Freesurfer

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30070 discussions

Statistical analysis
by Laura Ferrero Montes 11 Jun '17

11 Jun '17

Dear FS team, Thank you very much for your help. Just a few more questions. I want to perform a statistical analysis between two groups:controls and patients, using age and IQ as covariates. First I have to test if there is an interaction between group and covariate using DODS. My questions are: Q1) Do I have to test age and IQ separately, or together? Q2) In case that there is not interaction in any of the covariates, can I use the same FSGD file but do I have tu run it as DOSS? How it could be done? I would appreciate if you could give me some hints or examples about the matrices and contrast files that I must use. Thank you, All the best, Laura

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cortical metrics description
by Aniqa Nisar 11 Jun '17

11 Jun '17

Hi All, Is there a full description on what these cortical metrics are and how are they derived ? How do I calculate sulcal depth ? Is it available already ? What does the ?h.curv mean ? Please suggest. Thanks Ani

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mri_cvs_register error: Symbol not found: ___emutls_get_address
by Elijah Mak 10 Jun '17

10 Jun '17

Hi Freesurfer Developers, I am trying use mri_cvs_register but I ran into an error (Mac OS SIERRA 10.12.2). The log is pasted below. Logfile for mri_cvs_register Sat 10 Jun 2017 17:58:48 BST --mov 16084 $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ dhcp-10-240-198-151.cp.wireless.private.cam.ac.uk Darwin dhcp-10-240-198-151.cp.wireless.private.cam.ac.uk 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 asegfname aseg Using m3z type morph files. mris_register -1 -dist 1.0 -inflated /Volumes/CITADEL/16084/surf/lh.sphere /Applications/freesurfer/subjects//cvs_avg35/surf/lh.sphere /Volumes/CITADEL/16084/surf/lh.cvs.tocvs_avg35.sphere.reg dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I have also tried to update the freesurfer binaries with sudo -E fs_update but the problem persists. Thanks for looking into this! Best Wishes, Elijah

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Re: [Freesurfer] Regarding: Group analysis of WMHs
by Elijah Mak 09 Jun '17

09 Jun '17

Hi Doug, I am referring to a rather old thread where you have provided some interesting suggestions to perform group-wise analysis of WMHs. I am trying to do something similar in patients and controls. First, mri_binarize was used to extract the individual WMH volumes from aseg.mgz. These volumes were subsequently warped into MNI305 space and smoothed (using mri_fwhm 8mm). The goal is to compare the spatial distributions of WMH between both groups. Finally, mri_concat --mean was used to visualise group averaged WMH volumes. The outputs can be found here: http://imgur.com/a/curYf Do these steps look alright? On a conceptual level, is it statistically valid to compare stacks of binarised lesion maps between groups (using mri_glmfit and then performing MC with FDR/mri_glmfit-sim)? On an individual level, I noticed that some WMH voxels show up inside the MNI305 ventricles for a few subjects. This happens despite a good-looking talairach registration. Thanks a lot for your time in advance and I’ll appreciate any thoughts you may have on this. Sincerely, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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methodological questions for manuscript
by Jacobs H (NP) 09 Jun '17

09 Jun '17

Hi! For my manuscript, the journal wants me to answer some questions on the methods that I used and I want to make sure I am giving correct information on how FreeSurfer calculates hippocampal volumes. Would it be possible to check my 4 answers and let me know if these are accurate? Question: How were the data normalized/standardizes? Answer: T1 data was intensity normalized using FreeSurfer's mri_normalize script Question: Describe the template used for normalization/transformation Answer: All data was kept in subject-specific space, no templates were used. FreeSurfer, volumes are defined in several steps during which a high-dimensional non-linear registration is done to the MNI305 template to increase the accuracy of the segmentation and to facilitate the segmentation and tissue-probability assessment for region labeling. Volumes of the hippocampus are ultimately extracted from a subject-specific subcortical volumetric atlas (aseg) in 1mm isotropic space. Question: Describe your procedure for artifact and structured noise removal Answer: The standard preprocessing pipeline of FreeSurfer incorporates motion correction, intensity correction and skull-stripping. Question: how are anatomical locations determined? Answer: In FreeSurfer a subject-independent probabilistic atlas (hand labeled atlas by neuroanatomists on a training set) and subject-specific measured values. Subject-specific segmentations of the hippocampus are based on these probabilities and on the white and pial surfaces. Many thanks! All the best Heidi

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Cortical thickness_Group analysis
by Ali Radaideh 09 Jun '17

09 Jun '17

Dear FS experts, I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for. I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness). Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis? Best regards and many thanks in advance, Ali -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis
by Tamara Tavares 09 Jun '17

09 Jun '17

Hello, I have ran my data through the default recon-all processing stream and am planning on analyzing ventricular volume and cortical thickness. I was wondering whether I need to use the Qdec to complete the ventricular volume and cortical thickness analysis, or can I export the data (txt files found in the stats folder) and complete the analysis on any statistical program such as SPSS or STATA? I also noticed that Qdec needs to have the data smoothed before analyzing cortical thickness or other surface information. Why does the data need to be smoothed after being ran through recon-all and before analysis? Does the smoothing just need to occur if I am running the analysis via Qdec or do I need to complete the smoothing before analyzing the data on any statistical program? Thank you in advance for your help! Best, Tamara

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Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis
by Tamara Tavares 09 Jun '17

09 Jun '17

Hi Douglas, The message stream indicates you replied to my email but I don't see your response in the email thread. I am not sure what happened. Can you please reply again? Thank you, Tamara On 6/6/17 11:50 AM, Tamara Tavares wrote: > Hello, > > I have ran my data through the default recon-all processing stream and > am planning on analyzing ventricular volume and cortical thickness. I > was wondering whether I need to use the Qdec to complete the > ventricular volume and cortical thickness analysis, or can I export > the data (txt files found in the stats folder) and complete the > analysis on any statistical program such as SPSS or STATA? you can export > > I also noticed that Qdec needs to have the data smoothed before > analyzing cortical thickness or other surface information. Why does > the data need to be smoothed after being ran through recon-all and > before analysis? Does the smoothing just need to occur if I am running > the analysis via Qdec or do I need to complete the smoothing before > analyzing the data on any statistical program? The data does not necessarily need to be smoothed, but people usually do because it improves stats. But I thought you were doing an ROI analysis based on the first question > > Thank you in advance for your help! > > Best, > Tamara >

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testing FS installation - apparent cursor RAS coordinate mismatch?
by Antonio Algaze Beato 09 Jun '17

09 Jun '17

Hello, I just installed FS 6 (mac OS) and followed Examples 1, 2, 3 and 4 under the "Test your FreeSurfer Installation" section here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I am getting a very different view of bert's brain when the cursor RAS coordinates are made to coincide with those on the figure shown in the tutorial. Is this a sign of a failed installation test? Thanks a lot for your help! Antonio

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Re: [Freesurfer] FW: F and p- values for non sig findings {Disarmed}
by Douglas Greve 09 Jun '17

09 Jun '17

Those will have the vertex-wise p-values. You can read them in to matlab with the MRIread() command. On 6/7/17 8:18 AM, Lim, Lena wrote: > > Dear Doug, > > Thanks very much for your reply. > > Sorry, I couldn’t read the files—would they show the non-significant F > and p values as I would find in the summary output if the results were > significant? Please could you kindly help? > > Many thanks again, > > Lena > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* 08 May 2017 16:03 > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] F and p- values for non sig findings > > If you look in the output folder, there will be a subfolder for each > contrast. In there there will be sig.mgh and F.mgh files > > On 5/8/17 9:06 AM, Lim, Lena wrote: > > Dear Freesurfer experts, > > I tried to do a group x gender interaction in QDEC and there is no > sig interaction, but how do I get the F or T and P values please > as requested by the reviewers? > > Many thanks, > > Lena > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > *MailScanner has detected a possible fraud attempt from > "emea01.safelinks.protection.outlook.com" claiming to be* > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr…> >

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