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30080 discussions

Extraction mean curvature values
by Carl Schultz 02 Nov '08

02 Nov '08

Dear all, I compared the mean curvature between two groups using the mri_glmfit command and the Monte carlo simulation. Is there a possibility to extract the smoothed average curvature values of the significant clusters for all subjects? Thank you in advance Best regards Christoph Schultz University of Jena Department of Psychiatry Germany ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Walter Bauer-Wabnegg; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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Error Log
by Kellen Mobilia 01 Nov '08

01 Nov '08

Hi Would anyone happen to know the location where Freesurfer hides its error logs? Especially for the "medit tool. Are the located in the local Freesurfer directory or are they located somewhere else, like in the individual; subject folder? Any help would be awesome. Also what would be even better, if anyone knows of a command log that keeps a record of all the commands the medit tools is executing in the background, it probably doesn't exist but it is worth a shot. I am running Freesurfer on a Linux. Thanks Kellen

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mris_calc
by Akram Bakkour 01 Nov '08

01 Nov '08

Hello, I have two thickness files I want to subtract one from the other, so I did: on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh #OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh \ and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' has wrong magic number." Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

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Re: [Freesurfer] mris_calc
by rudolph＠nmr.mgh.harvard.edu 31 Oct '08

31 Oct '08

mris_calc currently only works with flat curvature files (eg ?h.curv, ?h.sulc, ?h.area, ?h.thickness, etc) and not on volumes. ------Original Message------ From: Akram Bakkour Sender: freesurfer-bounces(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] mris_calc Sent: Oct 31, 2008 20:13 Hello, I have two thickness files I want to subtract one from the other, so I did: on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh #OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh \ and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' has wrong magic number." Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Sent via BlackBerry from T-Mobile

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Re: [Freesurfer] Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 29 Oct '08

29 Oct '08

When I look in the contrast folder, there is only one gamma.mgh image, but I have two groups. I am assuming this is the mean thickness, or the mean difference in thickness between groups. How do I get it to save out one file for each group? Where is there a good explanation of the output files from qdec? Thanks Jen On Oct 28, 2008, at 4:30 PM, Doug Greve wrote: If you go into the qdec output directory, you will find a contrast for each group (class). In the contrast directory, you will find a file called gamma.mgh. This will be the average thickness for the group. You can load it into tksurfer, something like: tksurfer fsaverage lh inflated -overlay gamma.mgh doug Bramen, Jennifer E. wrote: Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Viewing atlas?
by Ryan Scotton 29 Oct '08

29 Oct '08

Hi Freesurfers, Some associates of mine are working on a pipeline that generates cortical parcellations and we are looking to compare its measurements to some measurements generated by the freesurfer pipeline. However, our pipeline parcellates broader regions which include several labels generated by the FS cortical parcellation process within each of our labels. What we need is to get a general idea of where every label generated by FS fits within the context of our broader labeling scheme. SO, this may be an obvious question, but how might i be able to view an atlas image volume with the FS parcellation/labeling scheme applied to it in order to get a general idea of how the separate labeling schemes match up? Thanks! Ryan

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Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 28 Oct '08

28 Oct '08

Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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FI and sulc -- how are they related?
by Rudolph Pienaar 28 Oct '08

28 Oct '08

> Dear Rudolph Pienaar, > could you please tell me if the Folding index and the sulc are in a way > correlated? > thank you Hi David - This question does not really have a simple yes or no answer, mostly because each measures different features. These features are both derived from the topology of the surface, but are not directly related. The 'sulc' measurement is the distance that a specific vertex is away from a hypothetical "mid-surface" that exists between the gyri and the sulci. This surface is chosen so that the "mean" of all the displacements is zero. The 'sulc' gives a indication then of linear *distance* and displacements: how "deep" and how "high" are the folds, but doesn't say much about how "sharply" folded they are, or in what manner are they folded (like cylinders, like spheres, etc). The FI is a *curvature* (not distance) measure. It uses the k1 and k2 principal curvatures at each vertex to calculate a value according to (per Van Essen/Drury 1997): FI_i = fabs(k1) * (fabs(k1) - fabs(k2)); Conceptually the FI tries to give a measure of how (relatively) tightly or sharply folded a gyrus is in a cylindrical sense. The more cylindrical a gyrus is, the more the FI increases along its length. For regions with spherical or saddle folding, k1 = k2 and the FI is zero. So it tells us more about how much like cylinders the folds are, but tell us nothing about how "deep" the folds extend. Essentially, the 'sulc' and the FI are related of course by the topology of the surface but they each measure conceptually different things. It is not possible to determine 'sulc' from the FI or vice versa. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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qdec patch
by Juranek, Jenifer 28 Oct '08

28 Oct '08

Nick, Just in case you're taking a head count, I would benefit from a patch for qdec which reads ?h.pial_lgi files as mentioned in response to Martin's posting yesterday. Cheers, Jenifer

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(no subject)
by david felps 28 Oct '08

28 Oct '08

Dear Rudolph Pienaar, could you please tell me if the Folding index and the sulc are in a way correlated? thank you _________________________________________________________________ Hotmail to go! Hol' Dir Hotmail aufs Handy! http://windowslivemobile.msn.com/BrowserServiceHotmail.aspx?lang=de-de

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