Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

mri_convert sort dicom files??
by Gennan Chen 13 Aug '10

13 Aug '10

Hi! Does mri_convert sort dicom files in a different way for Siemens' dicom file? I have dicom files from GE, Philips and Siemens. They have the same ImagePositionPatient and SliceLocation tags. But volume from Siemens flip in the 3rd dimension? Why is it?? I know it doesn't matter as long as vxl2ras is correct. But I am just curious why this happens only to siemens' dicom? Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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loading surfaces in freeview
by ythomas 13 Aug '10

13 Aug '10

Hi, when I try to load my own generated surfaces in freeview (e.g. generated from cerebellum), I am getting the following printed errors even though it did save out the images I want. Seems like freeview is assuming that ?h.inflated, etc has the same dimensions as the surfaces I am loading. freeview -v mri/norm.mgz:opacity=0.5 -f surf/lh.cerebellum_gm_surf -f surf/rh.cerebellum_gm_surf -ss test.png -slice 128 128 60 mrisReadTriangleFile(surf/lh.white): surface doesn't match surf/ lh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from white mrisReadTriangleFile(surf/lh.pial): surface doesn't match surf/ lh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from pial mrisReadTriangleFile(surf/lh.orig): surface doesn't match surf/ lh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from orig mrisReadTriangleFile(surf/lh.inflated): surface doesn't match surf/ lh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from inflated MRISreadNewCurvature: incompatible vertex number in file surf/lh.curv No such file or directory could not read curvature from curv mrisReadTriangleFile(surf/rh.white): surface doesn't match surf/ rh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from white mrisReadTriangleFile(surf/rh.pial): surface doesn't match surf/ rh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from pial mrisReadTriangleFile(surf/rh.orig): surface doesn't match surf/ rh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from orig mrisReadTriangleFile(surf/rh.inflated): surface doesn't match surf/ rh.cerebellum_gm_surf No such file or directory mrisReadTriangleFile failed. No such file or directory could not load surface from inflated MRISreadNewCurvature: incompatible vertex number in file surf/rh.curv No such file or directory could not read curvature from curv --Thomas

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Re: [Freesurfer] medialorbitofrontal_area
by Michael Waskom 13 Aug '10

13 Aug '10

Hi Jose, If you're using Freesurfer 4.5, the aparcstats2table program has a known bug that causes the columns to be written in a random order. Depending on how you create a database from these files, it could lead to what looks like a large asymmetry, when really you're just comparing columns from different regions. Best, Mike ---------- Forwarded message ---------- From: "Pedro Paulo de Magalhães Oliveira Junior" <ppj(a)netfilter.com.br> To: Jose Soares <zmsoares(a)yahoo.com.br> Date: Fri, 13 Aug 2010 10:01:39 -0300 Subject: Re: [Freesurfer] medialorbitofrontal_area It's not unusual to have asymmetries in some patients. I have seen some myself in AD. Have you checked the segmentation in those areas? --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Fri, Aug 13, 2010 at 07:12, Jose Soares <zmsoares(a)yahoo.com.br> wrote: > Hi all, > > I am doing a study about the medialorbitofrontal, and I am having some > strange area results in a lot of subjects. > > The rh areas are much higher than the lh areas of medialorbitofrontal: Some > examples: > > lh rh > 1714.0 2822.0 1720.02632.0 1728.0 2675.0 1877.02733.0 1498.0 2719.0 > 2067.02542.0 1870.0 2666.0 1554.02263.0 1535.0 2566.0 1794.02392.0 1487.0 > 2547.0 > Why is this happening, any idea? Should I do any correction? > > Thanks for the help, > > Miguel. > > > _______________________________________________ > 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. 2010/8/13 <freesurfer-request(a)nmr.mgh.harvard.edu> > ---------- Forwarded message ---------- > From: "Pedro Paulo de Magalhães Oliveira Junior" <ppj(a)netfilter.com.br> > To: Jose Soares <zmsoares(a)yahoo.com.br> > Date: Fri, 13 Aug 2010 10:01:39 -0300 > Subject: Re: [Freesurfer] medialorbitofrontal_area > It's not unusual to have asymmetries in some patients. I have seen some > myself in AD. Have you checked the segmentation in those areas? > > --------------------------------------------------------------------- > Pedro Paulo de Magalhães Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br > -- For mobile: http://www.netfilter.com.br/mobile > > > > > On Fri, Aug 13, 2010 at 07:12, Jose Soares <zmsoares(a)yahoo.com.br> wrote: > >> Hi all, >> >> I am doing a study about the medialorbitofrontal, and I am having some >> strange area results in a lot of subjects. >> >> The rh areas are much higher than the lh areas of medialorbitofrontal: >> Some examples: >> >> lh rh >> 1714.0 2822.0 1720.0 2632.0 1728.0 2675.0 1877.0 2733.0 1498.0 >> 2719.0 2067.0 2542.0 1870.0 2666.0 1554.0 2263.0 1535.0 2566.0 >> 1794.0 2392.0 1487.0 2547.0 >> Why is this happening, any idea? Should I do any correction? >> >> Thanks for the help, >> >> Miguel. >> >> >> _______________________________________________ >> 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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Error in selxavg3-sess with -sf option
by Shahin 13 Aug '10

13 Aug '10

Hi, I ran the selxavg3-sess with -sf to process a group of 12 sessions (see below). selxavg3-sess -sf Sessid -a Analysis.rh After hours, it finished without any error. The last message was: rawfunc2surf-sess completed then: then/endif not found. But there is no "Analysis.rh" folder in the session folders. When I applied the same command to each indivisual session by: "selxavg3-sess -s Session1 -a Analysis.rh", it works perfectly and generates the Analysis.rh folder. Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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autorecon2
by Mareen Kussatz 13 Aug '10

13 Aug '10

Hi to all, after correcting white matter problems, we saved the wm as aux volume and we tried also to save it as main volume. And than, we started recon-all -autorecon2-wm -subjid (subject file name). The process ends without any error for both conditions but after checking the tkmedit, there weren´t any corrections visible and actually there were no change at all.??? We just want to know if it is a syntax problem or if there is something wrong with the freesurfer itself. thanks and best regards. Mareen Kussatz -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail

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Talairach xform problem
by Tricia Merkley 13 Aug '10

13 Aug '10

Hi Freesurfers, Is there a solution for fixing a bad talairach transform as shown in the attached figures? Recon-all completed without error (with the -notal-check included, v4.5.0), and the output looks pretty good. However I'm concerned that the 'IntraCranialVol' value will be off since it is based on the tal xform. I've tried to fix it as described at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, but to no avail. I'd appreciate any suggestions. Thanks, Tricia

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overlaying surfaces on volumes in freeview
by ythomas 12 Aug '10

12 Aug '10

Hi, when we load a mri volume and a surface at the same time, such as: freeview -v mri/norm.mgz -f surf/lh.white should we expect to see the lh.white surface be on top of the norm.mgz volume? I certainly do not see the surface unless I "unhighlight" the volume. Thanks, Thomas

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activity time course
by Shahin 12 Aug '10

12 Aug '10

Hi, Would you tell me how can I see time-course of activities within one ROI (averaged over voxels) for each experiment condition? Should I use matlab commands? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Coordinates for DTI tractography
by Lena Palaniyappan 12 Aug '10

12 Aug '10

Hi all I want to use a freesurfer parcellation as a seed point in DTI analysis using a non-FSL DTI tractography tool. I have the raw DTI images for around 40 subjects (20 scz 20 controls). From the structural MPRAGEs that correspond to these subjects, I have an average image where I have my defined ROI (which is a freesurfer atlas based parcellation). The ROI has numerous vertices whose MNI coordinates are available to me. Please correct me if I have understood this properly 1. I have to process the raw DTI images to obtain FA/trace images first for each subject 2. each FA/trace image should be registered to the average structural MPRAGE of the group How do I then go on to obtain the coordinates for my label on the DTI space? Many thanks Lena > > _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH 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.

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Transferring surface coordinates to functional data coordinates
by Patrik Ahvenainen 12 Aug '10

12 Aug '10

Dear FreeSurfer experts, For the past few days I have been struggling with how to transform points in FreeSurfer surface coordinates to points in functional data (SPM t-values) coordinates. I can coregister the functional data with FreeSurfer anatomical image using tkregister2. What I'm having trouble with is how to transform FreeSurfer surface coordinates to (any) volume coordinates that can be coregistered with the anatomical image. I have looked at the FreeSurfer wiki page about the coordinates, but I have not been able to understand fully which transformations are needed and where the related matrices are. I believe that the center of the RAS-coordinate systems (mri_info spmT_0001.img --cras; mri_info wm.mgz --cras) could be helpful as well as a transformation from voxel (volume) coordinates to RAS-coordinates (mri_info spmT_0001.img --vox2ras). What I'm looking for is the matrix-multiplication that would transform the FreeSurfer surface coordinates (such as those in ?h.white) to the functional data volume coordinates (in spmT_0001.img). I need to know what these matrices are (and where to get them) and in which order to apply the transformation matrices. I would like to do this with Matlab as much as possible. I have a large number of points and therefore I cannot do it manually for each point. Any help would be greatly appreciated. Sincerely, Patrik Ahvenainen AMI centre Helsinki University of Technology

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Freesurfer August 2010