476 0.1321 -28.652 >> -0.058117 -0.180136 1.09158 31.7066 >> 0 0 0 1 >> >> The voxel size of the volume is 1.17x1.17x1.2, so it shouldn't be a >> problem of resolution. >> >> When I converted the volume to mgz (mri_convert 20070404.nii >> mri/orig/001.mgz), the orientation was wrong; but changing it using >> the Volume Tools in tkmedit did not alter the outcome... >> >> Finally, I also used the --notal-check switch in recon-all, but then >> the script failed before completing skull stripping... >> >> thank you very much in advance for your help! >> >> roberto >> >> ___ >> 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
Re: [Freesurfer] Surface area and curvature
this reference may be relevant: Discrete Differential-Geometry Operators for Triangulated 2-Manifolds (Mark Meyer, Mathieu Desbrun, Peter Schröder and Alan H. Barr), VisMath 2002 the pdf is available at: www.multires.caltech.edu/pubs cheers, roberto On Wed, Apr 29, 2009 at 9:17 PM, Richard Frye wrote: > > What is the best reference regarding the calculation of surface area and > surface curvature and are there any studies looking at the reliability of > these measures? > Thanks > > Best Wishes, > > Richard E. Frye, M.D., Ph.D., F.A.A.P. > Assistant Professor of Pediatrics and Neurology > University of Texas Medical School at Houston > 7000 Fannin -- UCT 2478 > Houston, TX 77030 > Office: 713-500-3245 > e-mail: richard.f...@gmail.com > > ___ > 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
[Freesurfer] grey/white
Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] grey/white
Thank you Bruce! I will try sampling 1mm above and bellow the surface using mri_vol2surf --projdist mmdist -1 and --projdist mmdist 1, and trilinear interpolation. Should also check that I'm not sampling beyond the grey matter... roberto On Mon, Jun 1, 2009 at 5:49 PM, Bruce Fischl wrote: > Hi Roberto, > you are probably better off using the surfaces for this. You can sample > inside and outside the gray/white surface and compute the contrast that way > using mri_vol2surf. > > cheers, > Bruce > > On Mon, 1 Jun 2009, roberto toro wrote: > >> Dear Freesurfers, >> Reading the surface segmentation paper, Dale et al 1999, it says >> that in freesurfer the grey/white matter boundary is detected first >> based on voxel intensity, and then by fitting locally a plane of list >> variance. Is there a way to use that data to assess how clear cut the >> grey/white border is? For example, to distinguish the superior >> temporal gyrus, which has often a very distinct GM/WM border, from the >> precentral gyrus, which is often more blurry? >> thank you in advance! >> roberto >> ___ >> 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
Re: [Freesurfer] grey/white
Hi Doug, I can't find the script in my version of freesurfer (freesurfer-Darwin-leopard-i686-stable-pub-v4.2.0) does it also work by sampling above and below the white matter surface? thanks, roberto On Mon, Jun 1, 2009 at 6:00 PM, Douglas N Greve wrote: > There's a script called pctsurfcon which will compute the percent gray/white > contrast at each vertex on the surface. > > doug > > Bruce Fischl wrote: >> >> Hi Roberto, >> you are probably better off using the surfaces for this. You can sample >> inside and outside the gray/white surface and compute the contrast that way >> using mri_vol2surf. >> >> cheers, >> Bruce >> >> On Mon, 1 Jun 2009, roberto toro wrote: >> >>> Dear Freesurfers, >>> Reading the surface segmentation paper, Dale et al 1999, it says >>> that in freesurfer the grey/white matter boundary is detected first >>> based on voxel intensity, and then by fitting locally a plane of list >>> variance. Is there a way to use that data to assess how clear cut the >>> grey/white border is? For example, to distinguish the superior >>> temporal gyrus, which has often a very distinct GM/WM border, from the >>> precentral gyrus, which is often more blurry? >>> thank you in advance! >>> roberto >>> ___ >>> 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 >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] New release, v4.4.0 on 64 bit : talairach_afd error
Hi Roman, did you check with tkregister2 what the transforms look like? (use tkregister2 --mgz --s mySubjectID --fstal) cheers, roberto On Wed, Jun 17, 2009 at 8:37 AM, romain valabregue < romain.valabre...@chups.jussieu.fr> wrote: > Hello > > I tried this new relase on 20 subject and I get the same error > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0001, pval=0. < threshold=0.0050) > Linux pclx16 2.6.23.1-42.fc8 #1 SMP Tue Oct 30 13:18:33 EDT 2007 x86_64 > x86_64 x86_64 GNU/Linux > > but it works ok with the 32 version. > Is it a problem of my installation ? > > Thanks > > Romain > > > > ___ > 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
Re: [Freesurfer] frontal gray matter and frontal white matter volumes
That will not be able to separate the only frontal WM from the rest of the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with an atlas of the lobes (that covers WM and GM) for that kind of job roberto On Tue, Aug 18, 2009 at 9:24 PM, Douglas N Greve wrote: > You can get the WM from our white matter segmentation (wmparc.mgz and > stats table wmparc.stats). You'd need to pick the cortical labels that > you want to define as the "frontal lobes". You should create a binary > mask with mri_binarize, passing the indices of the segments you want to > use with the --match option, then load the mask in tkmedit to see > whether it is what you expect. You can do a similar thing with the gray > matter, but you can get the volumes from the ?h.aparc.astats > > doug > > Jared Price wrote: >> Hi freesurfer gurus, >> We are doing some freesurfer processing for a collaborating lab and the >> PI has asked us for a measure of gray matter volume and a measure of >> white matter volume, both of which need to be specific to just the >> frontal lobes. Does anyone know of a simple, and accurate, way of >> acquiring these measures from freesurfer? >> Thanks. >> Jared >> >> ___ >> 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > 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
Re: [Freesurfer] frontal gray matter and frontal white matter volumes
fantastic! I didn't know of that feature :) thanks, roberto On Wed, Aug 19, 2009 at 4:07 PM, Bruce Fischl wrote: > actually, Doug's wm parcellation tool should be able to parcel out the > frontal white matter from a lobar segmentation. > > cheers > Bruce > On Wed, 19 Aug 2009, roberto toro wrote: > >> That will not be able to separate the only frontal WM from the rest of >> the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with >> an atlas of the lobes (that covers WM and GM) for that kind of job >> >> roberto >> >> On Tue, Aug 18, 2009 at 9:24 PM, Douglas N >> Greve wrote: >>> >>> You can get the WM from our white matter segmentation (wmparc.mgz and >>> stats table wmparc.stats). You'd need to pick the cortical labels that >>> you want to define as the "frontal lobes". You should create a binary >>> mask with mri_binarize, passing the indices of the segments you want to >>> use with the --match option, then load the mask in tkmedit to see >>> whether it is what you expect. You can do a similar thing with the gray >>> matter, but you can get the volumes from the ?h.aparc.astats >>> >>> doug >>> >>> Jared Price wrote: >>>> >>>> Hi freesurfer gurus, >>>> We are doing some freesurfer processing for a collaborating lab and the >>>> PI has asked us for a measure of gray matter volume and a measure of >>>> white matter volume, both of which need to be specific to just the >>>> frontal lobes. Does anyone know of a simple, and accurate, way of >>>> acquiring these measures from freesurfer? >>>> Thanks. >>>> Jared >>>> >>>> ___ >>>> 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 >>> >>> In order to help us help you, please follow the steps in: >>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> >>> ___ >>> 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 >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] crop neck
Dear Freesurfers, I have some mri volumes with too much neck, and I would like to crop them. I have been trying with mri_convert --cropsize, but it does not work. It seems that --cropsize is cropping around the center, so when I cut the neck I also cut the top of the head... I tried changing the center using -ic, but it doesn't seem to do anything... thank you in advance, roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] colin27 skullstrip problem
Hello, I am also very interested in having a copy of colin27's FS data! roberto On Tue, Dec 1, 2009 at 2:53 AM, Bruce Fischl wrote: > Hi Mishkin, > > yes, I generates surfaces for the Colin27 dataset. It actually doesn't > have great gray/white contrast, probably due to differential B0 > distortions in the different sessions. Maybe we should include it as part > of our release? In any case, I can send it to you. > > cheers > Bruce > > > On Mon, 30 Nov 2009, Mishkin > Derakhshan wrote: > >> Hi, >> I'm trying to get the surfaces for the colin27 brain that is included >> with the mni packages. Has anyone managed to do this before? >> >> I thought I would have an easy time given that this linear average of >> 27 brains has very good signal to noise and nice contrasts, and even >> though recon-all completes without errors, the surfaces are way off. >> The main problem appears to be the skull stripping. >> >> My input volume is here: >> http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz >> >> These are the steps I took and where I think the problem might be: >> 1. gunzip colin27_t1_tal_lin.mnc.gz >> 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 >> 3. tkmedit conlin27 orig/001.mgz >> At this point the image the brightness and contrast levels of the >> image look very washed out. I am hoping this is only a display issue >> and that the underlying intensities of the image are still intact and >> is not a result of something going on in mri_convert, but maybe this >> is what is causing the downstream skull strip to fail. Can someone >> take a look? >> http://opus.bic.mni.mcgill.ca/public/001.mgz >> 4. recon-all -autorecon1 -subjid colin27 >> 5. tkregister2 --mgz --s colin27 --fstal >> Results are not perfect but reasonable ie. about the same as many >> other runs I've had that have passed so I don't think it is the >> registration. >> 6. tkmedit colin27 brainmask.mgz -aux T1.mgz >> It is clear this is where the problem is. >> http://opus.bic.mni.mcgill.ca/public/brainmask.mgz >> http://opus.bic.mni.mcgill.ca/public/T1.mgz >> 7. I have subsequently tried: >> recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid >> colin27 (basically extract the entire head) >> recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid >> colin27 (basically extracted the entire head) >> recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted >> the brain, but left large chunks of skull) >> recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted >> the brain, but left quite a few chunks of skull) >> >> I'm concerned that the -wsthresh is so low in order to get a >> reasonable result, that's why I think the intensities might be off >> (see step 3). >> >> I'm re-running -autorecon2/3 now to see if the surfaces are better, >> but if someone could take a look at my input file and the converted >> 001.mgz to see if it isn't a problem there it would be much >> appreciated. >> >> thanks, >> mishkin >> ___ >> 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] A basic question about visualising data
Just a guess: if you are using a Mac, the path for the directory should be something like /Users/yourname/Desktop/ etc. instead of just /Desktop/ etc. hope this helps, roberto On Thu, Feb 18, 2010 at 10:15 PM, Douglas N Greve wrote: > The SUBJECTS_DIR is where you want the result of the freesurfer analysis > to go. This is usually not /usr/local/freesurfer/subjects because you > usually don't have write permissions. Try setting it to a place where > you have some space, then run recon-all something like > > recon-all -s yoursubject -i /Desktop/Allimages/MRIscan... and the full > path till DICOM/dicomfile > > the output will then be in $SUBJECTS_DIR/yoursubject > > doug > > Janani Dhinakaran wrote: >> My data is on the desktop. The subjects directory is under >> usr/local/freesurfer/subjects. >> I tried setting desktop as SUBJECTS_DIR by using 'export >> SUBJECTS_DIR="/Desktop/Allimages/MRIscan... and the full path till >> DICOM" ' but apparently it didn't work because when I tried to run >> recon, it says >> SUBJECTS_DIR /Desktop/Allimages/MRIscan/.../DICOM does not exist >> >> If I can't get SUBJECTS_DIR to change to Desktop path, how can I >> introduce my data into usr/local/freesurfer path? >> I notice Bert has everything in order. If I mkdir Mine in SUBJECTS_DIR >> and put my MRI files in there , will it work? >> >> >> ___ >> 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Volumes of four major cortical lobes
Hi, I have an label volume of the four lobes, right and left hemispheres, plus diencephalon, brain stem and cerebellum (drawn over Colin27). I would be happy to send it to you, and very interested in receiving any comments (in particular, the occipital-parietal-temporal junction is quite tricky). best, roberto On Tue, Mar 2, 2010 at 10:16 PM, Bruce Fischl wrote: > David Salat was going to draw these, but I'm not sure if he ever did. > David? > > > On Wed, 3 Mar 2010, caoaize wrote: > > >> Hi, Bruce, >> >> >> >> We want calculate the four major cortical lobe volumes, i.e. frontal, >> parietal, temporal, and occipital, to see the relationship between them and >> some ROIs. I did fully run recon-all, but not clear which file should be >> used and what cortical areas should be included in these four lobes >> seperatively. May you please give me some instruction? Thanks. >> >> >> >> Aize >> >> _ >> MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ >> http://kaba.msn.com.cn/?k=1 > > > ___ > 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. > > ___ 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.
[Freesurfer] Command for making a picture
hello, Is there a command line tool for making a picture of a surface with labels superimposed? thanks in advance! roberto ___ 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.
[Freesurfer] vertex coordinates / volume coordinates
Hello, I have a C code that reads FS surfaces and does some processing on them. I would like to map this back to the original MRI volume. Googling around I found that vertex coordinates may correspond to coordinates in the COR volume but COR volumes are now deprecatedso two questions: 1. what is the relationship between vertex coordinates and volume coordinates? 2. is there a special volume where vertex coordinates just map volume coordinates? thank you very much! roberto This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] vertex coordinates / volume coordinates + Folding Index
Hi, one more question: 3. can I use mris_curvature to compute the folding index only for a particular label (and not allways for the complete hemisphere)? I've been using mris_curvature path_to_mesh/lh.white, to get ICI and FI, and -min - max -w to get the min, max, gaussian and mean curvatures. thanks again! roberto This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] vertex coordinates / volume coordinates + Folding Index
On 25 Nov 2006, at 15:08, Bruce Fischl wrote: Hi Roberto, no, nothing built in, but you could always mask it to the label in matlab. I guess we could provide an mris_mask utility if that would be helpful. thanks Bruce, I've been trying to compute the folding index (FI) based on the max/ min files generated by mris_curvature, but I'm obtaining different values . When I load a surface the np vertices are in p[], the nt triangles in t[], then max/min curvatures are in max[] and min[] respectively. This is what I'm doing next FI=0; for(i=0;ifor every triangle the algorithm computes the value of FI at the vertices and integrates over the triangle. The values I'm obtaining are larger than those reported by mris_curvature (4585 instead of 2537, or 4408 instead of 2750, for example). Furthermore, in the paper where Van Essen introduces the FI, he reports a value of 510 for a hemisphere of the Visible Man! Is there something tha I'm missing? thanks in advance! roberto This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] smoothing thickness
Hi! I'm trying to smooth thickness data using mri_surf2surf. The thickness vectors are mapped onto ico7, and I would like to smooth the thickness there (ico7). But when I add the --fwhm option to mri_surf2surf (equivalent to --fwhm-trg), mris_surf2surf looks for a real subject called "ico" (ie $SUBJECTS_DIR/ico/surf/lh.white) instead of the oversampled icosahedron... This is the type of command I'm using (with freesurfer-Darwin-tiger- stable-pub-v3.0.2, mac os 10.4.8): mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness -- src_type curv --trgsubject ico --trgicoorder 7 --fwhm 30 -- trgsurfval /Users/roberto/Desktop/bertest-lh.mgh --trg_type mgh without --fwhm everything goes ok, but including it produces at the end an error like this: (...) MRISread(/freesurfer/subjects/ico/surf/lh.white): could not open file No such file or directory ERROR: could not read /freesurfer/subjects/ico/surf/lh.white It looks for a subject ico. I think that I could use --fwhm-src to do the smoothing on bert/ lh.white, but then different brain sizes would have different fwhm values after mapped over ico7... Is there a way of giving an absolute path to the surface used for smoothing? (to /Applications/freesurfer/lib/bem/ic7.tri). Am I doing something wrong? A last little thing how is the number of iterations (à la -- nsmooth) computed from the given fwhm? thanks in advance! (and have a happy new year :) roberto This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] brain size
Hello, I would like to measure the size of a bunch of surface reconstructions (ventral-dorsal, posterior-anterior, medial-lateral), but I wouldn't like that the different orientation of the subject's head may affect the measurements (if the head is tilted, for example). Is there a simple way of doing this? ... otherwise, which of the talairach transforms should I use to recover the orientation of the brain (among talairach.xfm, .lta, etc) thank you very much in advance! roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] brain size
On 14 Mar 2007, at 00:28, Bruce Fischl wrote: Hi Roberto, the tal xforms will have scaling normalization in them, which I assume you don't want? Bruce Hi Bruce, you are right. I would like to know only the orientation of the head and then compute the hemisphere size from the reconstructions. If I compute the eigenvalues of the rotation part of the matrix (the first 3 columns) I can recover the scaling factors, and then I should be able to get the rotation matrix by dividing the rows by their corresponding eigenvalue, isn't it? thanks for your help, roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsaverage and mni305
Hi, I'm trying to figure out how to go from a coordinate in mni305 space to a vertex index in fsaverage. In the README file that comes with fsaverage it's stated that surface coordinates are in talairach space, so they align with the MNI305 volume (and the talairach.xfm is the identity). But when I select a vertex in fsaverage (using tksurfer) I have three different coordinates. For example, vertex 62176 gives 1. the actual 3d coordinate of the vertex in the mesh -2.4876, -5.1338, 10.0494 2. the RAS coordinate -1.97, -4.48, 10.51 3. the Talairach coordinate (which I suppose are in fact MNI305 coordinates..) -1.95, -3.85, 9.87 this doesn't seem to be just a translation because when I compare actual 3d and talairach, the difference between the x coord (for example) of different vertices is not the same... how does tksurfer convert to talairach coordinates? thanks in advance! roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage and mni305
On 3/30/07, Doug Greve <[EMAIL PROTECTED]> wrote: What do you mean by the "actual 3d coordiantes in the mesh"? The RAS coord is the MNI305 coord. You can have tksurfer display it with View->Information->VertexMNITal. In this case it will be the same as the RAS. The Talairach coord is the MNI coord adjusted with Mathew Brett's algorithm, which is more than just a translation. doug Hi Doug, Thanks for the clarification. If you load fsaverage in tksurfer and click in a vertex, the interface will display the RAS and talairach coordinates, but you can read a different set of coordinates in the terminal window (X11). When I read fsaverage lh.pial directly with C code, the coordinates of the vertices are these coordinates that tksurfer displays in the terminal window., that's why I call them the "actual 3d coordinates in the mesh". tksurfer has to be using a transformation to convert the actual coordinates into the RAS, MNI or talairach coordinates displayed in the interface. this is an example of tksurfer display for vertex 98832: % surfer: dmin=0.2498, vno=98832, x=50.3003, y=14.1151, z=-32.7580 % surfer: curv=0.00, fs=0.00 % surfer: val=0.00, val2=0.00 % surfer: amp=0.00, angle=0.00 deg (0.00) % surfer: vertex 98832 marked (curv=0.00, stat=0.00) x = (50.3, 14.1, -32.8), n = (0.4, 0.9, -0.2). % The MNI Talairach coordinates for the same vertex are (48.08 11.30 -31.69) So, I would like to know which is the transformation matrix used to go from the actual to the MNI coordinates. thanks in advance! roberto On Fri, 30 Mar 2007, roberto toro wrote: > Hi, > > I'm trying to figure out how to go from a coordinate in mni305 space > to a vertex index in fsaverage. In the README file that comes with > fsaverage it's stated that surface coordinates are in talairach space, > so they align with the MNI305 volume (and the talairach.xfm is the > identity). But when I select a vertex in fsaverage (using tksurfer) I > have three different coordinates. For example, vertex 62176 gives > > 1. the actual 3d coordinate of the vertex in the mesh > -2.4876, -5.1338, 10.0494 > 2. the RAS coordinate > -1.97, -4.48, 10.51 > 3. the Talairach coordinate (which I suppose are in fact MNI305 > coordinates..) >-1.95, -3.85, 9.87 > > this doesn't seem to be just a translation because when I compare > actual 3d and talairach, the difference between the x coord (for > example) of different vertices is not the same... > > how does tksurfer convert to talairach coordinates? > > > thanks in advance! > > roberto > ___ > 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] convert mnc->analyze->mgz
Hi, The problem was Neurolens' display of .mgz files. mri_info of P.mnc and P.mgz is the same, and the display in Scuba is correct. Thanks Bruce and Doug you for your help! (Note for Olivier: Scuba's display [at least in my computer] is radiological, i.e., negative X coordinates are to the right) roberto On 9/28/07, Bruce Fischl <[EMAIL PROTECTED]> wrote: > p.s. and how did you create the .mnc in the first place? The safest thing > by far is to go right from the dicoms. Does the .mnc show up properly in > tkmedit and/or scuba? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] license
Hi, I asked (twice, using [EMAIL PROTECTED]) for a license to use freesurfer the last week and haven't had any answer is this delay normal? thanks in advance! roberto This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Output of mris_anatomical_stats
Hi, I found the reference to D. Van Essen's paper: Van Essen, D and Drury, H (1997) "Structural and functional analyses of human cerebral cortex using a surface-based atlas" J Neurosci 17 (18):7079-7102 and the folding index is defined (from that paper) as "the integral of the product of the maximum principal curvature and the difference between maximum and minimum curvature, divided by 4*pi", ie, FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA is this what freesurfer is using? thanks, roberto On 8 Feb 2006, at 16:39, Bruce Fischl wrote: the Gaussian and mean curvature are differential geometric measures and you can find them in any standard textbook (e.g. do Carmo). The folding indices come from one of David Van Essen's papers - sorry, I don't have the reference offhand, but it shouldn't be too hard to find. Bruce On Wed, 8 Feb 2006, Goradia, Dhruman D wrote: Hi, The output of function "mris_anatomical_stats" contains the following measurements: integrated rectified mean curvature, integrated rectified Gaussian curvature, folding index and intrinsic curvature index. Can someone please give me a brief explanation of what these measurements are or suggest some reading material. -Dhruman Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 Phone: 412-586-9017 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Output of mris_anatomical_stats
three more quick questions: (1). do you know of a paper using the folding index successfully? (2). is it possible to access k_max and k_min for every vertex? (3). is it possible to access the mean curvature and the gaussian curvature for every vertex? (... to obtain (2)...) thanks, roberto On 15 Feb 2006, at 17:28, Bruce Fischl wrote: yes. On Wed, 15 Feb 2006, Roberto Toro wrote: Hi, I found the reference to D. Van Essen's paper: Van Essen, D and Drury, H (1997) "Structural and functional analyses of human cerebral cortex using a surface-based atlas" J Neurosci 17(18):7079-7102 and the folding index is defined (from that paper) as "the integral of the product of the maximum principal curvature and the difference between maximum and minimum curvature, divided by 4*pi", ie, FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA is this what freesurfer is using? thanks, roberto On 8 Feb 2006, at 16:39, Bruce Fischl wrote: the Gaussian and mean curvature are differential geometric measures and you can find them in any standard textbook (e.g. do Carmo). The folding indices come from one of David Van Essen's papers - sorry, I don't have the reference offhand, but it shouldn't be too hard to find. Bruce On Wed, 8 Feb 2006, Goradia, Dhruman D wrote: Hi, The output of function "mris_anatomical_stats" contains the following measurements: integrated rectified mean curvature, integrated rectified Gaussian curvature, folding index and intrinsic curvature index. Can someone please give me a brief explanation of what these measurements are or suggest some reading material. -Dhruman Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 Phone: 412-586-9017 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
