Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

[TENURE-TRACK POSITION IN CLINICAL NEUROSCIENCE AT OHIO STATE UNIVERSITY]
by Herring, Elizabeth J. 07 Sep '17

07 Sep '17

[POSTED ON BEHALF OF RUCHIKA PRAKASH] Dear Colleagues: The Department of Psychology at Ohio State University is looking to hire a tenure-track assistant professor in the area of clinical neuropsychology/neuroscience. We are specifically looking for candidates with the potential to establish a solid program of research in the field of clinical neuropsychology. We are seeking an individual that is pushing the boundaries of traditional cognitive/neuropsychological assessments. Researchers who employ a variety of methods including brain imaging and/or computational modeling are encouraged to apply. Please see below for more details on the job posting: https://jobs.psychologicalscience.org/job/761/assistant-professor-clinical-… Please note that this position is different from the one advertised at the Department of Psychiatry at Ohio State University. Our interest is in research-focused candidates who can contribute to our mission of conducting research and training in clinical sciences. Please feel free to contact me if you have any questions about the position or would like to learn more about the clinical area, the department of psychology, or our interdisciplinary brain imaging center, Center for Cognitive and Behavioral Brain Imaging - Ruchika Prakash @ Prakash.30(a)osu.edu<mailto:Prakash.30@osu.edu> Best, -Ruchika Prakash Ruchika Prakash, Ph.D. Associate Director, Center for Cognitive and Behavioral Brain Imaging Director, Clinical Neuroscience Laboratory Department of Psychology The Ohio State University Email: Prakash.30(a)osu.edu<mailto:Prakash.30@osu.edu> Phone: (614) 292-8462<tel:(614)%20292-8462>

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Error while running recon-all
by Ritesh Mahajan 06 Sep '17

06 Sep '17

Hello guys, I am trying to run recon-all command, i am getting the following error: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory Can anyone help me out with this. Thanks, Ritesh Mahajan

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Re: [Freesurfer] Fixed Effects Analysis on Single Subject's Brain
by Taylor, Johnmark 06 Sep '17

06 Sep '17

Registered to the subject's anatomical volume (which registers to the surface for free anyways, if I understand correctly). On Wed, Sep 6, 2017 at 1:38 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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: controlling for Sex in a model using two continuous > variables onto CTh (Douglas N Greve) > 2. Re: Multi-Subject Comparison in FreeSurfer (Douglas N Greve) > 3. Re: group interaction with one continuous covariate and three > nuisance variables (two continuous, one dichotomous) (Douglas N > Greve) > 4. Re: Interpretting Brain Segmentation Volume to eTIV ratio > (Douglas N Greve) > 5. Problem with ambiguous voxels? (Del Re, Elisabetta) > 6. Re: patch for ribbon mgz failure (Douglas N Greve) > 7. Re: upsampling ?h.curv (Douglas N Greve) > 8. Re: Map of covariance (Douglas N Greve) > 9. Fixed Effects Analysis on Single Subject's Brain > (Taylor, Johnmark) > 10. Re: Freesurfer Preliminary Questions (Douglas N Greve) > 11. Re: Occipital Cortex Segmentation (Douglas N Greve) > 12. Re: How to estimate the Intracranial area? (Douglas N Greve) > 13. Re: Combining Echo Frames Error (Douglas N Greve) > 14. Re: individual mri_segstats waveforms for vertices or face in > label (Douglas N Greve) > 15. Re: Fixed Effects Analysis on Single Subject's Brain > (Douglas N Greve) > 16. Re: Reliability of labeling procedure in the same scan > (Mike Schmidt) > 17. Re: Problem with ambiguous voxels? (Bruce Fischl) > 18. Re: controlling for Sex in a model using two continuous > variables onto CTh (Uquillas, Federico D'Oleire) > 19. MNI average brain in Freesurfer space (Anna Kasdan) > 20. R: Re: Map of covariance (stdp82(a)virgilio.it) > 21. Re: MNI average brain in Freesurfer space (Douglas N Greve) > 22. Re: controlling for Sex in a model using two continuous > variables onto CTh (Douglas N Greve) > 23. Re: R: Re: Map of covariance (Douglas N Greve) > 24. Re: Cortical thickness (Douglas N Greve) > 25. Re: sub-cortical analysis (Douglas N Greve) > 26. Error with TRACULA using dcm and nii (Ferrier, Christopher Q.) > 27. Re: controlling for Sex in a model using two continuous > variables onto CTh (Uquillas, Federico D'Oleire) > 28. Re: controlling for Sex in a model using two continuous > variables onto CTh (Douglas N Greve) > 29. Re: controlling for Sex in a model using two continuous > variables onto CTh (Uquillas, Federico D'Oleire) > 30. Talairach registration error (Ariana Vajdi) > 31. Ventricle Volumes Decreasing over time? (Tamara Tavares) > 32. Re: Ventricle Volumes Decreasing over time? (Bruce Fischl) > 33. Re: Talairach registration error (Douglas Greve) > 34. ??: ROI (Jin Bo) > 35. Re: wm topological defects (Ruotsalainen, Ilona) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Sep 2017 12:01:32 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] controlling for Sex in a model using two > continuous variables onto CTh > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <c94e8853-6171-8520-1786-e46c2746e870(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > can you send the fsgd file for the analysis that is failing? > > > On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote: > > Dear FreeSurfer experts, > > > > We have run a vertex-wise analysis regressing a continuous variable > > onto cortical thickness on the surface, and would like to verify that > > our contrast that uses Age and Sex as covariates was defined > > correctly, especially since there is probably more than one way to > > control for a binary variable like Sex. > > > > On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it > > suggests to make two regressors, one for Males, and one for Females, > > where for the former a 1 is indicative of the Male category, and a 1 > > on the latter is indicative of the Female category. However, using > > that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the > > error: matrix is ill-condition or badly scaled, condno=2.01889e+07. > > We believe this may be due to the fact that Male and Female categories > > are autocorrelated and Freesurfer likes variables to be de-meaned. > > Running a FSGD file with only Age and our variable of interest via a > > DOSS contrast of [0 1 0] works without any errors. > > > > We thus created an FSGD file where we have Sex as our third variable > > (in addition to our continuous variable of interest and one demeaned > > continuous covariate), coding 1s for Males and 0s for Females, and we > > used a DOSS contrast of [0 1 0 0]. This provided us with a map that > > makes sense with our expectations. > > > > We would like to verify if this is doing what we believe it is doing; > > that is, looking at the relationship of our continuous variable or > > interest after accounting for age and sex. > > Any thoughts would be greatly appreciated. > > > > Thank you so much. > > > > Best, > > > > Fred > > > > > > > > > > > > _______________________________________________ > > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 2 > Date: Tue, 5 Sep 2017 12:03:27 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Multi-Subject Comparison in FreeSurfer > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <36414cb1-e5cb-b192-d1a6-80259da31da4(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > You will need to run 500 different recon-all jobs. Obviously, if you run > them on a single computer, it will take a long time, so you will need > access to a cluster. Or you can buy time on a cloud service. > > > On 08/29/2017 02:54 PM, Sherrill, John T wrote: > > > > I am a new grad student and have been assigned a project in our Brain > > Imaging Research Center. I would be taking the time to push through > > and find these answers on my own but our program gives us 5 weeks of > > half days in a lab for a trial. So I am in a bit of a time crunch. > > > > I have been given a database of about 500 .nii files and been asked to > > find duplicates or likely duplicates. (Some subjects were > > duel-consented so they may have multiple scans.) What is the best way > > to recon-all all of the files? Individually, in small groups, or in > > one larger group? If I do it in groups do I need to list each file or > > can I just recon-all the entire directory? And if a recon-all on 1 > > file takes 6-20hr, will doing a recon-all on the entire data set take > > 500*(6-20hr)=3000-10,000hr? Any help is greatly appreciated. > > > > John Sherrill > > jtsherrill(a)uams.edu > > john_sherrill(a)me.com > > (870) 761-0580 > > ------------------------------------------------------------------------ > > Confidentiality Notice: This e-mail message, including any > > attachments, 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 e-mail and > > destroy all copies of the original message. > > > > > > _______________________________________________ > > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 3 > Date: Tue, 5 Sep 2017 12:05:42 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] group interaction with one continuous > covariate and three nuisance variables (two continuous, one > dichotomous) > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <db68777a-81ed-d750-5075-cd6b35992588(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > try looking at the FSGD examples for a case that you can generalize > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > > On 08/29/2017 08:59 PM, Ines M?rner-Lavanchy wrote: > > > > Dear FS experts, > > > > I would like to test if the correlations between thickness/area and > > cognition differ between two groups, while age, socioeconomic status > > (continuous) and gender (dichotomous) should be nuisance variables. > > > > To look at the effect of cognition in one group only, I made a model > > with 8 regressors: > > > > - sex male > > - sex female > > - age male > > - age female > > - cognition male > > - cognition female > > - ses male > > - ses female > > > > With the contrast 0 0 0 0 0.5 0.5 0 0: how does cognition correlate > > with Cth/CSA, controlled for age, sex, and ses. > > > > Now how do I model this, if I have *two* groups and want to look at > > the interaction of group*cognition? I have trouble setting up the fsgd > > and design matrix. > > > > Any help is appreciated, > > > > Thanks in advance, > > > > Ines > > > > > > > > _______________________________________________ > > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 4 > Date: Tue, 5 Sep 2017 12:07:41 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Interpretting Brain Segmentation Volume to > eTIV ratio > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <3b478464-8cc5-e338-170a-0786a153e40a(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > I put that in there mainly as a quality check to automatically flag > something that has gone wrong. I think something went wrong if the value > is 0.65 (unless you have very atrophied subjects). You will have to take > a look to see what might have gone wrong. > > > > On 08/29/2017 09:03 PM, Mehta, Chintan wrote: > > > > Dear FreeSurfer community, > > > > > > I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted > > from FreeSurfer version 5.2.0. In my sample of normally developing > > adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for > > 98% of subjects. However, the value is less than 0.65 for 2% of subjects. > > > > > > Could this reflect actual feature of brain volume to eTIV? > > > > > > Or is this a reflection of poor scans, poor overall FreeSurfer > > processing, or inaccurate eTIV estimates for these subjects? Subjects > > with BrainSegVol.to.eTIV ratios less than 0.65 tended to all be > > females. They had Brain Segmentation volumes falling in normal ranges > > of females in the full sample. However, their eTIV was on the > > upper-end among eTIVs of females in the sample. If the eTIVs for these > > subjects were over-inflated, then it makes sense the ratios are > > especially low. > > > > Thank you. > > > > Best, > > Chintan > > > > > > > > > > _______________________________________________ > > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 5 > Date: Tue, 5 Sep 2017 16:07:37 +0000 > From: "Del Re, Elisabetta" <Elisabetta_DelRe(a)hms.harvard.edu> > Subject: [Freesurfer] Problem with ambiguous voxels? > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: "Somes, Nathaniel G." <NSOMES(a)BWH.HARVARD.EDU> > Message-ID: > <CY4PR07MB2837476706EFA64ABABA2CAEB3960@CY4PR07MB2837. > namprd07.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear FS Team, > > We are running recon-all for a large dataset and 5 of the cases keep > getting stuck at the exact same spot. It is the point at which the > following has just been displayed on the screen: > > #@# WM Segmentation Wed Aug 30 17:34:40 EDT 2017 > > mri_segment brain.mgz wm.seg.mgz > > doing initial intensity segmentation... > using local statistics to label ambiguous voxels... > computing class statistics for intensity windows... > WM (107.0): 105.5 +- 6.4 [91.0 --> 125.0] > GM (78.0) : 81.0 +- 6.1 [56.0 --> 94.0] > setting bottom of white matter range to 87.1 > setting top of gray matter range to 93.2 > doing initial intensity segmentation... > using local statistics to label ambiguous voxels... > > > > For these 5 cases it will sit at this step apparently still running for > over a week without any change before I cancel the job. There does not seem > to be anything special about these 5 cases either in terms of their header > information or visually. We have not found any artifacts in the images > except for some minor ringing which is present in many images in the > dataset, not just these. The rest of the cases of the dataset all ran to > completion and produced all of the files we were expecting, but a subset of > them seem to have a related issue where most of the wmparc.mgz labelmap is > unsegmented white matter. Only the very edges and the very center are > getting designated as something other than this label. The rest of the > files in the "mri" directory such as aparc+aseg.mgz and so on are equally > as affected by this. Do you know what could be going on here? I would be > happy to give you any more information that could be helpful. > > Best, > Elisabetta and Nate > > > > > Elisabetta C. del Re, Ph.D. > Assistant Professor of Psychiatry, > Department of Psychiatry > Harvard Medical School > phone 617 9675569 > mail elisabetta_delre(a)hms.harvard.edu > > > >

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wm topological defects
by Manuel Delgado 06 Sep '17

06 Sep '17

Dear all: Regarding wm edits, it is shown in the tutorial how to proceed with "holes" that appear in the smoothwm.nofix. However, those holes do not necessarily affect the wm matter surface. So is it recommendable to check if holes in the smoothwm.nofix surface affect the real wm surface before correcting them? And, what is the purpose of the smoothwm.nofix, is it used for other issues? Thank you -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain*

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Re: [Freesurfer] Ventricle Volumes Decreasing over time?
by Tamara Tavares 06 Sep '17

06 Sep '17

Hi Bruce, Thank you for your quick reply! The decrease in percent difference vary. I have listed the range here for each region: Left Lateral Ventricle: -26 to -0.06 Left inferior ventricles: -67 to -0.2 Third ventricle: -23 to -0.06 Fourth ventricle: -7 to -0.142 Right lateral ventricle: -21 to -0.04 Right inferior ventricle: -59 to -0.68 I had a chance to examine one brain that showed -16% difference score in the left lateral ventricles between the longitudinal and baseline scan. The scans seemed to show a smaller left lateral ventricle at time 2. Do you know whether the variability of Freesurfer (version 5.1) may contribute to some of the decreases I am seeing? Thank you in advance for your help. Best, Tamara Message: 32 Date: Tue, 5 Sep 2017 21:43:23 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Ventricle Volumes Decreasing over time? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1709052142520.4038(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Tamara have you visualized the multiple time points of a subject whose ventricular volume is decreasing? How big a decrease are you seeing? cheers Bruce On Tue, 5 Sep 2017, Tamara Tavares wrote: > Hello, > I used the default longitudinal stream to calculate ventricular volumes over time. When I examined > the difference score (longitudinal-baseline) I noticed that for some participants ventricular > volumes decreased. The same site, scanner and scanning protocol was used for both baseline and > longitudinal scans. I processed the cross, template and longitudinal time points on the same > computer using the same Freesurfer version (v 5.1). Furthermore, this decrease in ventricular volume > is evident before and after manual corrects were made to the aseg file. Is it common to see an > decrease in ventricular volume over time? Can this be due to Freesurfer variability or slight > differences in the scanner over the two time points? > > Thank you in advance for your help. > > Best, > Tamara

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Philips and Toshiba dicom tag Read - error
by M Janani 06 Sep '17

06 Sep '17

Hi Team, We would like to process the MRI data obtained using Philips and Toshiba scanners. Can we do it using Freesurfer? Thought the reconstruction process got completed successfully, we got DICOM read error while fetching DWI parameters in the beginning of the reconstruction process. Can I neglect that error? Attached log for reference. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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rh.white and rh.pial surface manual edit
by Farhad Ghaseminejad 06 Sep '17

06 Sep '17

Hello FreeSurfer experts, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha… <https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha…> Best, Farhad

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Talairach registration error
by Ariana Vajdi 05 Sep '17

05 Sep '17

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck. These are the errors I receive: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would appreciate your help. Thank you! Warmly, Ariana

2 1

Ventricle Volumes Decreasing over time?
by Tamara Tavares 05 Sep '17

05 Sep '17

Hello, I used the default longitudinal stream to calculate ventricular volumes over time. When I examined the difference score (longitudinal-baseline) I noticed that for some participants ventricular volumes *decreased*. The same site, scanner and scanning protocol was used for both baseline and longitudinal scans. I processed the cross, template and longitudinal time points on the same computer using the same Freesurfer version (v 5.1). Furthermore, this decrease in ventricular volume is evident before and after manual corrects were made to the aseg file. Is it common to see an *decrease *in ventricular volume over time? Can this be due to Freesurfer variability or slight differences in the scanner over the two time points? Thank you in advance for your help. Best, Tamara

2 1

controlling for Sex in a model using two continuous variables onto CTh
by Uquillas, Federico D'Oleire 05 Sep '17

05 Sep '17

Dear FreeSurfer experts, We have run a vertex-wise analysis regressing a continuous variable onto cortical thickness on the surface, and would like to verify that our contrast that uses Age and Sex as covariates was defined correctly, especially since there is probably more than one way to control for a binary variable like Sex. On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it suggests to make two regressors, one for Males, and one for Females, where for the former a 1 is indicative of the Male category, and a 1 on the latter is indicative of the Female category. However, using that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the error: matrix is ill-condition or badly scaled, condno=2.01889e+07. We believe this may be due to the fact that Male and Female categories are autocorrelated and Freesurfer likes variables to be de-meaned. Running a FSGD file with only Age and our variable of interest via a DOSS contrast of [0 1 0] works without any errors. We thus created an FSGD file where we have Sex as our third variable (in addition to our continuous variable of interest and one demeaned continuous covariate), coding 1s for Males and 0s for Females, and we used a DOSS contrast of [0 1 0 0]. This provided us with a map that makes sense with our expectations. We would like to verify if this is doing what we believe it is doing; that is, looking at the relationship of our continuous variable or interest after accounting for age and sex. Any thoughts would be greatly appreciated. Thank you so much. Best, Fred

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Freesurfer September 2017