Freesurfer

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30086 discussions

intensity normalization fails?
by Frank Scharnowski 18 Jun '10

18 Jun '10

Dear Freesurfers, When importing a 3T MDEFT structural scan into freesurfer with 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark (see attached tkmedit snapshot). The results of recon all are suboptimal, probably due to the bad intensity normalization. In SPM the structural looks just fine. Is there a way to correct for this? Many thanks for your help, frank

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segmentation fix question
by Natalia Bilenko 16 Jun '10

16 Jun '10

Hi all, I have a question about fixing surface segmentation errors while doing an anatomical reconstruction. When I try to fix some white matter surface errors by deleting/adding points to wm.mgz and running recon-all -autorecon-wm, they sometimes get fixed only partially or not at all. I was just wondering if there is any way to predict whether a certain volume fix is going to alter a segmentation, or if the only way to find out is to fix the volume and wait for the results of autorecon2. Thanks! Natalia

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Volume to RAS transformation for electrode coordinates
by ckeller＠nmr.mgh.harvard.edu 16 Jun '10

16 Jun '10

Hi Freesurfers, This may be a very simple question but I am having some problems sorting it out and any help would be much appreciated. I am trying to coregister the pial surface (from a freesurfer reconstruction of the preoperative MRI sequence) with intracranial electrodes pulled from a postoperative CT scan. The electrode coordinate gathering from the CT and transformation to preopMR space was done in bioimage suite already. I believe the problem is that there is a transformation needed from voxel space to surface RAS coordinates in order to plot the pial surface in the same space as the electrodes. As of now I am plotting the pial surface with read_surf and tripatch commands in matlab. Does anyone know where I can find this transformation matrix or how to construct it? Thanks in advance. Best, Corey

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transversetemporal data is missing in rh.aparc.stats
by Guang Zeng 16 Jun '10

16 Jun '10

Hi, there, I have a subject which is processed through FreeSurfer longitudinal stream, and I found that in the rh.aparc.stats file, the data of transversetemporal is not included. So, when FreeSurfer can not detect a ROI, it will not write it into ?h.aparc.stats ? Thanks! Guang _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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Demeaning TIV
by Nasim Maleki 16 Jun '10

16 Jun '10

Hi all, I have a question with regards to using the TIV as a covariate in comparing the subcortical volumes between the two cohorts. In particular I'm wondering: 1-Should you demean the TIV at all or not? 2-1-If you are using both age and TIV as your covariates, will it make sense to demean the age but not demean the TIV? 2-If you do demean each or both, should you demean these for each of the cohorts separately or use the mean of all of your subjects? I should add that the mean age of both of my cohort are pretty much the same and I'm just interested in seeing if there is a difference in the subcortical volumes between the two cohorts. Thanks for your advices in advance, Nas

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Local gyrification index error
by Dankner, Nathan (NIH/NIMH) [F] 15 Jun '10

15 Jun '10

Hi All, I'm running the lGI script on my subjects, and recently received this error: ... remeasuring lGI value for vertex iV = 64101. It may take a few minutes. WARNING -- Problem for vertex iV = 64101, lGI value is aberrantly high (lGI=59.4571)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/misc/data14/jen/SurfaceStats/BCM/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Linux thalamos 2.6.18-194.3.1.el5 #1 SMP Thu May 13 13:08:30 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jun 14 19:20:30 EDT 2010 I've gone to the offending vertex in tkmedit and tksurfer to try to determine if there was some manual editing that needed to be done, but the area appeared to be fine. Any ideas on what the cause/solution might be? Thanks, Nathan

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Changing tkmedit settings
by Mehul Sampat 15 Jun '10

15 Jun '10

Hi Folks, In tkmedit, the keyboard commands to view main and aux volume are 'Ctrl+1' and Ctrl+2'. Is it possible for me to change them to just '1' and '2' respectively ? (like how only 'n' is required for the navigation tool) Thanks Mehul

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Re: [Freesurfer] R: R: How means all the output file from a segmentation?
by Michael Waskom 15 Jun '10

15 Jun '10

Hi Leonardo, You might want to check out 3D slicer: http://www.slicer.org/ It sounds like it might be able to do what you're looking for. Best, Mike On Sun, 13 Jun 2010, Leonardo Chesi wrote: Hi bruce, my goal is to obtain a 3D surface of the hippocampal region for a visual comparison with a manual segmentation made by a neuroradiologist. Today I managed to extract the volume with mri_binarize but I can't transform it in a surface that tkurfer can visualize. For that I try to use mri_vol2surf but I obtain a surface with 0 vertices. Can you help me?? Cheers Leonardo

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Antw: Re: V5/MT label anatomical borders
by Carl Schultz 15 Jun '10

15 Jun '10

Hi Bruce, thank you for your fast reply. Is that the work you referred to ? Cytoarchitectonic analysis of the human extrastriate cortex in the region of V5/MT+: a probabilistic, stereotaxic map of area hOc5. Malikovic A, Amunts K, Schleicher A, Mohlberg H, Eickhoff SB, Wilms M, Palomero-Gallagher N, Armstrong E, Zilles K. Cereb Cortex. 2007 Mar;17(3):562-74. Best regards Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 15.06.10 14.56 Uhr >>> Hi Christoph, the V5/MT label we distribute is based on the work of Karl Zilles and Katrin Amunts who defined it histologically. I don't have the reference handy, but it shouldn't be too hard to find. cheers Bruce On Tue, 15 Jun 2010, Carl Schultz wrote: > Dear all, > > is there an anatomical description for the V5/MT label? > (Freesurfer Version 4.0.5) > > Thank you in advance > > > Christoph > > Christoph Schultz, MD > University of Jena > Department of Psychiatry > 07743 Jena > Germany > > Dr. C. Schultz > Universitätsklinik für Psychiatrie und Psychotherapie > Philosophenweg 3 > 07743 Jena > > ____________________ > Universitätsklinikum Jena > Körperschaft des öffentlichen Rechts und Teilkörperschaft der > Friedrich-Schiller-Universität > Jena Bachstraße 18, 07743 Jena > Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; 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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micro-parcellation
by Christian Lambert 15 Jun '10

15 Jun '10

Hello, I've been through the threads and can't find the answer to this one. Problem: - Subdivide the cortex into 5000++ (ideally>10,000) units per hemisphere I've tried using mris_divide_parcellation but unfortunately it got very upset trying to find a "unique rgb colour" after I had managed to achieve >2700 new labels (also I was not entirely sure how to transfer these annot labels to the annot.mgz but that's a side issue): CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid .. etc., I'm not really bothered about visualising the result per se, I just want each small area_ through _the cortical mantel to be assigned an unique value (like in the annot.2009s.mgz images but with many many more areas) so I can then convert to nifti and run numerous MATLAB scripts across multiple coregistered scans. Is this approach going to work?? Cheers, - Chris

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