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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

xhemi installation
by Sofie Valk 08 Jan '14

08 Jan '14

Dear FreeSurfers, I have a question regarding the installation of xhemi (I am using FreeSurfer 5.1) I tried to follow the guide on: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi to install the necessary files, however the following files do not seem to be present on the ftpserver: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.{… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol.{… What could be wrong? Thank you very much!! Kind regards, Sofie Valk, ... PhD Candidate, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany

3 4

Re: [Freesurfer] pial erosion/downsampling
by Octavian Lie 08 Jan '14

08 Jan '14

Thank you, I want to merge the pial eroded (of white expanded) and downsampled surfaces of the two hemispheres in a new surface (generate a new, continuous, surface/mesh, no holes, no self intersections). The question is whether pial freesurfer atlases and spherical registration would be applicable to this surface too, Octavian On Wed, Jan 8, 2014 at 11:54 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you cc the list? I don't know what you mean by "merge" > > On Wed, 8 Jan 2014, Octavian Lie wrote: > >> Thank you, >> >> I want to merge the pial eroded (of white expanded) and downsampled >> surfaces of the two hemispheres in a new surface. The question is >> whether pial freesurfer atlases and spherical registration would be >> applicable to this surface too, >> 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. >

2 1

surface reorientation in sinc with volume
by Octavian Lie 08 Jan '14

08 Jan '14

Dear All I reoriented a volume on exporting to analyze format for an application mri_convert -i path to file/T1.mgz --out_orientation PSR -o path to file/T1reoriented.mgz mri_convert -ot analyze -i path to file/T1reoriented.mgz -o path to file/T1reorientedPSR.img I need to reorient from the command line the original pial surfaces (?h.pial) generated from the recon-all process to new surfaces to match the new T1 orientation (T1 reorientedPSR). Thank you, please advise, Octavian

1 0

longitudinal hippocampal subfields analysis
by Salil Soman 08 Jan '14

08 Jan '14

Hi, I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated. Thank you. Salil Soman, MD, MS

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