Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Bug Reporting: recon-all -s 001 exited with ERRORS
by Rosalia Dacosta Aguayo 13 Nov '17

13 Nov '17

Hello FreeSurfer Developers, I am attempting to compute autorecon1 in a subject to see how it works recon-all in a stepwise as described in the tutorial. Sorry if this is a very naive question but it is the first time I am trying to run an analysis with FreeSurfer. After running: *r* *econ-all -subjid 001 -autorecon1 -i S_001.nii.gz* I have found that it crashes with the following warning: *recon-all -s 001 exited with ERRORS at dom * I have seen that the problem comes from orig_nu.log Does anyone have any thoughts on how to trouble-shoot this problem? I have attached the recon-all.log and the orig_nu.log in case it is of any use. Kind regards, Rosalia

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[FSL] Tenure-Track Research Fellowships in Precision Imaging - University of Nottingham (fwd)
by Bruce Fischl 13 Nov '17

13 Nov '17

FYI ---------- Forwarded message ---------- Date: Mon, 13 Nov 2017 10:59:30 +0000 From: Stamatios Sotiropoulos <stamatios.sotiropoulos(a)NDCN.OX.AC.UK> Reply-To: FSL - FMRIB's Software Library <FSL(a)jiscmail.ac.uk> To: FSL(a)jiscmail.ac.uk Subject: [FSL] Tenure-Track Research Fellowships in Precision Imaging - University of Nottingham Dear All A number of unique opportunities are available for Tenure-track Research Fellowships in the University of Nottingham in the field of Precision Imaging. Potential topics include Neuroimaging-based disease biotyping, Imaging-based neuromodulation, and MR Spectroscopy. More details can be found online: http://www.nottingham.ac.uk/research/researchwithus/fellowships/beacon-fell owships.aspx The deadline for applications is Monday 4 December 2017. Best wishes Stam ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Stamatios N Sotiropoulos, PhD *Associate Professor Sir Peter Mansfield Imaging Centre School of Medicine, Queens Medical Centre The University of Nottingham, NG72UH *Honorary Research Fellow Centre for Functional MRI of the Brain (FMRIB) University of Oxford t: 0115 82 31027 w: www.nottingham.ac.uk/medicine/people/stamatios.sotiropoulos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Freesurfer] Fw: Multiple comparison, color maps and contrast
by Douglas N Greve 13 Nov '17

13 Nov '17

can you send pics of the two patterns? Also, please remember to post to the list! doug On 11/10/2017 06:16 PM, Fabrizio Pizzagalli wrote: > Hi Douglas, > > I am not obtaining the same pattern testing for Group A > Group B > (c=[1 -1]) and Group A < Group B (c=[-1 1]). > That's why I am a bit confused. > > Thank you very much! > fab > > On Fri, Nov 10, 2017 at 12:29 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > the sig is signed by the sign of the contrast so that you can see > both sides. The p-values is two-sided > > > > On 11/10/17 3:25 PM, Fabrizio Pizzagali wrote: > > Hello, > When comparing 2 groups I obtain negative sig.mgh values > testing for Group A > Group B. > Shouldn't I get positive values of sig.mgh when testing for > Group A < Group B? > > Thank you. > Best, > fab > > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- 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/

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7 T analysis - does GPU help?
by Melanie Ganz 13 Nov '17

13 Nov '17

Dear list, especially Bruce and Jon, We are starting to acquire images on the local 7T Philips scanner and would like to run them through FS. We did some pilot runs following what's described on http://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon and in http://www.sciencedirect.com/science/article/pii/S105381191730808X. That took approximately 42 hours. It looked reasonable but I estimate from the pilot run that some manual edits will be in order. This is quite tedious to do if the turnaround time is 2 days and we are looking at quite a few number of patients we want to run. Would we actually get any speedup if we utilize the -use-gpu flag (we don't have access to a gpu yet, but are getting one soon). I looked at the speedup factors and especially mris-inflate doesn't speed up too much (https://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide) . Kind regards, Mel

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"Halo" of low values around pial surface in Apparent Diffusion Coefficient maps from DWI registered to CVS template
by Mehta, Chintan 13 Nov '17

13 Nov '17

Dear FreeSurfer users, I'm using FS 6.0. I registered DWI scans to the CVS registrations of T1-weighted MRI scans as described at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0. The average diffusion coefficient (ADC) maps registered to CVS have a "halo" of very low values around the brain (right outside the pial surface of the cortex), which diverges from the expectation that ADC be lowest in white matter. See attached image of ADC in CVS space for one sample: adc-ANAT+CVS-to-avg35.png On the other hand, this halo of low values is not as apparent in the ADC maps in diffusion space (masked to voxels in subject's aseg in diffusion space): See attached image of ADC in diffusion space: diffusionSpace-adc.png For comparison, also attached are the subject's T1-weighted images registered to CVS space (final_CVSmorphed_tocvs_avg35_norm.png) and to diffusion space (diffusionSpace-brainmask.png) that underlay these spatial maps. On the other hand, fractional anisotropy (FA) maps in either CVS space or diffusion space look reasonable --- with FA highest along white matter fiber tracts. See attached screenshots for FA in CVS space (fa-ANAT+CVS-to-avg35.png) and FA in Diffusion space (fa-diffusionSpace.png; masked to aseg in diffusion space). This phenomena is typical across all samples. Is the halo of very low values surrounding the brain, adjacent to cortical gray matter, typical in ADC spatial maps registered to CVS? If so, is there a way to remove this halo of low values for ADC maps in CVS space? For example, the depth of this halo decreases when masking the ADC maps with the aseg.mgz for the CVS average template. The halo decreases furthermore when masking by the subject-specific aseg registered to CVS generated by mri_cvs_register ("final_CVSmorphed_tocvs_avg35_aseg.mgz"). In either case, the halo does not disappear. I'm concerned that these ADC mis-measurement e boundary may yield significant issues in GLM analysis. If there is no way to remove this halo, is a GLM of ADC maps in CVS space more reliable for voxels masked to white matter? Thank you. Best, Chintan

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TRACULA
by 郑凤莲 13 Nov '17

13 Nov '17

Hi Professor, Thank you for looking at my e-mail in your busy time. I am a student studying TRACULA in Freesurfer. But I got into troubles in my study. Could you help me resolve some problems? 1. When I do the first step, after the ‘bbregister done’, it say 'with errors', as the following picture. Do you know what it means? How to solve it? 2. In another computer, I finished the first step with out errors. But in the second errors, I met a trouble again. Does it because of the version of Freesurfer? I really need your help. If I don't describe my problem clearly, please contact me at any time. I am looking forward to your reply. Thank you very much. Sincerely, Zheng

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Re: [Freesurfer] Adding control points to aparc+aseg
by Nicholas Goh 13 Nov '17

13 Nov '17

I have still been having trouble with fixing the white matter of the aparc+aseg.mgz file for a subject. I have tried using recon-all -autorecon2-cp -autorecon3 -subjid XXXX recon-all -autorecon2-wm -subjid XXXX recon-all -autorecon2-wm -autorecon3 -subjid XXXX None of these have solved the issue, and I was hoping for help in finding a way to fix this? There are other more extreme examples, but this one seems to have an error at [-7, 114, 133] Thank you for the help, Nicholas Goh On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh <ngoh95(a)gmail.com> wrote: > Ping, is this okay to do? I Think it is but wanted to check before sending > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: Thu, Sep 28, 2017 at 5:23 PM > Subject: Re: [Freesurfer] Adding control points to aparc+aseg > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > > Hi Nicholas > > why don't you tar, gzip and upload your subject and we will take a look. > Make sure to tell us the coordinates of where you are trying to fix things > > cheers > Bruce > > > On Thu, 28 Sep 2017, Nicholas Goh wrote: > > I am still having trouble with getting the aparc+aseg to recognize sections >> that should be white matter as such. Using the control points paired >> withrecon-all -autorecon2-cp -autorecon3 -subjid XXXX >> >> did not work, after 4 or 5 attempts with different control points, and >> using >> recon-all -autorecon2-wm -s XXXX >> also did not yield appreciable results. Is there anything else that I >> might >> be able to try to fix this? >> Thank you for all the help, >> >> Nicholas Goh >> >> On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak <fkm24(a)medschl.cam.ac.uk> >> wrote: >> Hi Nicholas, >> >> In such situations, I have learned that autorecon2-wm after adding WM >> voxels seems to work pretty well. Hope that helps. >> >> Best Wishes, >> Elijah >> >> On 27 September 2017 at 16:46:43, Nicholas Goh (ngoh95(a)gmail.com) >> wrote: >> >> Bruce, >> Thank you for the response. Attempting to use this method has >> not produced results, and I am unsure how to proceed or if I had >> performed it improperly. I have attached an example of the >> control points being placed, if that helps any. >> Thank you, >> >> Nicholas Goh >> >> On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Nicholas >> >> yes, possibly, depending on why you are missing >> chunks. If the white matter in the regions you are >> missing has intensity values significantly < 110 >> then what you are doing should help. The control.dat >> file must be place in the subject/tmp dir for us to >> find it. >> >> cheers >> Bruce >> On Wed, 27 Sep 2017, Nicholas Goh wrote: >> >> I am attempting to fix the >> aparc+aseg.mgz file for an image, and >> wanted to check to see if I am >> doing it correctly.What I was doing >> which seemed to be ineffective was >> 1)create a new point set of control >> points labelled control.dat >> 2)place control points along what should >> be white matter >> 3)save point set >> 4)run recon-all -autorecon2-cp >> -autorecon3 -subjid XXXX >> >> Is this the correct way to go about >> fixing aparc+aseg files that are missing >> chunks of the brain? Is >> there a better way to go about this? >> Thanks for the help, >> >> Nicholas Goh >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for >> the person to whom it is >> addressed. If you believe this e-mail was sent to >> you in error and the e-mail >> contains patient information, please contact the >> Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the >> e-mail was sent to you in error >> but does not contain patient information, please >> contact the sender and properly >> dispose of the e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person >> to whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >

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[FSL] Microstructural Imaging Jobs in CUBRIC, Cardiff (fwd)
by Bruce Fischl 12 Nov '17

12 Nov '17

FYI ---------- Forwarded message ---------- Date: Mon, 13 Nov 2017 01:38:46 +0000 From: Derek Jones <JonesD27(a)CARDIFF.AC.UK> Dear All, Please find below links to three jobs in microstructural imaging at CUBRIC, Cardiff University (available immediately). Obviously, a large part of this will be exploring the benefits of using the ultra-strong gradients on the Connectom scanner, but we’re also interested to see what 7T offers in terms of microstructure. As an update, we’re pretty pleased with the current performance of the Connectom scanner and getting some really nice results out, so I think there is a really good opportunity for people that want to explore cutting edge diffusion / multi-contrast approaches with ultra-strong gradients. Anyway, I’d be very happy to discuss any of these with you. Please feel free to pass on the details to other people that you think may be interested. Here’s the links: Research Associate: https://goo.gl/a6bRVe Research Fellow: https://goo.gl/ZqgMKY Thanks for reading! Derek Jones __________________________________________ Derek Jones Director CUBRIC Cardiff University +44-29-2087-9412 [IMAGE] http://sites.cardiff.ac.uk/cubric Yr Athro Derek Jones Cyfarwyddwr Canolfan Delweddu Prifysgol Caerdydd er Ymchwil yr Ymennydd (CUBRIC) Coleg Y Gwyddorau Biofeddygol Prifysgol Caerdydd Ffôn: + 44(0)2920879412

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Re: [Freesurfer] Creating cached versions of Xhemi registrations
by Mehta, Chintan 12 Nov '17

12 Nov '17

Dear Doug, I'm performing a linear regression over one sample with a design matrix including columns for one continuous-valued predictor whose effect on neural measures I'm interested in testing, several covariates to adjust for (continuous- or binary-valued such as age, sex, total intracranial volume, and other demographic groupings), and an intercept. The contrast matrix I'll be testing will have 1 in the column corresponding to the column in the design matrix containing the predictor of interest and zeros in all other columns. In addition, I was interested in performing the same linear regressions over subsets of the group to determine whether the pattern associated with the predictor-of-interest is persistent. That's why I want to stack surfaces for different sets of subjects (without recreating surfaces registered to fsaverage_sym for each subjects' laterality indices for each instance). This way I could repeat the same contrast, except subsetting rows of the design matrix for subjects in the given sample. Thank you. Best, Chintan >Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 10 Nov 2017 11:28:52 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> > That looks right, though I'm not sure what is in the design matrix. Is it a column of +1 and -1?

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mean cortical thickness map
by John Anderson 12 Nov '17

12 Nov '17

Dear Freesurfer community, I want to visualize the mean cortical thickness map of 20 subjects. I ran the command recon-all on the the T1 images. How can I visualize the mean cortical thickness of one group. Thanks for any advice John

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Freesurfer November 2017