Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18
by Eriksen, Jeffrey (Portland) 16 Aug '10

16 Aug '10

Sure. Right now I would like to extract the corpus callosum, as defined by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like to pick a voxel in the center of the CC and grow a region around it picking up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted single irregular ROI of the CC. I am more of an EEG person, and have done this with EEG tools like EMSE and Brain Voyager. Thanks, -Jeff -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Tuesday, August 10, 2010 5:35 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 78, Issue 18 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Red Hat vs. CentOs (Paul Raines) 2. Exec format error. Wrong Architecture. (Kristina Fanucci) 3. Re: Red Hat vs. CentOs (Don Hagler) 4. [freesurfer] a puzzling installation error (Glen Lee) 5. region seeding and growing (Eriksen, Jeffrey (Portland)) 6. Re: region seeding and growing (Bruce Fischl) 7. surface-based aal template (Zhangyuanchao) 8. File Format for talairach.m3z (Soon Hock Wei) ---------------------------------------------------------------------- Message: 1 Date: Mon, 9 Aug 2010 15:42:57 -0400 (EDT) From: Paul Raines <raines(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Red Hat vs. CentOs To: dahlia(a)nmr.mgh.harvard.edu Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <Pine.LNX.4.62.1008091542210.9461(a)gate.nmr.mgh.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Yes, it should be almost no different. On Mon, 9 Aug 2010 dahlia(a)nmr.mgh.harvard.edu wrote: > Hi, > > I'd like to make sure that a Dell desktop with pre-installed RHEL would > work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? > > Thanks, > Dahlia. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- --------------------------------------------------------------- Paul Raines email: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA ------------------------------ Message: 2 Date: Mon, 9 Aug 2010 15:44:07 -0400 From: Kristina Fanucci <kfanucci(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Exec format error. Wrong Architecture. To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <AANLkTimJ2QWFpH3Vy-_NgzN6zeSMK8powGj6GBb745uM(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, I finished running autorecon1 pbsubmit -m kfanucci -l nodes=1:opteron -c "recon-all -i /autofs/cluster/mscat/users/kristina/MS-freesurfer/ms-dicom/MS_pt20_dico m/MEMPRAGE_4e/008/255000-000008-000049.dcm -subjid MS_pt20_recon -autorecon1" and then tried to look at the skull strip tkmedit MS_pt20_recon brainmask.mgz -aux T1.mgz but received this error: /autofs/cluster/mscat/users/kristina/MS-freesurfer/frozen-freesurfer-ver s03082010/stable/bin/tkmedit.bin: Exec format error. Wrong Architecture. Where did I go wrong? Thanks, Kristina

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preserving control points and wm edits
by Mira Michelle Raman 16 Aug '10

16 Aug '10

Hi, I want to re-run subjects in 5.0 that have been edited in 4.5(wm.mgz, brainmask.mgz, control points). What command should I use to preserve these edits? -Mira

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Cluster Correction in Freesurfer
by Pye, Brandon (NIH/NIMH) [F] 16 Aug '10

16 Aug '10

Hi all, I have a question about performing a cluster correction. I have gone through the Group Analysis tutorial on the FsTutorial website, but it walks through the process of doing a glm analysis to compare different conditions of data. I have a mask file (.mgh) that contains activation levels below a certain significance threshold, and I want to use freesurfer to find the true clusters in the data, find the center of each cluster (either the talairach coorindate or something to help localize where the cluster is centered), then create an ROI of a predetermined size and/or shape to the coordinates/areas discovered from the the cluster correction analysis. So, essentially, I want to take an overlay file of significance regions, and extract out the true clusters and define ROIs at the epicenter of these true clusters. How would I best go about doing this? I have seen the examples of cluster correction using mri_glmfit-sim, but I don't want to do a glm analysis. Is there a stand-alone cluster correction analysis program in freesurfer? Thanks, Brandon --------------------------------------------------------------------- Brandon Pye Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 402-3893 Fax: (301) 402-0921 brandon.pye(a)nih.gov

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Re: [Freesurfer] question regarding minimum p-values in cortical thickness
by Michael Waskom 16 Aug '10

16 Aug '10

Hi Heidi, You can use mri_segstats on the surface. You can either use the --label option or, if you have a lot of labels, you can merge them into an annotation with mris_label2annot and then use the --annot option to extract from all at once (values are extracted from each region separately; this just might save some time/typing). Note that the file you're extracting from (the one after the --i flag) must be stored as a surface. Best, Mike On Mon, Aug 16, 2010 at 10:46 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Hi, > > Last year, I have been working for four months with David Salat and so, I > have learnt a lot, including the dt_recon command. > From David, I also learnt to use mri_segstats command in order to get > minimum p-values for each label in my volume. > However, now I have performed cortical thickness analyses. Based on the > results on the inflated surface, I created labels and deprojected them to > native space, to get the statistics. > Now, I also would like to have the minimum p-value of each label in the > cortical thickness analyses. However, the mri_segstats command is not > suitable for surfaces. > Do you have any idea how I can extract these minimim p-values? > > Thank you very much. > > Best > Heidi. > > * > > * > > *Heidi Jacobs * > *PhD student > Faculty of Health, Medicine and Life Sciences* > *School for Mental Health and Neurosciences* > *Alzheimer Center Limburg* > *Division Cognitive Neuropsychiatry and Clinical Neurosciences* > *h.jacobs(a)np.unimaas.nl > *www.maastrichtuniversity.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 126 F +31 43 38 84 092 > > > *Please consider your environmental responsibility before printing this > e-mail.* > >

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question regarding minimum p-values in cortical thickness
by Jacobs H (NP) 16 Aug '10

16 Aug '10

Hi, Last year, I have been working for four months with David Salat and so, I have learnt a lot, including the dt_recon command. >From David, I also learnt to use mri_segstats command in order to get minimum p-values for each label in my volume. However, now I have performed cortical thickness analyses. Based on the results on the inflated surface, I created labels and deprojected them to native space, to get the statistics. Now, I also would like to have the minimum p-value of each label in the cortical thickness analyses. However, the mri_segstats command is not suitable for surfaces. Do you have any idea how I can extract these minimim p-values? Thank you very much. Best Heidi. [cid:202094614@16082010-0DEF] Heidi Jacobs PhD student Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Alzheimer Center Limburg Division Cognitive Neuropsychiatry and Clinical Neurosciences h.jacobs(a)np.unimaas.nl <mailto:h.jacobs@np.unimaas.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 [cid:202094614@16082010-0DF6] Please consider your environmental responsibility before printing this e-mail.

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Real world orientation in tksurfer
by Michael Waskom 14 Aug '10

14 Aug '10

Hi Bruce et al, Is there any way to control the orientation of the brain in TKsurfer according to some "real world" coordinate system? While I can manipulate the orientation in the tcl prompt from the initial display orientation, it's hard to line left and right hemispheres up in particular ways. Alternatively, if you know the starting orientation in real world coordinates, I could probably work backwards from there. Thanks, Mike

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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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