Freesurfer September 2011

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Folding Index and Gyrification index
by Alan Francis 28 Sep '11

28 Sep '11

Hi Bruce, Nick & Doug: How does Folding index differ from Gyrification index? thanks, Alan BIDMC

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Re: [Freesurfer] Error with mri_glmfit-sim
by Douglas N Greve 28 Sep '11

28 Sep '11

again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with "--cache 2 sign" where sign is pos, neg, or abs doug Antonella Kis wrote: > Hi Doug, > > Thanks again for helping. I am trying to use QDEC but there are no > clusters surviving after FDR (it says statics cannot be done so gives > me error by running FDR). So I am trying to get the thickness values > only for the clusters that are formed in QDEC after setting up a > threshold = 2 (before running FDR). In order to do this you suggested > me to run mri_glmfit-sim on the QDEC results. The only problem is that > I cannot run the -sim if there is no FDR data (stats) so I cannot > cache the clusters formed only by thresh 2 in QDEC. Is theer a way to > do it? > > Many thanks, > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, September 28, 2011 12:06 PM > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > What does FDR have to do with it? FDR should not come into play in this. > doug > > Antonella Kis wrote: > > Good morning Doug, > > > > I tried running the -sim on my QDEC output (as you recommended me last > > days) but for some data the FDR gives me error (cannot calculate > > clusters statistics) so mri_glmfit-sim is not working either since the > > corrections by multiple comparisons is not working. What should I do > > in this case so I can get as output my cortical thickness values for > > the formed clusters at threshold 2, before multiple comparison? > > > > Many thanks, > > AK > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit
by Ilana Hairston 28 Sep '11

28 Sep '11

Hi Doug, Sorry, that this is turning into a saga. The xhemireg command ran, but then recon-all failed (we used recon-all -all). Also it seems there are missing surfaces, we can't load wm and pial, the surf directory is empty. Although that maybe because the recon didn't run. Thanks i. ---------- Forwarded message ---------- From: Chelsea Cummiford <chelsea.cummiford(a)gmail.com> Date: Thu, Sep 22, 2011 at 4:35 PM Subject: Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit To: Ilana Hairston <hairstonster(a)gmail.com> [chelsea@hypnos ilanagroup]$ recon-all -all -subjid FlippedFS091205dc/ Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/FS51/subjects/ilanagroup Actual FREESURFER_HOME /usr/local/FS51 -rw-rw-r-- 1 chelsea ZL 16132 Sep 22 15:37 /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Thu Sep 22 16:35:06 EDT 2011 ERROR: no run data found in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri. Make sure to have a volume called 001.mgz in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FlippedFS091205dc exited with ERRORS at Thu Sep 22 16:35:06 EDT 2011 For more details, see the log file /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Thu, Sep 22, 2011 at 4:32 PM, Ilana Hairston <hairstonster(a)gmail.com>wrote: > can you paste in the errors? i'll forward them to the freesurfer list > > > On Thu, Sep 22, 2011 at 3:43 PM, Chelsea Cummiford < > chelsea.cummiford(a)gmail.com> wrote: > >> ok, so the xhemireg command ran fine, but I can't run recon-all -all - it >> exits with errors. says that there is no 001.mgz file. >> >> I can pull it up in tkmedit (albeit, none of the control points or >> grey/white matter lines show up). the brain is flipped compared to the >> original though. >> >> >> On Thu, Sep 22, 2011 at 3:30 PM, Chelsea Cummiford < >> chelsea.cummiford(a)gmail.com> wrote: >> >>> oh, got it. i thought you meant check both commands... will do. >>> >>> >>> On Thu, Sep 22, 2011 at 3:26 PM, Ilana Hairston <hairstonster(a)gmail.com>wrote: >>> >>>> no this one, to invert the brains that are already processed >>>> >>>> xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg >>>> >>>> >>>> On Thu, Sep 22, 2011 at 3:24 PM, Chelsea Cummiford < >>>> chelsea.cummiford(a)gmail.com> wrote: >>>> >>>>> do you mean running the --in-orientation ras command and then running >>>>> recon-all?? because we did that and it looks fine in tkmedit and tksurfer - >>>>> right heng? this is what FS00wh is... >>>>> >>>>> >>>>> On Thu, Sep 22, 2011 at 2:57 PM, Ilana Hairston < >>>>> hairstonster(a)gmail.com> wrote: >>>>> >>>>>> Seems like we need to be 100% sure that our analyze/nifti is RAS. >>>>>> Chelsea, could you check the second command, followed by recon-all (i >>>>>> assume recon-all all) ? >>>>>> thx >>>>>> i >>>>>> >>>>>> >>>>>> >>>>>>> We think that in order to avoid this in future we should add a >>>>>>> --in-orientation ras flag to mri_convert. Is that correct? >>>>>>> >>>>>> >>>>>> That might work. The orientation string is actually more specific than >>>>>> just "RAS". You data might in an RAS cooridnate system, but this means that >>>>>> the orientation string could be RAS, or it could be SAR, or ARS, or ARS, >>>>>> etc. See what I mean? If it shows up correctly in tkmedit, then you're got >>>>>> it right (assuming that you are sure that it is really in an RAS coordinate >>>>>> system). >>>>>> >>>>>> >>>>>>> The other question is - now that we have processed some 50 subjects, >>>>>>> is there a way of flipping the results so that we wont have to start from >>>>>>> scratch (this is a longitudinal study and participants will be scanned >>>>>>> again).? >>>>>>> >>>>>> You can try using >>>>>> xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg >>>>>> >>>>>> This script was never intended for this purpose, so I don't know >>>>>> whether it will work fully or not. It should at least reverse all the >>>>>> volumes after which you can run recon-all on it. It should keep any edits >>>>>> you have made, but the control points won't be copied (and would be wrong in >>>>>> the reversed subject). >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Thanks >>>>>>> Ilana >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>>> ****************************** >>>>>>>> Ilana Hairston ,PhD >>>>>>>> Research Assistant Professor >>>>>>>> 4250 Plymouth Rd. (rm 2439) >>>>>>>> Psychiatry Department, Addiction Research Center >>>>>>>> University of Michigan, Ann Arbor MI 48109-2700 >>>>>>>> Tel: 734-232-0232; Mobile: 650-906-8449 >>>>>>>> >>>>>>>> ******************** >>>>>>>> Reminder: Women do 66% of the work worldwide, earn 10% of the >>>>>>>> income, and own 1% of the world's property >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>> >>>>>> >>>>>> >>>>>> 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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> ****************************** >>>>>> Ilana Hairston ,PhD >>>>>> Research Assistant Professor >>>>>> 4250 Plymouth Rd. (rm 2439) >>>>>> Psychiatry Department, Addiction Research Center >>>>>> University of Michigan, Ann Arbor MI 48109-2700 >>>>>> Tel: 734-232-0232; Mobile: 650-906-8449 >>>>>> >>>>>> ******************** >>>>>> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >>>>>> and own 1% of the world's property >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> >>>> ****************************** >>>> Ilana Hairston ,PhD >>>> Research Assistant Professor >>>> 4250 Plymouth Rd. (rm 2439) >>>> Psychiatry Department, Addiction Research Center >>>> University of Michigan, Ann Arbor MI 48109-2700 >>>> Tel: 734-232-0232; Mobile: 650-906-8449 >>>> >>>> ******************** >>>> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >>>> and own 1% of the world's property >>>> >>>> >>>> >>> >> > > > -- > > ****************************** > Ilana Hairston ,PhD > Research Assistant Professor > 4250 Plymouth Rd. (rm 2439) > Psychiatry Department, Addiction Research Center > University of Michigan, Ann Arbor MI 48109-2700 > Tel: 734-232-0232; Mobile: 650-906-8449 > > ******************** > Reminder: Women do 66% of the work worldwide, earn 10% of the income, and > own 1% of the world's property > > > -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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GM, WM and CSF segmentation for partial volume correction
by _andreia_＠sapo.pt 28 Sep '11

28 Sep '11

Hello list, Following this email that I found in the archives: "(...) For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview… You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson" I need to obtain the different % of tissue (GM, WM and CSF) inside one defined voxel. Does FS has a file that can be exported to Matlab to then get these values? Or only FSL/FAST and SPM have this type of info? Thanks! Andreia

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Error with mri_glmfit-sim
by Antonella Kis 28 Sep '11

28 Sep '11

Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK

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analysis.cfg not generated by mkanalysis-sess
by Po-Jang (Brown) Hsieh 28 Sep '11

28 Sep '11

Dear all, I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate analysis.cfg. The only file I can see after running this is analysis.info. When I ran mkanalysis-sess.new, both analysis-info and analysis.cfg are generated as fine. Could any one know how to solve this problem? ps. I'm running freesurfer5.1.0 on Mac OS X 10.6.8 (the mkanalysis-sess.new is a copy from freesurfer4.5.0). Thanks! Brown

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correction
by Oertel, Viola 28 Sep '11

28 Sep '11

Dear Freesurfers, could you please give me detailed information about the Bonferroni or clusterwise correction we can do in Freesurfer? How much iterations? Is that cluster- oder voxelwise? Is there anywhere a detailed description about the correction options? Best regards, Viola

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fieldsign-sess: ERROR Surf/src mismatch
by Michelle Umali 28 Sep '11

28 Sep '11

Dear Freesurfers, This is related to my retinotopy analysis tksurfer-sess dimension mismatch error message. So another subject had these errors come up during fieldsign-sess selxavg3-sess -a rtopy.self.lh -s sjXX -force (which ran without error) then I ran fieldsign fieldsign-sess -a rtopy.self.lh -occip -s sjXX and got: ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. What may have caused this? Thanks. Michelle

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aparc.annot question from August
by Keefe, Helen L 28 Sep '11

28 Sep '11

Hi Everyone, I have not received a response on this question from August -= cold we revisit it please? thanks, Helen [Freesurfer] Saving annotation and stats after expand boundary of region Keefe, Helen L helen-keefe at uiowa.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Saving%20annotation%20and%20stats%20after%20expand%20boundary%20of%0A%09region&In-Reply-To=%3C353409BC97D32F48B41827FF380DD9A105F2DC%40hc-mailboxc1-n4.healthcare.uiowa.edu%3E> Tue Aug 16 12:10:25 EDT 2011 * Previous message: [Freesurfer] update v5.1 and trac-all command <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019884.h…> * Next message: [Freesurfer] Abnormal segmentation of hippocampal subfields <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019832.h…> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/date.htm…> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/thread.h…> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/subject.…> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/author.h…> ________________________________ Hi Bruce, Doug, and All, I have corrected a boundary between lh corpuscallosum and caudalanteriorcingulate. I have overwritten the label/lh.aparc.annot as per Bruce's email below. However, doesn't this leave a number of files with incorrect information now in the stats directory? Do I need to rerun something to bring these up to date? Thanks, Helen ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Retinotopy tksurfer-sess: ERROR: mask and surf dimensions don't match
by Michelle Umali 27 Sep '11

27 Sep '11

Hi Doug and Freesurfers I didn't change any of the structural After the retinotopy analysis. First, I ran recon-all -all. Second, I made edits to to brainmask.mgz and wm.mgz and then ran autorecon2-wm and autorecon3. Third, I cut the occipital patches in tksurfer and then flattened them. Finally, after all of this, I ran the retinotopy analysis (please see below) on the functional images. Where would the dimsension mismatch of the mask and surf occur in this pipeline? How does one overcome this? I would really be very grateful for any assistance. Thanks very much. Michelle ________________________ TERMINAL OUTPUT Here are the analysis commands I used the error output for viewing the map is below it : mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj07 -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sj07 -force selxavg3-sess -a rtopy.self.rh -s sj07 -force fieldsign-sess -a rtopy.self.lh -occip -s sj07 fieldsign-sess -a rtopy.self.rh -occip -s sj07 This is the output when I tried to view in tksurfer-sess BOTANICA:/usr/local/freesurfer/subjects/retinotopy> tksurfer-sess -a rtopy.self.lh -s sj07 -map angle Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Tue Sep 27 06:37:33 EDT 2011 /usr/local/freesurfer/bin/tksurfer list eccen polar con/map eccen /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz con/map polar /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz maplist /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz mri_concat /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz --o /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii cd /usr/local/freesurfer/subjects/retinotopy setenv SUBJECTS_DIR /usr/local/freesurfer/subjects tksurfer ld07 lh inflated -overlay /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 -mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz -mask-thresh 2 -fthresh .01 Contrasts 0 eccen 1 polar setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 mrismaskfile /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz... setting mrismaskthresh to 2.0000 setting fthresh to 0.0100 subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/retinotopy checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=156145, faces=312286 tkmedit: Trying to open /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.dat surfer: Interpreting overlay volume /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii as registered functional volume. surfer: curvature read: min=-3.127128 max=2.364444 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 8162 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(ld07) Reading mris mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz ERROR: dimension mismatch between mask and surf

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Freesurfer September 2011