Freesurfer

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30132 discussions

contrast matrix
by Meng Li 29 Aug '12

29 Aug '12

Hi Freesurfers, My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender, the contrast matrix is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 so I can get the clusters that have significant interaction. When I perform the main effect of dignosis, is the following matrix used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 (I think it regressed out the effect of genotype and gender, that is take the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5) to perform the main effect of diagnosis. Am I correct? Any help will be very appreciated. Best wishes, Meng Li

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(no subject)
by Hugh Pemberton 28 Aug '12

28 Aug '12

Hi Freesurfers, Have had this error come up after recon-all for a number of subjects and was wondering if you know what the issue is..? I have attached the recon-all.log too FYI. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ MRISread(/home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix): could not open file reading input surface /home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix... No such file or directory mris_fix_topology: could not read input surface /home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix No such file or directory As the error suggests cannot read lh.qsphere, there is indeed nothing at all in the surf folder. Thanks for all your help, Hugh

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mri_convert feature request?
by dgw 28 Aug '12

28 Aug '12

Hi, I'm not sure if this is a bug report or a feature request. I have been using mri_convert to convert dicoms to nii.gz and mgz files, and I have noticed some discrepancies when reading the volumes in with MRIread in either matlab or octave. The volumes differ in their support of the flip angle, tr, te, and ti fields (I realize some of this may be due to file type differences). Thought the standard output of mri_convert shows the expected values. In the mgz file the TR seems to be rounded i.e. 50 instead of 50.000000745058060 in the nii.gz In the mgz file the flip angle and te are recorded FA 0.52.... while in the nii.gz it is 0 te 10.39... while in the nii.gz it is 0 The ti value appears strange to me in the mgz ti = -1 while in the nii.gz it is 0 I have generated two files using mri convert off of the same MR volume as a test case: /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/877000-000020-000003.dcm /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/volume.nii.gz /cluster/hbot/agario_p2_2/dcm/test.mgz These files were generated using /usr/local/freesurfer/stable5_1_0/ Thanks, D

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fswiki down?
by Satrajit Ghosh 28 Aug '12

28 Aug '12

looks like the freesurfer wiki is down. cheers, satra

2 1

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

2 2

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

2 1

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. ---------------------------------------------------------------------

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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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