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fswiki down?
by Satrajit Ghosh 28 Aug '12

28 Aug '12

looks like the freesurfer wiki is down. cheers, satra

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How to load specific color label for rois
by Dalwani, Manish 27 Aug '12

27 Aug '12

Hi Freesurfer's, How can I load color labels for specific for display purposes? Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado

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Error with annot file
by Antonella Kis 27 Aug '12

27 Aug '12

Hi, I am trying to run the mri_label2vol but I am getting the following error. I am not sure which annot file I should use for my QDEC clusters. I tried to use my annot file from mri_glmfit-sim but it didn't work. I was running: mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh 0 --subject fsaverage --hemi lh --annot /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh --o /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/sig2MNI.nii and my error: Number of labels: 0 Annot File: /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh Template Volume: MNI152_T1_1mm_brain.nii.gz Outut Volume: /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/sig2MNI.nii Registration File: /usr/local/freesurfer//average/mni152.register.dat Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 91.000; -0.000 -0.000 -1.000 109.000; -0.000 1.000 -0.000 91.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Loading registration from /usr/local/freesurfer//average/mni152.register.dat RegMat: -------- 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.998 0.007 -0.018 90.043; 0.015 1.001 -0.002 127.550; -0.013 -0.009 0.997 73.184; 0.000 0.000 0.000 1.000; INFO: loading surface /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/fsaverage/surf/lh.white nvertices = 163842 Reading thickness /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/fsaverage/surf/lh.thickness Loading annotations from /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh MRISreadAnnotationIntoArray: vertex index out of range: 163842 i=00000001, in_array_size=163842 annot file: /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh reading colortable from annotation file... colortable with 1 entries read (originally ) annotidmax = 0 ERROR: load annot file /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh Thanks, AK

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tracula-snowleopard updates
by Cat Chong 27 Aug '12

27 Aug '12

Hello Experts, Just a quick question: Do the Tracula updates(dmri_mergepaths, etc) for snow_leopard replace the 'old' ones in freesurfer's "bin" directory? cheers, Cat

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Control points and errors
by Herting, Megan 27 Aug '12

27 Aug '12

Hi, I have been using freesurfer on a large dataset and I am having some trouble. Sometimes the temporal lobes are not fully covered, so I will go back to add a few control points based on the recommendations of freesurfer (voxels that are <110 and not next to a gray matter voxel) and send it through again. This will often correct the previous error, but then ends up creating new errors in a different region (frontal lobe, temporal lobe in the other hemisphere) etc. This has happened on a large fraction of my data (~25%). What is recommended to fix this? Should I continue to try to add cp to these new regions and send it through again, and continue to do this until it looks good? Is there another method? Thank you! Megan --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

2 2

Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space
by Antonella Kis 27 Aug '12

27 Aug '12

Hi Doug, Thank you very much for your reply and help. If I am not doing cluster by cluster how I can know which cluster is which when I overlay the file onto MNI152? Is the following correct I am not sure how to input (using which option) my sig.mgh from QDEC: mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh 0 --subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh--hemi lh --annot lh.aparc.annot --o sig2MNI.nii Many thanks, Antonella ________________________________ From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Monday, August 27, 2012 10:23 AM Subject: Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space You should use mri_label2vol. If you want to do it label by label, then you need to convert the cluster annotation (the .annot file) into labels with mri_annotation2label. Or you can feed the annotation directly into mri_label2vol to create a segmentation volume. You don't need to specify a subject (but it you were, it would be fsaverage). Leave fillthresh at 0; the clusters cannot overlap. doug On 8/27/12 4:17 PM, Antonella Kis wrote: > > > > > > Hi, > > I want to overlay my QDEC clusters on the connectivity maps in FSL on the MNI ( this is the template I use for my connectivity maps). I am not sure how I can mention the label of my clusters, the uncorrected clusters. >Should I use the sig.mgh as subject id, my clusters were obtained from all my subjects or it should be the fsaverage? Should I use mri_label2vol or mri_surf2vol? > > >How I can identify the label of my clusters more exactly how I can keep only the clusters (name and size) from QDEC as in thefollowing table or > > where I can find for each QDEC's cluster the label so I can use it under --label option ? > >mri_label2vol > --label ??? > --temp MNI152_T1_1mm_brain.nii.gz > --reg $FREESURFER_HOME/average/mni152.register.dat > --fillthresh .5 > --subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh --hemi lh > --o precentral-lh.nii > > > > >Also is the 0.5 the threshold I need to use with mri_label2vol under option --fillthresh if I want to get my uncorrected clusters? How can I do this if as below I have two clusters in the same region? > > > Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 >ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation >--------- --- ------ --------- ---- ---- ---- ----- ---------- > 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral > 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal > 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal > 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula > 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine > 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal > 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole > 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal > 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral > 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate > 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal > 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal > 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts > 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal > 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal > 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis > 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal > 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital > 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral > 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal > > > > > > > >________________________________ > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >To: freesurfer(a)nmr.mgh.harvard.edu >Sent: Tuesday, August 21, 2012 4:55 PM >Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space > >You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat >doug > >On 08/21/2012 11:06 AM, Antonella Kis wrote: >> Dear All, >> >> Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain >> template? >> >> Thank you. >> Antonella >> >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > > > > > > > > > > > > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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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Command line to get BA stats with the thresholds
by _andreia_＠sapo.pt 27 Aug '12

27 Aug '12

Hi! Is there a command line to obtain the BA values with the recommended thresholds from all subjects at once? Thank you, Andreia Pereira

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Fw: Convert QDEC clusters on the MNI_152_T1 space
by Antonella Kis 27 Aug '12

27 Aug '12

Hi Doug, Many thanks for your help. Can you please take a look and see if this is the correct way to do it. I want to overal in fact my QDEC clusters on the connectivity maps in FSL but I got them by registering on the MNI 152 so I suppose I can just transform or move my QDEC clusters on the MNI space since this is the template I use for my connectivity maps. I am not sure if I need to mention the label of my clusters for example the uncorrected clusters. Should I use the sig.mgh or I just run: mri_label2vol --label lh-precentral --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh .5 --o precentral-lh.nii Also what threshold should I use with mri_label2vol if this are my uncorrected clusters? How can I do this if as below I have two clusters in the same region? Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: > Dear All, > > Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain > template? > > Thank you. > Antonella > > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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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Fwd: Surface statistics for PET
by Daniel Tarquinio 26 Aug '12

26 Aug '12

Hi Bruce, I'm sorry I didn't ask the correct question - I was able to generate the .mgh file with mri_vol2surf without problem. The issue was that "qsurfer" gives me an error stating it couldn't find the .w file. According to usage it needs a file ending in -?h.w. Is there a way to use a .mgh file with qsurfer, or is there a better way to view inflated functional data than with qsurfer? Thank you again, Daniel Sent from my iPhone On Aug 26, 2012, at 12:50 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > sure, use mgh as the output format of mri_vol2surf. > > cheers > Bruce > On Sun, 26 Aug 2012, Daniel Tarquinio wrote: > >> Thank you Doug, that worked perfectly. >> Regarding the .w file, to view the functional data inflated I used this >> tutorial: >> http://poc.vl-e.nl/distribution/manual/fsl-3.2/freesurfer/index.html >> Is there a workaround to view inflated functional data mapped using >> mri_vol2surf with a .mgh file? >> Thank you again, >> Daniel >> Message: 6 >> Date: Fri, 24 Aug 2012 18:57:55 -0400 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Surface statistics for PET >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <503806F3.50807(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> You can use mri_segstats for this, something like >> mri_segstats --annot subject lh aparc --i lh.pet.mgh --sum sum.dat >> where lh.pet.mgh is the surface-sampled pet >> BTW, unless you need a .w for something, use a .mgh file (the .w is becoming obsolete). >> doug >> On 08/23/2012 07:27 PM, Daniel Tarquinio wrote: >> > I would like to calculate average PET intensities for specific labels > (using the aparc.annot label files). >> > >> > I have coregistered and used mri_vol2surf to assign PET values to the > FS generated surface, and viewed the results using qsurfer. >> > >> > The next step is to take the values from the .w files and calculate > label-specific stats. I've tried mris_anatomical_stats but I don't > think this is the right command. >> > >> > Any advice? >> > >> > Thank you in advance, >> > Daniel >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -----Original Message----- >> From: freesurfer-request <freesurfer-request(a)nmr.mgh.harvard.edu> >> To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Sat, Aug 25, 2012 12:00 pm >> Subject: Freesurfer Digest, Vol 102, Issue 27 >> 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. Control points and errors (Herting, Megan) >> 2. Re: 3rd level surface analysis of fMRI data (Douglas N Greve) >> 3. Re: In Qdec, what does the 'area' mean within 'Measure' menu >> in 'Design' tab (Jeff Sadino) >> 4. Re: problem with tksurfer (Douglas N Greve) >> 5. Re: In Qdec, what does the 'area' mean within 'Measure' menu >> in 'Design' tab (Douglas N Greve) >> 6. Re: Surface statistics for PET (Douglas N Greve) >> 7. Re: mri_segstats error (Douglas N Greve) >> 8. Re: qdec analyses without interaction effect (Douglas N Greve) >> 9. tracula trac-all error malloc_error_break (Cat Chong) >> 10. Re: creating labels, new atlas (Bruce Fischl) >> 11. Re: creating a gca file from .mgz files (Bruce Fischl) >> 12. Re: Control points and errors (Bruce Fischl) >> ---------------------------------------------------------------------- >> Message: 1 >> Date: Fri, 24 Aug 2012 18:45:54 +0000 >> From: "Herting, Megan" <mherting(a)chla.usc.edu> >> Subject: [Freesurfer] Control points and errors >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> Message-ID: >> <7C6AFE602753B44C84DC09C4D69F17B6A41058(a)CHLAEXMBH01.LA.AD.CHLA.ORG> >> Content-Type: text/plain; charset="us-ascii" >> Hi, >> I have been using freesurfer on a large dataset and I am having some trouble >> . Sometimes the temporal lobes are not fully covered, so I will go back to add >> a few control points based on the recommendations of freesurfer (voxels that a >> re <110 and not next to a gray matter voxel) and send it through again. This wi >> ll often correct the previous error, but then ends up creating new errors in a different region (frontal lobe, temporal lobe in the other hemisphere) etc. This has happened on a large fraction of my data (~25%). What is recommended to f >> ix this? Should I continue to try to add cp to these new regions and send it through again, and continue to do this until it looks good? Is there another >> method? >> Thank you! >> Megan >> --------------------------------------------------------------------- >> CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidentia >> l >> or legally privileged information. Any unauthorized review, use, disclosure >> or distribution is prohibited. If you are not the intended recipient, please >> contact the sender by reply e-mail and destroy all copies of this original message. --------------------------------------------------------------------- >>

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Re: [Freesurfer] Surface statistics for PET
by Daniel Tarquinio 26 Aug '12

26 Aug '12

Thank you Doug, that worked perfectly. Regarding the .w file, to view the functional data inflated I used this tutorial: http://poc.vl-e.nl/distribution/manual/fsl-3.2/freesurfer/index.html Is there a workaround to view inflated functional data mapped using mri_vol2surf with a .mgh file? Thank you again, Daniel Message: 6 Date: Fri, 24 Aug 2012 18:57:55 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Surface statistics for PET To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <503806F3.50807(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You can use mri_segstats for this, something like mri_segstats --annot subject lh aparc --i lh.pet.mgh --sum sum.dat where lh.pet.mgh is the surface-sampled pet BTW, unless you need a .w for something, use a .mgh file (the .w is becoming obsolete). doug On 08/23/2012 07:27 PM, Daniel Tarquinio wrote: > I would like to calculate average PET intensities for specific labels > (using the aparc.annot label files). > > I have coregistered and used mri_vol2surf to assign PET values to the > FS generated surface, and viewed the results using qsurfer. > > The next step is to take the values from the .w files and calculate > label-specific stats. I've tried mris_anatomical_stats but I don't > think this is the right command. > > Any advice? > > Thank you in advance, > Daniel > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -----Original Message----- From: freesurfer-request <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Sat, Aug 25, 2012 12:00 pm Subject: Freesurfer Digest, Vol 102, Issue 27 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. Control points and errors (Herting, Megan) 2. Re: 3rd level surface analysis of fMRI data (Douglas N Greve) 3. Re: In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab (Jeff Sadino) 4. Re: problem with tksurfer (Douglas N Greve) 5. Re: In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab (Douglas N Greve) 6. Re: Surface statistics for PET (Douglas N Greve) 7. Re: mri_segstats error (Douglas N Greve) 8. Re: qdec analyses without interaction effect (Douglas N Greve) 9. tracula trac-all error malloc_error_break (Cat Chong) 10. Re: creating labels, new atlas (Bruce Fischl) 11. Re: creating a gca file from .mgz files (Bruce Fischl) 12. Re: Control points and errors (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Aug 2012 18:45:54 +0000 From: "Herting, Megan" <mherting(a)chla.usc.edu> Subject: [Freesurfer] Control points and errors To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <7C6AFE602753B44C84DC09C4D69F17B6A41058(a)CHLAEXMBH01.LA.AD.CHLA.ORG> Content-Type: text/plain; charset="us-ascii" Hi, I have been using freesurfer on a large dataset and I am having some trouble. Sometimes the temporal lobes are not fully covered, so I will go back to add a few control points based on the recommendations of freesurfer (voxels that are <110 and not next to a gray matter voxel) and send it through again. This will often correct the previous error, but then ends up creating new errors in a different region (frontal lobe, temporal lobe in the other hemisphere) etc. This has happened on a large fraction of my data (~25%). What is recommended to fix this? Should I continue to try to add cp to these new regions and send it through again, and continue to do this until it looks good? Is there another method? Thank you! Megan --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

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