Freesurfer

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Question about Monte Carlo and significant clusters
by Maller, Jerome 09 Jan '14

09 Jan '14

Hi everyone, I have a question related to Monte Carlo tests of multiple comparisons. When I conduct some of my analyses, there is no difference between before and after Monte Carlo (i.e. same size and coloured regions appear on the inflated brain after I click on the analysis in the Description box), whereas for other analyses I get large matt coloured clusters with significance values stated for those clusters in the terminal. Also, I have completed one analysis whereby the before and after Monte Carlo coloured clusters are the same but only one of the clusters is stated as significant in the terminal. Does anyone know whether the clusters that appear after Monte Carlo simulation, but are not stated as clusters in the terminal, are significant? Thankyou! Jerome Maller -- Dr Jerome J Maller BSc,GradDipPsych,MSc,PhD Neuroscientist NHMRC Industry Career Development Fellow (CDF) CETBIR (Centre for Excellence in Traumatic Brain Injury) Postdoctoral Research Fellow Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School, Monash University and Alfred Hospital 4th Floor, 607 St Kilda Rd, Melbourne VIC Adjunct Associate Professor Centre for Research on Ageing, Health and Wellbeing, Research School of Population Health, ANU College of Medicine, Biology and Environment at the Australian National University. Phone: +61 3 9076 2404 Fax: +61 3 9076 6588 Mobile: +61 419 221 454

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Fwd: Anatomical segmentation - question
by Rotem Saar 09 Jan '14

09 Jan '14

Dear freesurfer experts, I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing step number 4 in the script below – from some reason, the two images don't fit. Should I use "scale brain" ? I know this is not recommended thus want to consult with u first – Can u please comment on why this is happening? Is there any value that corresponds to "how good is the segmentation" ? if yes, where can I find it ? My script is written below. Thanks, Rotem Anatomical segmentation: first step- 23 hours: *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s FOLDER-NAME* second step:(gyrus=green, sulcus=red) *tksurfer -curv FOLDER-NAME lh/rh inflated* third step: (talairch registretion) *tkmedit FOLDER-NAME brainmask.mgz* File-> transforms-> load transform AUX-> Browse-> talairch.xfm forth step: (simetry - allows changing 12df transformation. if we made any changes we should click "save reg" and run this command again) *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME fifth step: (scalp removal: if removed too much, rise up from the value 25: *recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME * to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white *) for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz* tools-> configure volume brush -> MARK: mode=clone, source=Aux tools-> configure brush info (for choosing brush size) click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing voxels : slice by slice. when finish, click: File-> save main volume sisxt step: (cp for correcting segmentation) *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white* seventh step: (done) *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

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Re: [Freesurfer] Freesurfer templates for cross-ethnicity comparisons
by Bruce Fischl 09 Jan '14

09 Jan '14

Hi Mike nice to be right once in a while :). You shouldn't have to register to an atlas brain to build the folding pattern template though - you can pick one of your own dataset to start with. cheers Bruce On Thu, 9 Jan 2014, Michael Chee wrote: > Hi Bruce and Linda, > > Yes, this is my work email. Pacific internet shut down email operations in > Singapore in Dec 2012… > > We built an ‘Asian Only’ template with around 30 Chinese participants but > the use of this template did not generate a result that differed from that > obtained using the stock MGH template. We were quite disbelieving of Bruce’s > prediction that this would be so but he proved to be correct. The caveat > (and its not a small one) is that to BUILD the template, one has to register > to an atlas brain which is presumably Caucasian weighted. > > The paper comparing predominantly Caucasian and Chinese brains using FS was > published in 2011 in J Cog Neurosci and can be found on my lab website. We > did not mention building the custom atlas in that work because of the lack > of a difference in using this vs. the standard template. > > Zheng Hui (copied) did all the hard work on this. > > > Michael Chee MBBS, FRCP(Edin) > Professor > Cognitive Neuroscience Laboratory > Neuroscience and Behavioral Disorders Program > Duke-NUS Graduate Medical School > 8 College Rd, #06-18 > Singapore 169857. > > email: michael.chee(a)duke-nus.edu.sg > office: (65) 65164916 > CNL Home page: http://www.cogneuro-lab.org > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: Thursday, 9 January, 2014 5:24 am > To: Linda Zhang <lzhang87(a)gmail.com> > Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu>, Michael Chee > <michael.chee(a)duke-nus.edu.sg> > Subject: Re: Freesurfer templates for cross-ethnicity comparisons > > Hi Linda > > I had an old address for Mike in the first email. I think this one is > correct. Building a folding atlas is pretty quick, depending on how many > subjects you have. You'll need to pick one subject, run mris_make_template > to build a single-subject template (for each hemi), register everyone to > it, rerun mris_make_template to build a multi-subject atlas, rerun > mris_register with the new atlas as the target and iterate this procedure > until it converges (atlas building and reregistering). Usually it does > after only one additional round. > > cheers > Bruce > > > > > On Wed, 8 Jan 2014, Linda Zhang wrote: > > Thanks Bruce! How long would it take to build an atlas? > > What are your thoughts Mike? > > > On 7 January 2014 14:38, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Linda > > I actually don't know the ethnicity of the subjects in our > atlas. I wouldn't > expect it to be an issue for folding patterns, but it is > possible. You could > build your own atlas and redo the analyses if you want to see if > that > changes things. I'll cc Mike Chee who I think has looked at this > question as > well. > > cheers > Bruce > > > > > > On Tue, 7 Jan 2014, Linda Zhang wrote: > > Hi Bruce, > > I've been using Freesurfer to compare subcortical volumes > and cortical > thickness between Caucasian and Chinese controls. There > are some > significant findings, but the question of whether or not > these may be > biased due to the template has been raised (the assumption > being that > the majority of subjects used in the template are > Caucasian). Is it > possible to reduce the weight of the atlas during > normalisation (or > some other method to address the issue)? I would greatly > appreciate > your thoughts on this. > > Cheers, > Linda > > > > > > 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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Fwd: questions about cortical thickness using qdec.
by yaya ya 09 Jan '14

09 Jan '14

Dear Greve, Thank you very much for your response. I am now a little more clear, although I still have some further questions. According to your suggestion, I just tried to test whether there is a difference between group age. I included age as a continuous variable in qdec. After running, I got the results arising from the contrast 0 0 1 -1 (which is called does the thickness-age correlation differ between two groups?). That is, the results revealed the thinner in some brain areas. But when I checked the results relating to the comparision of groups (1 -1 0 0 ), the results were the same expect the opposite pattern. That is, the results became thicker in the same region. Does this imply that there is an age effect? It means I could not use DOSS to do analysis, right? Best, Lickey On Thu, Jan 9, 2014 at 12:32 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > On 01/08/2014 04:28 PM, yaya ya wrote: > > Dear Freesurfer experts, > > > > I have a question about cortical thickness analysis using freesurfer. > > Since I don't know how to post my question in freesurfer mailing > > list, that is why I am writing to you to get some help. Hopefully, my > > email will not cause you any troubles. > Thanks for posting to the list. > > > > My question is : When I compared thickness from two groups (a patient > > group and a healthy contrl group), that is say I got the thinner in a > > subdivision of a particular brain region in patients than that in > > controls. But when I added age as a nusiance factors (not in the > > continuous covariate because I want to control for or regress out the > > age effect) in qdec, the results changed. In the same region, the > > thickness became thicker in the patients than that in the controls. I > > have no idea what happened. Which of them do I need to trust? The age > > between two groups has been matched. > It depends on several things. It might be that there is an interaction > between group and age. Try testing for a difference between the age > slopes of the two groups. If there is no difference, then re-run using > DOSS (DOSS was removed from QDEC so you'll have to create an FSGD file > and use mri_glmfit). > > > > In addition, when I do FDR correction on the results, the min in the > > threshold jumped to more than 5 , making all the clusters disappear. I > > think this correction is too high, unabling the genious effects to > > show up. How to deal with it? > Try using a cluster correction instead of FDR. > doug > > > > > By the way, our lab's IT staffs install the lastest released > > freesurfer. But when I use the qdec, I could not find the option of > > DODS and DOSS, as discussed in the mailing list. I am wondering if it > > has been deleted in this new version. > > > > I really appreciate your help in advance. > > > > Best, > > Lickey > > > > > > _______________________________________________ > > 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/ > > _______________________________________________ > 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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Re: [Freesurfer] absolute value of effect size
by Douglas N Greve 08 Jan '14

08 Jan '14

Several potential problems. It makes the statistics non-gaussian and the abs(ces) becomes noise dependent (and so there will be a noise dependent bias). This makes interpretation more difficult (eg, is a difference between groups a difference in ces or a difference in noise?). The non-gaussianity could be addressed with a permutation test. doug On 01/08/2014 07:11 PM, shahin(a)nmr.mgh.harvard.edu wrote: > Exactly! I need ces and cesvar files for a second order analysis. More > specifically, I need to subtract this absolute map from another map. > Would you be more specific about what I should check when I am doing this > second order analysis? > > > >> You can do it to the sig file (the p-value already assumes a two-sided >> test). Why do you want to do it with the ces and cesvar files? If you >> are planning to use the abs(ces) for a higher level analysis then you >> need to be very careful as you can get some unintended effects >> doug >> >> >> >> >> On 01/07/2014 03:46 PM, SHAHIN NASR wrote: >>> Hi, >>> I have two related questions. I have two conditions (e.g. C1 and >>> C2) and I want to generate a map that shows all voxels that can >>> differentiate C1 from C2 _irrespective_ of whether C1>C2 or C1<C2. I >>> think it can be done easily by: >>> >>> mris_calc -o sig.nii abs_sig.nii abs >>> >>> If I am right, then: >>> 1) Can I apply the same command to ces.nii file to have the absolute >>> value of the effect size (i.e. abs(C1-C2 effect size)) or should I >>> consider other factors? >>> 2) Do I need to apply the same routine to cesvar? >>> >>> Thanks >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >> -- >> 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/ >> >> >> > -- 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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absolute value of effect size
by SHAHIN NASR 08 Jan '14

08 Jan '14

Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 *irrespective* of whether C1>C2 or C1<C2. I think it can be done easily by: mris_calc -o sig.nii abs_sig.nii abs If I am right, then: 1) Can I apply the same command to ces.nii file to have the absolute value of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other factors? 2) Do I need to apply the same routine to cesvar? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
by Muhammad Naveed Iqbal Qureshi 08 Jan '14

08 Jan '14

Thank you Bruce, Please guide me how can I use mri_surf2vol command on lh/rh.thickness files to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you Best Regards, Muhammad Naveed Iqbal Qureshi > From: freesurfer-request(a)nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 119, Issue 6 > To: freesurfer(a)nmr.mgh.harvard.edu > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > 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. erroneuos segmentation labeling of skull outside of brain > (Yuliya Yoncheva) > 2. Re: erroneuos segmentation labeling of skull outside of brain > (Bruce Fischl) > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > 4. Re: erroneuos segmentation labeling of skull outside of brain > (Yuliya Yoncheva) > 5. Re: erroneuos segmentation labeling of skull outside of brain > (Bruce Fischl) > 6. Re: recon-all exited w/errors (Bruce Fischl) > 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) > 8. converting .thickness files of T1 MRI from FreeSurfer into > AFNI (Muhammad Naveed Iqbal Qureshi) > 9. brain orientation in qdec (L. Schweren) > 10. Re: converting .thickness files of T1 MRI from FreeSurfer > into AFNI (Bruce Fischl) > 11. recon-all error (Emad Ahmadi) > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 5 Jan 2014 15:14:39 -0500 > From: Yuliya Yoncheva <yuliya.yoncheva(a)gmail.com> > Subject: [Freesurfer] erroneuos segmentation labeling of skull outside > of brain > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear FreeSurfer community, > > I am visually inspecting the quality of my recon -all output for a large > dataset and have a rookie question. > > In some instances, when skull stripping ended up leaving some of the skull, > these voxels are associated with a "sgmtn label" (cerebral cortex). In > other instances, although there are a small number of skull voxels that > were not removed automatically, these voxels do not have an associated > "sgmnt label" available in TkMedit Tools. > > Is it the case that only the voxels for which there is a segmentation label > are actually added to the total grey volume estimate? > > Thus, voxels, which have not been automatically labelled would not impact > volume computations? > > Thank you kindly for your help. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/3… > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: ExCerCor.png > Type: image/png > Size: 81100 bytes > Desc: not available > Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/3… > > ------------------------------ > > Message: 2 > Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull > outside of brain > To: Yuliya Yoncheva <yuliya.yoncheva(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1401051539450.16518(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Yuliya > > they are included if they are inside of the ?h.pial surface. We don't use > the cortex aseg label as it is in general less accurate than the surfaces. > > cheers > Bruce > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > Dear FreeSurfer community, > > I am visually inspecting the quality of my recon -all output for a large > > dataset and have a rookie question. > > > > In some instances, when skull stripping ended up leaving some of the skull, > > these voxels are associated with a "sgmtn label" (cerebral cortex). In other > > instances, although there are a small number of skull voxels that were not > > removed automatically, these voxels do not have an associated "sgmnt label" > > available in TkMedit Tools. > > > > Is it the case that only the voxels for which there is a segmentation label > > are actually added to the total grey volume estimate?? > > > > Thus, voxels, which have not been automatically labelled would not impact > > volume computations? > > > > Thank you kindly for your help. > > > > > > ------------------------------ > > Message: 3 > Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR > To: Octavian Lie <octavian.lie(a)gmail.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1401051554470.16518(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Octavian > > it's not so easy to reduce the bandwidth in the T2-space sequences, but > certainly you can try. Geometry-matched just means that the FOV and > matrix sizes are the same. > > cheers > Bruce > On Fri, 3 Jan 2014, Octavian Lie wrote: > > > Dear Bruce, > > > > Best wishes for 2014! > > > > I will heed your advice and cc to the list. Indeed, the MGH protocol I > > obtained from Andre has one acquisition (NSA). > > Related, I cc this post: > > > > We have been trying adaptations of the T2spaceFLAIR MGH protocol on > > our Phillips 3T scanners (sequences called VISTA). Incorporation of > > the T2 space FLAIR has been mostly successful at editing out the dura > > from the pial surface. The only concern are minute differences > > occasionally appearing as small indentations (at most times <1-2mm) > > between the woFLAIR.pial and the final pial surfaces, including in > > intrasulcal (duraless) areas; the amount of these small mismatches is > > variable from patient to patients, with some trials with almost > > perfect overlap, and others with visible, if small, differences. I > > wonder if this has been your experience too, and if this is due mostly > > to bb registration limits or to differences in pixel bandwidth between > > mprage and space flair sequences (in our case, see below). > > In FSwiki, the recommendation is that T2 space flair ?should be > > bandwidth, geometry and readout matched to the mprage?. > > > > 1. Speaking about pixel bandwidth, logistics most likely would not > > allow application of a MEMPR sequence on our Phillips. According to > > Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple echo > > sequence is not available, one should choose a bandwidth of 195 > > Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio MPRAGE > > protocol as if the MEMPR is not available, how one would adjust the > > bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens > > space flair and MEMPR protocols) to "match" it to the "simple" MPRAGE > > protocol (decreasing it to 195 ?). Would it be a workaround? (Please > > comment on the Siemens case, obviously, I do not expect any light on > > Phillips without further testing). > > 2. Could you clarify what geometry matched means? > > Please advise, > > > > Thank you, > > > > Octavian > > > > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Octavian > >> > >> can you cc the list so that others can answer? What is NSA? We don't have a > >> ton of experience with it, but 1 has seemed ok (not sure if we've ever tried > >> two) > >> Bruce > >> > >> > >> > >> On Thu, 2 Jan 2014, Octavian Lie wrote: > >> > >>> Dear Bruce, > >>> > >>> Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a > >>> consistent difference in results, with the 2-NSA run obviously doubling > >>> the > >>> scan time. Is there a preferred number of NSA you recommend, or we should > >>> be > >>> fine with one? Both are at resolution 1X1X1 mm. > >>> Thank you, > >>> > >>> Octavian > >>> > >>> > >>> > >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >>> wrote: > >>> Hi Octaviaan > >>> no, not really. You should motion correct and average them using > >>> something like mri_motion_correct* > >>> > >>> We do typically bandwidth/readout match them to the memprages so > >>> that there is no differential distortion > >>> > >>> cheers > >>> Bruce > >>> > >>> > >>> On Wed, 1 Jan 2014, Octavian Lie wrote: > >>> > >>> Dear All, > >>> > >>> We recently implemented pial correction using T2 > >>> space FLAIR with freesurfer > >>> v 5.3, mostly successfully. We use 2-3 MPRAGE > >>> (sagittal + axial and/or > >>> coronal) volumes as 001.mgz, 002/003.mgz for the > >>> motion correction step in > >>> recon-all pipeline. > >>> The typical times for acquiring space FLAIR in our > >>> settings vary from 2.5 to > >>> 6 min, depending on the resolution/NSA no. I was > >>> wondering how freesurfer > >>> deals with motion artifacts in the space FLAIR > >>> sequence (especially with > >>> longer acquisition times), and if there is a > >>> strategy to minimize motion > >>> distortion with these (such as getting second runs > >>> for averaging, etc). > >>> Please advise, > >>> > >>> Octavian. > >>> > >>> > >>> > >>> > >>> 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. > >>> > >>> > >>> > >> > > > > > > > > ------------------------------ > > Message: 4 > Date: Sun, 5 Jan 2014 19:25:53 -0500 > From: Yuliya Yoncheva <yuliya.yoncheva(a)gmail.com> > Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull > outside of brain > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Bruce, > > thank you very much for your fast response and clarifying that potential > voxels outside the pial surface do not impact cortical measures. > > Best, > Yuliya > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > > > Hi Yuliya > > > > they are included if they are inside of the ?h.pial surface. We don't use > > the cortex aseg label as it is in general less accurate than the surfaces. > > > > cheers > > Bruce > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > Dear FreeSurfer community, > >> I am visually inspecting the quality of my recon -all output for a large > >> dataset and have a rookie question. > >> > >> In some instances, when skull stripping ended up leaving some of the > >> skull, > >> these voxels are associated with a "sgmtn label" (cerebral cortex). In > >> other > >> instances, although there are a small number of skull voxels that were not > >> removed automatically, these voxels do not have an associated "sgmnt > >> label" > >> available in TkMedit Tools. > >> > >> Is it the case that only the voxels for which there is a segmentation > >> label > >> are actually added to the total grey volume estimate? > >> > >> Thus, voxels, which have not been automatically labelled would not impact > >> volume computations? > >> > >> Thank you kindly for your help. > >> > >> > >> > > > > 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. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/e… > > ------------------------------ > > Message: 5 > Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull > outside of brain > To: Yuliya Yoncheva <yuliya.yoncheva(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1401052028520.16518(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > exactly, or measures derived them them like whole-brain volume > > cheers > Bruce > > On Sun, 5 Jan 2014, Yuliya > Yoncheva wrote: > > > Hello Bruce, > > thank you very much for your fast response and clarifying that potential > > voxels outside the pial surface do not impact cortical measures. > > > > Best,? > > Yuliya > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > wrote: > > Hi Yuliya > > > > they are included if they are inside of the ?h.pial surface. We > > don't use the cortex aseg label as it is in general less > > accurate than the surfaces. > > > > cheers > > Bruce > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > Dear FreeSurfer community, > > I am visually inspecting the quality of my recon > > -all output for a large > > dataset and have a rookie question. > > > > In some instances, when skull stripping ended up > > leaving some of the skull, > > these voxels are associated with a "sgmtn label" > > (cerebral cortex). In other > > instances, although there are a small number of > > skull voxels that were not > > removed automatically, these voxels do not have an > > associated "sgmnt label" > > available in TkMedit Tools. > > > > Is it the case that only the voxels for which there > > is a segmentation label > > are actually added to the total grey volume > > estimate?? > > > > Thus, voxels, which have not been automatically > > labelled would not impact > > volume computations? > > > > Thank you kindly for your help. > > > > > > > > > > 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. > > > > > > > > > > ------------------------------ > > Message: 6 > Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all exited w/errors > To: "Boric, Katica A." <KBORIC(a)mgh.harvard.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1401052049480.16518(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Katica > > what format was the input image to recon-all? Can you verify that tkmedit > has the directions correct (that is what it labels as anterior is actually > anatomically anterior, etc...). If so, then the talairach just failed and > you will need to either try an alternative (like the MNI or SPM talairachs) > or generate it manually. > > cheers > Bruce > > > > On Thu, 2 Jan 2014, Boric, Katica A. > wrote: > > > Happy New Year freesuerfers! > > I run into this error while doing?recon-all : > > > > 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 really appreciate if someone could give me some advice on how to fix > > this error. > > > > Thank you very much! > > > > Katica Boric, > > > > > > ps:?Here is the error log: > > > > #@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > INFO: Attempting MINC mritotal to perform Talairach align > > #-------------------------------------------- > > #@# Talairach Thu Jan ?2 14:20:33 EST 2014 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > > orig.mgz --o orig_nu.mgz? > > > > > > ?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm? > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > /usr/local/freesurfer/bin/talairach > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > Thu Jan ?2 14:21:30 EST 2014 > > tmpdir is transforms/tmp.talairach.34005 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc > > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc? > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from orig_nu.mgz... > > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 > > i_ras = (-1, -9.03383e-08, 0) > > j_ras = (-1.3411e-07, 2.66591e-08, -1) > > k_ras = (1.59256e-07, 1, -5.93718e-09) > > writing to transforms/tmp.talairach.34005/src.mnc... > > -------------------------------------------- > > mritotal -verbose -debug -clobber -modeldir > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm > > transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm > > Legacy library shellwords.pl will be removed from the Perl core distribution > > in the next major release. Please install it from the CPAN distribution > > Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, > > line 460. > > ? > > ? > > Thu Jan ?2 14:21:43 EST 2014 > > talairach done > > > > ?cp transforms/talairach.auto.xfm transforms/talairach.xfm? > > > > #-------------------------------------------- > > #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014 > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > 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. > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan ?2 14:21:45 EST > > 2014 > > > > > > > > > > > > > > ------------------------------ > > Message: 7 > Date: Sun, 5 Jan 2014 23:35:55 -0800 > From: Frank Hsieh <two.frank(a)gmail.com> > Subject: [Freesurfer] ROI masks created in FreeSurfer used in FSL?? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear FreeSurfer Users, > > I ran recon -all on my structural image and created ROI masks (using > mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use > these masks for further analysis with FSL. However, it seems that the ROI > masks generated with mri_label2vol have different header information than > that of the original structural image. As a result, I was unable to carry > out further analysis with FSL (e.g., converting these ROI masks into > functional space with hires2example_func.mat). I was wondering if there is > a way to solve this issue. > > Many thanks in advance. > Frank > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/a… > > ------------------------------ > > Message: 8 > Date: Mon, 6 Jan 2014 17:11:54 +0900 > From: Muhammad Naveed Iqbal Qureshi <mniqureshi(a)hotmail.com> > Subject: [Freesurfer] converting .thickness files of T1 MRI from > FreeSurfer into AFNI > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <BLU174-W27296B6C59F4D34F89293AC4B70(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > Hi, > I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format > I tried the following Command but it gives error > > > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... > AFNI BRIK write unsupported > ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > UN:/media> > > Please let me help me to solve this problem > Thank you :) > > > > Best Regards, > > Muhammad > Naveed Iqbal Qureshi > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/1… > > ------------------------------ > > Message: 9 > Date: Mon, 6 Jan 2014 10:45:52 +0100 > From: "L. Schweren" <l.j.s.schweren(a)umcg.nl> > Subject: [Freesurfer] brain orientation in qdec > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <005601cf0ac4$16bda9b0$4438fd10$(a)umcg.nl> > Content-Type: text/plain; charset="us-ascii" > > Dear experts, > > > > I ran recon-all with qcache. When loading the right hemisphere of fsaverage > (or any other surface reconstruction) into tksurfer (for example command: > tksurfer fsaverage rh white), the left hemisphere surface is displayed, and > it is upside down. When I import annotations they load in the same > orientation as the surface. However, the coordinates and the labels, > displayed in the Tksurfer Tools window, are not. For example, when I move > the cursor to the temporal lobe, the label says it's postcentral. I do not > mind manually turning the surfaces in tksurfer, but I do need to be sure I > am looking at the correct hemispheres, coordinates and labels. > > I hope you can help me solve this. Thank you in advance. > > > > Best wishes, > > Lizanne > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/5… > > ------------------------------ > > Message: 10 > Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] converting .thickness files of T1 MRI from > FreeSurfer into AFNI > To: Muhammad Naveed Iqbal Qureshi <mniqureshi(a)hotmail.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1401060840550.16518(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > Hi Muhammad > > try: > > set sdir=/home/naveed/freesurfer/subjects/CHR01/surf > mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik > > cheers > Bruce > > On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: > > > Hi, > > I want to know that how can I convert FreeSurfer .thickness files to AFNI > > readable format > > I tried the following Command but it gives error > > > > > > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... > > AFNI BRIK write unsupported > > ERROR: failure writing > > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik > > UN:/media> > > > > Please let me help me to solve this problem > > Thank you :)? > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > ------------------------------ > > Message: 11 > Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) > From: "Emad Ahmadi" <emad(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] recon-all error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <63234.172.19.2.113.1389022843.squirrel(a)mail.martinos.org> > Content-Type: text/plain; charset="iso-8859-1" > > Hello & Happy New Year! > > I'm running recon-all for one subject on MGH clusters (ERISone), and it > exits with error. I would appreciate it if you help me figure out what the > problem is. The log file is attached. > > All the best throughout 2014! > Emad > > > Emad Ahmadi, MD > ------------------------------------------------ > Research Fellow > Department of Radiology > Massachusetts General Hospital > Harvard Medical School > > 25 New Chardon Street, Suite 400 > Boston, MA 02114 > Tel: 617 726 5237 > Email: emad(a)nmr.mgh.harvard.edu > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: recon-all.log > Type: application/octet-stream > Size: 20022 bytes > Desc: not available > Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/e… > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: recon1job.bash > Type: application/octet-stream > Size: 1555 bytes > Desc: not available > Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/e… > > ------------------------------ > > Message: 12 > Date: Mon, 6 Jan 2014 17:51:18 +0200 > From: Rotem Saar <saar.rotem(a)gmail.com> > Subject: [Freesurfer] Fwd: Anatomical segmentation - question > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA(a)mail.gmail.com> > Content-Type: text/plain; charset="windows-1252" > > Dear freesurfer experts, > > I'm performing anatomical segmentation for Philips dicoms (3T scanner). I > got these two images from the same slice while performing step number 4 in > the script below ? from some reason, the two images don't fit. Should I use > "scale brain" ? I know this is not recommended thus want to consult with u > first ? Can u please comment on why this is happening? Is there any value > that corresponds to "how good is the segmentation" ? if yes, where can I > find it ? > > My script is written below. > > Thanks, > > Rotem > > Anatomical segmentation: > > first step- 23 hours: > > *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s > FOLDER-NAME* > > second step:(gyrus=green, sulcus=red) > > *tksurfer -curv FOLDER-NAME lh/rh inflated* > > third step: (talairch registretion) > > *tkmedit FOLDER-NAME brainmask.mgz* > > File-> transforms-> load transform AUX-> Browse-> talairch.xfm > > forth step: (simetry - allows changing 12df transformation. if we made any > changes we should click "save reg" and run this command again) > > *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* > > IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: > recon-all -all -subjectid FOLDER-NAME > > fifth step: (scalp removal: if removed too much, rise up from the value 25: > > *recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s > FOLDER-NAME * > > to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux > T1.mgz -aux-surface rh.white *) > > for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz* > > tools-> configure volume brush -> MARK: mode=clone, source=Aux > > tools-> configure brush info (for choosing brush size) > > click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing > voxels : slice by slice. > > when finish, click: File-> save main volume > > sisxt step: (cp for correcting segmentation) > > *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface > rh.white* > > seventh step: (done) > > *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* > > > > > > Rotem Saar-Ashkenazy > Department of Brain and Cognitive Science > Ben Gurion University of the Negev > Beer-Sheva 84105 > Israel > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/3… > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 3.png > Type: image/png > Size: 299694 bytes > Desc: not available > Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140106/3… > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 119, Issue 6 > ******************************************

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brain orientation in qdec
by L. Schweren 08 Jan '14

08 Jan '14

Dear experts, I ran recon-all with qcache. When loading the right hemisphere of fsaverage (or any other surface reconstruction) into tksurfer (for example command: tksurfer fsaverage rh white), the left hemisphere surface is displayed, and it is upside down. When I import annotations they load in the same orientation as the surface. However, the coordinates and the labels, displayed in the Tksurfer Tools window, are not. For example, when I move the cursor to the temporal lobe, the label says it's postcentral. I do not mind manually turning the surfaces in tksurfer, but I do need to be sure I am looking at the correct hemispheres, coordinates and labels. I hope you can help me solve this. Thank you in advance. Best wishes, Lizanne

2 1

questions about cortical thickness using qdec.
by yaya ya 08 Jan '14

08 Jan '14

Dear Freesurfer experts, I have a question about cortical thickness analysis using freesurfer. Since I don't know how to post my question in freesurfer mailing list, that is why I am writing to you to get some help. Hopefully, my email will not cause you any troubles. My question is : When I compared thickness from two groups (a patient group and a healthy contrl group), that is say I got the thinner in a subdivision of a particular brain region in patients than that in controls. But when I added age as a nusiance factors (not in the continuous covariate because I want to control for or regress out the age effect) in qdec, the results changed. In the same region, the thickness became thicker in the patients than that in the controls. I have no idea what happened. Which of them do I need to trust? The age between two groups has been matched. In addition, when I do FDR correction on the results, the min in the threshold jumped to more than 5 , making all the clusters disappear. I think this correction is too high, unabling the genious effects to show up. How to deal with it? By the way, our lab's IT staffs install the lastest released freesurfer. But when I use the qdec, I could not find the option of DODS and DOSS, as discussed in the mailing list. I am wondering if it has been deleted in this new version. I really appreciate your help in advance. Best, Lickey

2 1

Freesurfer templates for cross-ethnicity comparisons
by Linda Zhang 08 Jan '14

08 Jan '14

Hi Bruce, I've been using Freesurfer to compare subcortical volumes and cortical thickness between Caucasian and Chinese controls. There are some significant findings, but the question of whether or not these may be biased due to the template has been raised (the assumption being that the majority of subjects used in the template are Caucasian). Is it possible to reduce the weight of the atlas during normalisation (or some other method to address the issue)? I would greatly appreciate your thoughts on this. Cheers, Linda

2 3

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