Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

question about Unpaired T-test group analysis
by kinson li 12 Oct '16

12 Oct '16

*Hello, * *Question 1: I would like to conduct an Unpaired T-test group analysis, I have two group of people, Group A8 age is 8 and Group A9 age is 9, and I to test the* change in thickness with age. But I am little confusion about the matirx and FSGD design. I am appreciated if you can take a look at my FSGD file and Matrix file. Please correct me if I am wrong, Question2 : I am using tksurfer to analysis the brain thickness, and I have a question about setting threshold, for I am not so sure about the relation between threshold and Min. is the equation Min = -log10(threshold) correct?( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) For example, if I want the threshold to be 0.05, and the Min will be set to 1.3 Please see the image attached in this email, and correct me if I am wrong. Thank you! Jincheng

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Using caudate as a seed
by Raney, Talia L. 12 Oct '16

12 Oct '16

Hi, Is there any way in FSFAST to use caudate as a seed for connectivity analysis? I was checking to see if it had a seg id for which I could run fc-seed-config, but it only had ids for caudate intensity abnormalities. Thank you! Best, Talia

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Should I use no-adjust in mri_surfcluster
by Mishra, Virendra 12 Oct '16

12 Oct '16

Hi, FreeSurfer Users. I am comparing cortical thickness of 2 groups controlled for certain variables of no interest. My contrast matrix is 1 -1 0 0 0 0 0 0 0 0 0 0 to check for group 1 thickness > group 2 thickness I get my sig.mgh and I want to run mri_surfcluster command to correct for FDR. I am confused as to whether I should use -no-adjust in mri_surfcluster. According to the help mri_surfcluster (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster) : I have to use -no-adjust if my sig.mgh is not a log(10) map and sig.mgh was created using a one-tailed test. Since my contrast is group1>group2 ; I am thinking my sig.mgh is a log(10) but a one-tailed. Hence I have to use -no-adjust. But then again, mri_glmfit (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) says if #of rows in Contrast matrix is 1 (which is true in my case), then the F-test reduces to a two-tailed t-test which means I should not use -no-adjust. I would appreciate any response regarding this. Thanks Regards Virendra =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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smoothing kernel inconsistency
by Qi Ting 12 Oct '16

12 Oct '16

Dear Freesurfer experts, I am trying to do the group analysis, before this I tried to smooth the data with the different smoothing kernel. However, when I checked the output dir, it turned out that data were smoothed with a larger smoothing kernel than I expected. For example, images intended to be smoothed with 5mm were actually smoothed with 8mm. So does anyone know why? Another thing is about the surface area in the analysis. I am a little confused which surface does the default cmd or the area in qdec indicate? Does it mean the area I got is white surface? If so, can I also get a pial surface? Technically, is the middle between the white surface and the pial surface the more reasonable one? Thank you in advance. Best regards, Ting

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how to exact the result of the stats filedir
by zhang yue 12 Oct '16

12 Oct '16

Hello FreeSurfer Developers, I’m attempting to exact the result of ‘stats’filedir, such as file ‘lh.aparc.stats’, I want to know you guys how to do this work. Your kind reply would be appreciated.

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Cortical thickness using qdec (between scanners)
by Martin Juneja 12 Oct '16

12 Oct '16

Hello FS experts, I have a data set of 20 subjects (patients) collected at location-1 with 3T Siemens scanner. Also, I have a set of age-matched 20 subjects (controls) collected at location-2 with 3T Siemens scanner. I am interested in comparing cortical thickness between controls and patients using FreeSurfer but I am not sure if I can do that since I have both the data sets collected at two different locations. I would really appreciate any inputs on this. I tried to find some papers on scanner differences but all I could find was between 1.5 T vs 3T or 3T vs 7T. Is there any special covariates I need to define for this purpose (if so then at which step during analysis?) or is it not possible at all? Thanks.

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Cortical Thickness Overlay Slice by Slice
by Sancgeetha Kulaseharan 12 Oct '16

12 Oct '16

Hello Freesurfer Experts, I am using Freeview to visualize cortical thickness with the command freeview -v mri/T1.mgz \ -f surf/lh.pial:overlay=lh.thickness While the cortical thickness overlay is visible in the 3-Dimensional display, I was wondering if it was possible to also view the cortical thickness map on a slice-by-slice case? Also where can I find topological information on ?h.thickness files? Thank you, Sancgeetha

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Re: [Freesurfer] [Dev Build] Processing very high resolution dataset
by Falk Lüsebrink 12 Oct '16

12 Oct '16

Dear all, using mris_topo_fixer instead of mris_fix_topology also results in a segmentation fault. The command line used was: mris_topo_fixer -mgz -warning -seed 1234 <subjID> lh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /surf/lh.orig... Before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, g=1022) Surface Diagnostics: eno=-2042 (nv=2743306, nf=5490696, ne=8236044) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 1022 loops (X=-2042) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 15 iterations identify defects... marking ambiguous vertices... 1475515 ambiguous faces found in tessellation segmenting defects... Segmentation fault Any suggestions or tips are highly appreciated. Best, Falk Von: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Falk Lüsebrink Gesendet: Donnerstag, 6. Oktober 2016 17:51 An: Freesurfer support list Betreff: [Freesurfer] [Dev Build] Processing very high resolution dataset Dear all, I am currently trying to process a MPRAGE with an isotropic resolution of 250 µm acquired in vivo. Downsampling the data to .5 and 1 mm resulted in no errors and surfaces look good. However, while processing the data at native resolution I receive a segmentation fault during topology fixation. May this be related to the number of vertices / faces? Surfaces look okay and not totally corrupted. Memory and disk space are available plentiful. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $ before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, g=1022) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 1461809 ambiguous faces found in tessellation segmenting defects... Segmentation fault Uploading of the dataset is currently not possible. Best, Falk

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Issues processing brain hemispherectomized patients
by Halbertsma, HN (ohk) 12 Oct '16

12 Oct '16

Dear all, I’m having troubles getting a good Freesurfer output from a hemispherectomised brain using recon-all. I was wondering whether there’s someone that has experience with running Freesurfer on such an unusual brain? The first couple of issues I bumped into were failures regarding the talaraich alignment which I solved using registration matrices from FSL. The issue I’m having now regards the labeling of subcortical structures. Apparently Freesurfer cannot deal with the fact that there’s just one hemisphere, and the fact that there is no clear corpus callosum. It looks like it’s trying to divide one hemisphere into two, which obviously messes up the subcortical labelling. Any ideas on how to work around this issues? Is there maybe a way to mirror the intact hemisphere pretending to form a full brain? Or are there any flags I can use to make sure the subcortical labelling works fine? Thanks in advance Hinke N. Halbertsma, MSc PhD Student University Medical Center Groningen (UMCG) Department of Ophthalmology NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124 T. (+31) 050 363 4431 E. h.n.halbertsma(a)umcg.nl<mailto:h.n.halbertsma@umcg.nl> ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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Hippocampal subfield analysis in FS 6.0
by Synne Aanes 12 Oct '16

12 Oct '16

Hello, I am about to start my project on hippocampal subfield analysis and realise that this function is highly improved in FS version 6.0. I have run my data in FS 5.3 before this came to my knowledge, and I am now wondering when version 6.0 will be released to the public so I can run them again? Sincerely, Synne Aanes

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