Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Getting Waveform from Label - dim mismatch
by ERIK JAHNER 12 Sep '16

12 Sep '16

(sorry if you got this multiple times this morning I had some server issues) I had not seen a post based on this email, so I am resending it. It is my understanding that I can use freesurfer and FSfast to get activation levels after data has been smoothed across the surface instead of 3D volume. Is the mir_segstats only able to use the 3D volume and not the surface data stored within vertices? Sorry if this questions is obvious to everyone. I want to basically get the average activation for a set of vertices at each time point included in a label from the surface mapped functional data. See below for additional details of the parameters I entered. Thanks Erik Jahner > On Sep 9, 2016, at 8:20 AM, ERIK JAHNER <erik.jahner(a)icloud.com <mailto:erik.jahner@icloud.com>> wrote: > > >> Dear Freesurfer experts, >> >> I am attempting to get the waveform from a subject (401)using the preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means of a label I created from the icosahedron 3 (lh.ic3.tri_vertex_638). This label was created from the subjects “sphere.reg" file. >> >> I am using the following command: >> >> mri_segstats >> --slabel 401 lh /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label >> --avgwf out.dat >> --id 1 >> --i /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz >> >> However I am getting the following error: >> >> ERROR: dimension mismatch between input volume and seg >> input 163842 1 1 >> seg 140104 1 1 >> >> Obviously there is something wrong with my file dimensions. But, I am unsure of how to fix this. I checked some of the files in my subject anatomical folder like the thickness file and they also have 140104 1 1 as the dimensions. But, as would be predicted the "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 163842 1 1 210. Is there an easy way to fix this problem? I am unsure what I did to create this discrepancy. >> >> Thanks for your continued support, >> Erik Jahner

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Re: [Freesurfer] Tracula movement
by Lars M. Rimol 12 Sep '16

12 Sep '16

Re: [Freesurfer] Tracula movement <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Anastasia Yendiki <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 12 Sep 2016 04:24:56 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi Lars - This sounds like the subject was trying to climb out of the scanner: 3cm average translational motion and 24% of the slices in the series have drop-out. How do the images look? a.y Hi, I don't have a lot of experience looking at dwi scans, but they don't seem crazy to me. I have attached screenshots of the dwi, FA, and brain_anat_mni images, and the gross anatomy looks fine to me. There are stripes in brain_anat_mni, which I would guess indicate motion.. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table
by Douglas N Greve 12 Sep '16

12 Sep '16

you can find it here fsaverage/surf/?h.white.avg.area.mgh On 09/12/2016 11:26 AM, Claudia Dacquino claudia.dacquino(a)gmail.com [martinos-tech] wrote: > Thanks Doug! > Yes, I realized I was wrong and I wrote to the freesurfer list too. > Just another question,as you were so prompt in replying... Where can I > find the average surface area of the inputsubjects? > Thanks. > Clauia > > > 2016-09-12 17:15 GMT+02:00 Douglas N Greve greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> [martinos-tech] > <martinos-tech(a)yahoogroups.com <mailto:martinos-tech@yahoogroups.com>>: > > Hi Claudia, it is better to post these things to the freesurfer > list as > martinos-tech is no longer active. The total cortical surface area > (65416.6mm2) is incorrect. The total should be 82219.960938. The > reported value is the actual surface area of the fsaverage white > surface. However, the average white surface has a much lower surface > area than areas of any of the input subjects because the surface > coordinate averaging causes minor folding to be smoothed out. To get > around this, we keep track of the average surface area of the input > subjects (rather than the surface area of the average surface, if > that > is not too confusing). The size of the cluster reported > (76467.08mm2) is > accurate. > > doug > > On 09/12/2016 07:52 AM, Claudia Dacquino > claudia.dacquino(a)gmail.com <mailto:claudia.dacquino@gmail.com> > > [martinos-tech] wrote: > > > > Hi all, > > > > I've run GLM surface analysis and I've got a summary table like > this: > > > > > > # Cluster Growing Summary (mri_surfcluster) > > > > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > > > > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > > > > # CreationTime 2016/09/12-08:47:18-GMT > > > > # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh > --csd > > > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd > > > --mask lh.Compr.glmdir/mask.mgh --cwsig > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot > aparc > > --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat > > --cwpvalthresh 0.05 --o > > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni > > --bonferroni 2 --surf white > > > > # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts > > > > # sysname Linux > > > > # hostname Piras-TC2 > > > > # machine x86_64 > > > > # FixVertexAreaFlag 1 > > > > # FixSurfClusterArea 1 > > > > # > > > > # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh > > > > # Frame Number 0 > > > > # srcsubj fsaverage > > > > # hemi lh > > > > # surface white > > > > # annot aparc > > > > # SUBJECTS_DIR /media/TREKSTOR/SUBJ > > > > # SearchSpace_mm2 65416.6 > > > > # SearchSpace_vtx 149953 > > > > # Bonferroni 2 > > > > # Minimum Threshold 4 > > > > # Maximum Threshold infinity > > > > # Threshold Sign pos > > > > # AdjustThreshWhenOneTail 1 > > > > # CW PValue Threshold: 0.05 > > > > # Area Threshold 0 mm^2 > > > > # CSD thresh 4.000000 > > > > # CSD nreps 10000 > > > > # CSD simtype null-z > > > > # CSD contrast NA > > > > # CSD confint 90.000000 > > > > # Overall max 1e+10 at vertex 3 > > > > # Overall min 0 at vertex 8 > > > > # NClusters 1 > > > > # Total Cortical Surface Area 65416.6 (mm^2) > > > > # FixMNI = 0 > > > > # > > > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > > CWPLow CWPHi NVtxs Annot > > > > 1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 > > 0.00000 0.00040 149953 rostralmiddlefrontal > > > > > > Is it possible to have a Cluster Size (76467.08 mm2) greater > than the > > Total Cortical Surface (65416.6 mm2). > > > > Are there some errors in this? > > > > Thanks a lot to all of you. > > > > Claudia > > > > > > -- > > > > Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia > > > > Laboratorio di Neuropsichiatria > > > > Dipartimento di Neurologia Clinica e Comportamentale > > > > IRCCS Fondazione Santa Lucia > > > > via Ardeatina 306 - 00179 Roma > > > > Tel. +39 (0)6 51501358 > > > > Fax +39 (0)6 51501575 > > > > web: http://www.neuropsichiatrialab.com > <http://www.neuropsichiatrialab.com> > > <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli > <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>> > > > > > > > > > > -- > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > 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. > > > > > -- > > Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia > > Laboratorio di Neuropsichiatria > > Dipartimento di Neurologia Clinica e Comportamentale > > IRCCS Fondazione Santa Lucia > > via Ardeatina 306 - 00179 Roma > > Tel. +39 (0)6 51501358 > > Fax +39 (0)6 51501575 > > web: http://www.neuropsichiatrialab.com > <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli> > > > > __._,_.___ > ------------------------------------------------------------------------ > Posted by: Claudia Dacquino <claudia.dacquino(a)gmail.com> > ------------------------------------------------------------------------ > Reply via web post > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/messages/58…> > • Reply to sender > <mailto:claudia.dacquino@gmail.com?subject=Re%3A%20%5Bmartinos-tech%5D%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20%5Bmartinos-tech%5D%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Start a New Topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/newtopic;_y…> > • Messages in this topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/topics/5882…> > (3) > > ------------------------------------------------------------------------ > Have you tried the highest rated email app? <https://yho.com/1wwmgg> > With 4.5 stars in iTunes, the Yahoo Mail app is the highest rated > email app on the market. What are you waiting for? Now you can access > all your inboxes (Gmail, Outlook, AOL and more) in one place. Never > delete an email again with 1000GB of free cloud storage. > ------------------------------------------------------------------------ > Visit Your Group > <https://groups.yahoo.com/neo/groups/martinos-tech/info;_ylc=X3oDMTJlYnY4dWI…> > > > Yahoo! Groups > <https://groups.yahoo.com/neo;_ylc=X3oDMTJkMnJybTJmBF9TAzk3NDc2NTkwBGdycElkA…> > > • Privacy > <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> • > Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> > > . > > __,_._,___ -- 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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visualize corrected results
by Caroline Beelen 12 Sep '16

12 Sep '16

Dear FS, I have a question on visualizing results from GLM analysis... How can I visualize corrected results in Freeview after having applied bonferroni/FDR correction (somewhere else)? I saw it is not possible (error: masking file missing) -and was told it is not necessary- to apply monte carlo simulation on results obtained via aparc-files from DK-atlas. Thank you very much! Regards, Caroline

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Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table
by Douglas N Greve 12 Sep '16

12 Sep '16

Hi Claudia, it is better to post these things to the freesurfer list as martinos-tech is no longer active. The total cortical surface area (65416.6mm2) is incorrect. The total should be 82219.960938. The reported value is the actual surface area of the fsaverage white surface. However, the average white surface has a much lower surface area than areas of any of the input subjects because the surface coordinate averaging causes minor folding to be smoothed out. To get around this, we keep track of the average surface area of the input subjects (rather than the surface area of the average surface, if that is not too confusing). The size of the cluster reported (76467.08mm2) is accurate. doug On 09/12/2016 07:52 AM, Claudia Dacquino claudia.dacquino(a)gmail.com [martinos-tech] wrote: > > Hi all, > > I've run GLM surface analysis and I've got a summary table like this: > > > # Cluster Growing Summary (mri_surfcluster) > > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > > # CreationTime 2016/09/12-08:47:18-GMT > > # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd > --mask lh.Compr.glmdir/mask.mgh --cwsig > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc > --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat > --cwpvalthresh 0.05 --o > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni > --bonferroni 2 --surf white > > # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts > > # sysname Linux > > # hostname Piras-TC2 > > # machine x86_64 > > # FixVertexAreaFlag 1 > > # FixSurfClusterArea 1 > > # > > # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh > > # Frame Number 0 > > # srcsubj fsaverage > > # hemi lh > > # surface white > > # annot aparc > > # SUBJECTS_DIR /media/TREKSTOR/SUBJ > > # SearchSpace_mm2 65416.6 > > # SearchSpace_vtx 149953 > > # Bonferroni 2 > > # Minimum Threshold 4 > > # Maximum Threshold infinity > > # Threshold Sign pos > > # AdjustThreshWhenOneTail 1 > > # CW PValue Threshold: 0.05 > > # Area Threshold 0 mm^2 > > # CSD thresh 4.000000 > > # CSD nreps 10000 > > # CSD simtype null-z > > # CSD contrast NA > > # CSD confint 90.000000 > > # Overall max 1e+10 at vertex 3 > > # Overall min 0 at vertex 8 > > # NClusters 1 > > # Total Cortical Surface Area 65416.6 (mm^2) > > # FixMNI = 0 > > # > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > 1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 > 0.00000 0.00040 149953 rostralmiddlefrontal > > > Is it possible to have a Cluster Size (76467.08 mm2) greater than the > Total Cortical Surface (65416.6 mm2). > > Are there some errors in this? > > Thanks a lot to all of you. > > Claudia > > > -- > > Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia > > Laboratorio di Neuropsichiatria > > Dipartimento di Neurologia Clinica e Comportamentale > > IRCCS Fondazione Santa Lucia > > via Ardeatina 306 - 00179 Roma > > Tel. +39 (0)6 51501358 > > Fax +39 (0)6 51501575 > > web: http://www.neuropsichiatrialab.com > <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli> > > > > __._,_.___ > ------------------------------------------------------------------------ > Posted by: Claudia Dacquino <claudia.dacquino(a)gmail.com> > ------------------------------------------------------------------------ > Reply via web post > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/messages/58…> > • Reply to sender > <mailto:claudia.dacquino@gmail.com?subject=Re%3A%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20Trobles%20witg%20GLM%20Surface-based%20Cluster%20Summary%20Table> > • Start a New Topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/newtopic;_y…> > • Messages in this topic > <https://groups.yahoo.com/neo/groups/martinos-tech/conversations/topics/5882…> > (1) > > ------------------------------------------------------------------------ > Have you tried the highest rated email app? <https://yho.com/1wwmgg> > With 4.5 stars in iTunes, the Yahoo Mail app is the highest rated > email app on the market. What are you waiting for? Now you can access > all your inboxes (Gmail, Outlook, AOL and more) in one place. Never > delete an email again with 1000GB of free cloud storage. > ------------------------------------------------------------------------ > Visit Your Group > <https://groups.yahoo.com/neo/groups/martinos-tech/info;_ylc=X3oDMTJlMjRnMGM…> > > > Yahoo! Groups > <https://groups.yahoo.com/neo;_ylc=X3oDMTJkNXQ3dWU2BF9TAzk3NDc2NTkwBGdycElkA…> > > • Privacy > <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> • > Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> > > . > > __,_._,___ -- 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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mris_anatomical_stats
by Arkadiy Maksimovskiy 12 Sep '16

12 Sep '16

Dear Freesurfer Experts, I am trying to run mris_anatomical_stats in order to extra thickness data from my participants' label files. However, I only have access to a subj_recon data (without wm.mgz in that folder). Does anyone know if there is a way to extract the thickness measures for every participant's label, without having the wm.mgz file? Would it be okay to copy that file from fsaverage, in order ot bypass this issue, or would that mess up the calculations of the thickness of the participants' labels? Thank you in advance for your help, Arkadiy

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Troubles witg GLM Surface-based Cluster Summary Table
by Claudia Dacquino 12 Sep '16

12 Sep '16

Hi all, I've run GLM surface analysis and I've got a summary table like this: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2016/09/12-08:47:18-GMT # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ cortex/fwhm15/pos/th40/mc-z.csd --mask lh.Compr.glmdir/mask.mgh --cwsig lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat --cwpvalthresh 0.05 --o lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts # sysname Linux # hostname Piras-TC2 # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /media/TREKSTOR/SUBJ # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign pos # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 1e+10 at vertex 3 # Overall min 0 at vertex 8 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 0.00000 0.00040 149953 rostralmiddlefrontal Is it possible to have a Cluster Size (76467.08 mm2) greater than the Total Cortical Surface (65416.6 mm2). Are there some errors in this? Thanks a lot to all of you. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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Tracula movement
by Lars M. Rimol 12 Sep '16

12 Sep '16

HI, Is there a rule-of-thumb upper level of acceptable head motion? The tutorial gives these values as examples: AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0.489419 0.00398925 0 1 I have a subject with AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore *30.018* 0.209 24 1.6 I plan, of course, to use the index described in Yendiki et al. (2013) but would such high levels nevertheless be considered disqualifying a priori? Thank you!

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Parcelation a2009 as mask for SPM analysis
by Matyáš Kuhn 12 Sep '16

12 Sep '16

Hi FreeSurfer experts, We would like to use Destrieux atlas for masking DLPFC in subjects, who uderwent fMRI and we used SPM to process the data. We want to find peaks in individuals according to some regions from the atlas (create individual mask). The problem I am facing is to get aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM and Freesurfer. I followed some discussions on mailing list and tried this: mni152reg --s $SUB mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \ --temp /.../spm/spmT_0001.nii \ --reg $SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \ --o aseg.$SUB.mni152.nii The process ended without errors, but while watching results in freeview - the results are not correctly aligned. Is FSL (which is part of mni152reg procedure) using some other MNI template than SPM? Any suggestions will be most appreciated. The freeview snapshot is here: https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a…

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white and pial surface crossin in the lingual gyrus
by Alain Imaging 12 Sep '16

12 Sep '16

Hello everybody, I am gladly starting my freesurfer adventure after the awesome last course in Copenhagen, but I have quickly realized that troubleshooting on your own is not as easy as with experts going around in a room. I was looking for errors after having run the recon all and I stumbled upon this crossing between white and pial surface in the lingual gyrus (see attached Figure1, green arrow). It seems to me that the problem may arise from the fact that in the WM volume (see attached Figure2) there are areas that have been categorized as WM hypointensities, and in particular on the right, the problem could be that the white matter surface, instead of going around these brighter voxels, just goes straight down (I hope I have explained myself). Is the fixing to this problem changing the value of those voxels (part of them, of course) in the WM volume ? If I look at the WM seg I see that indeed they are left out from the mask. Or should I do something else ? I am working with freesurfer version Linux-centos6_x86_64-stable-pub-v5.3.0, with Linux version 3.10.0-327.4.5.el7.x86_64 (Red Hat 4.8.3-9). Thanks in advance for any suggestion Alain

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