Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

slice timing correction and motion correction order
by Katie Bettencourt 01 Feb '13

01 Feb '13

Can you tell me the order of the slice timing and motion correction steps in preproc-sess (freesurfer v 4.5)? From the wiki it looks like motion correction is done first (For MC the input will be f and the output will be fmc For STC the input will be fmc and the output will be fmcstc". However, wouldn't doing the motion correction first cause an issue? Because, otherwise, after motion correction, the slices are realigned and the timing of a slice at a particular location is no longer what it is before, correct? Can you clarify this for me?

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mrisReadTriangleFile failed
by Jonathan Holt 01 Feb '13

01 Feb '13

Experts, Having an issue with this error. It's complaining about rh.pial not matching rh.white, indicates there's no such file or directory and that mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I tried loading rh.pial manually, but upon loading it immediately removes every surface on the LH. Wasn't an issue before I ran recon-all. Worth noting this brain was generated from a particularly low contrast MRI scan, and freesurfer had trouble generating correct surfaces from the get go. Jon

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about ROI to SPSS
by xiangbo_2010 01 Feb '13

01 Feb '13

Dear experts I has obtained two ROIs (corrected FDR) difference between AA and GG regressing out the effect of age and gender using the QDEC with attachment, following extract the average surface area of two ROIs to analysis using SPSS, in which I used the Univariate Analysis of Variance to find the difference between AA and GG, gender and age as covariates, but find that there no significant in these ROIs, I want to know why there were significant difference in QDEC, but no significant difference in SPSS? I hope that have experts to help me, thanks! Bo Xiang

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Postdoc position
by Direktion, Institut f. Schlaganfall- und Demenzforschung 01 Feb '13

01 Feb '13

Dear Sirs, please find attached a postdoc advert for posting. Thank you for your assistance. With best regards, Lilo Viele Grüße Lilo Thomas Assistentin der Institutsleitung Institut für Schlaganfall- und Demenzforschung (ISD) Klinikum der Universität München Heiglhofstraße 55 D-81377 München Telefon: +49 (0)89 7095 - 7801 Fax: +49 (0)89 7095 - 8729 E-Mail: lilo.thomas(a)med.uni-muenchen.de<mailto:lilo.thomas@med.uni-muenchen.de> Internet: www.isd.klinikum.uni-muenchen.de<http://www.isd.klinikum.uni-muenchen.de/>

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R: Re: R: Re: R: Re: bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Yes Anastasia. To check it, I'm attaching the last bvals,bvecs files (original) and bvals.norot (in my dmri).Thank you very much for your kindness. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 1-feb-2013 0.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: bvecs tracula Hi Stefano - I'm sorry that you're frustrated. Do you mean that you arranged the bvecs as 3 columns (not 3 rows) and are still getting the same error? a.y On Fri, 1 Feb 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > I'm frustrated because I'm checking to resolve this problem anywhere but the error is the same. Can it depend from interaction > between fs and new iMAC version (Mountain Lion)? > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 31-gen-2013 22.53 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: bvecs tracula > > > Hi Stefano - See "Specifying Diffusion Gradient Table" in the tracula > tutorial for the correct format: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > a.y > > On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > I attach the bvecs that I'm using. The second is produced in the dmri. > > You are noting that the first is in 3 rows, the second contains only 3 row with a 0 > > > > This is the last error > > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 > > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3 > > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff > > #------------------------------------- > > #@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CET > > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref > > /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo > > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat > > #------------------------------------- > > #@# Masks Gio 31 Gen 2013 22:41:55 CET > > #------------------------------------- > > #@# Tensor fit Gio 31 Gen 2013 22:41:55 CET > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > > Error: bvecs and bvals don't have the same number of entries > > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; > root:xnu-2050.20.9~1/RELEASE_X86_64 > > x86_64 > > > > trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET > > > > Thanks, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 31-gen-2013 21.43 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] bvecs tracula > > > > > > Hi Stefano - Are the original bvecs (that you specify in your > > configuration file) arranged in 3 rows or 3 columns? > > > > a.y > > > > On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Hi list, > > > I'm running trac-all -prep -c > > > > > > but I have this error > > > > > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > > > Error: bvecs and bvals don't have the same number of entries > > > > > > I'm noting that my original bvecs are > > > > > > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460 > > > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301 > > > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 > > > > > > and in dmri > > > > > > 0 > > > 0 > > > 0 > > > > > > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? > > > > > > Thank you very much, I really appreciate your patience. > > > > > > Stefano > > > > > > > > >_______________________________________________ > > 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 > > > 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 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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R: Re: R: Re: bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Hi Anastasia, I'm frustrated because I'm checking to resolve this problem anywhere but the error is the same. Can it depend from interaction between fs and new iMAC version (Mountain Lion)? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 31-gen-2013 22.53 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: bvecs tracula Hi Stefano - See "Specifying Diffusion Gradient Table" in the tracula tutorial for the correct format: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula a.y On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > I attach the bvecs that I'm using. The second is produced in the dmri. > You are noting that the first is in 3 rows, the second contains only 3 row with a 0 > > This is the last error > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff > #------------------------------------- > #@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CET > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref > /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat > #------------------------------------- > #@# Masks Gio 31 Gen 2013 22:41:55 CET > #------------------------------------- > #@# Tensor fit Gio 31 Gen 2013 22:41:55 CET > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 > x86_64 > > trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET > > Thanks, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 31-gen-2013 21.43 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] bvecs tracula > > > Hi Stefano - Are the original bvecs (that you specify in your > configuration file) arranged in 3 rows or 3 columns? > > a.y > > On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > I'm running trac-all -prep -c > > > > but I have this error > > > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > > Error: bvecs and bvals don't have the same number of entries > > > > I'm noting that my original bvecs are > > > > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460 > > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301 > > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 > > > > and in dmri > > > > 0 > > 0 > > 0 > > > > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? > > > > Thank you very much, I really appreciate your patience. > > > > Stefano > > > > > >_______________________________________________ > 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 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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R: Re: bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Hi Anastasia, I attach the bvecs that I'm using. The second is produced in the dmri.You are noting that the first is in 3 rows, the second contains only 3 row with a 0 This is the last errorfslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gzbet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff#-------------------------------------#@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CETflirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfoconvert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat#-------------------------------------#@# Masks Gio 31 Gen 2013 22:41:55 CET#-------------------------------------#@# Tensor fit Gio 31 Gen 2013 22:41:55 CETdtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifitError: bvecs and bvals don't have the same number of entriesDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 31-gen-2013 21.43 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] bvecs tracula Hi Stefano - Are the original bvecs (that you specify in your configuration file) arranged in 3 rows or 3 columns? a.y On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > Hi list, > I'm running trac-all -prep -c > > but I have this error > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > > I'm noting that my original bvecs are > > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460 > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301 > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 > > and in dmri > > 0 > 0 > 0 > > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? > > Thank you very much, I really appreciate your patience. > > Stefano > > >_______________________________________________ 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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bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Hi list, I'm running trac-all -prep -c but I have this error dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifitError: bvecs and bvals don't have the same number of entries I'm noting that my original bvecs are 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.4600 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.3010 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 and in dmri 000 bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? Thank you very much, I really appreciate your patience. Stefano

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slice timing correction and motion correction order
by Maryam Vaziri Pashkam 31 Jan '13

31 Jan '13

Hi Doug, Two questions: 1) In fsfast preprocessing is STC done first or MC? is there a way to control the order? 2) Also if STC is not mentioned in the analysis line and only done in the preprocessing would the analysis be run on the STC data automatically? or should I specify STC in the analysis for the selxavg3-sess to use the stc corrected data? Thanks, M

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Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
by Douglas N Greve 31 Jan '13

31 Jan '13

The threshold must be in the form of -log10(pthreshold). So, if you want pthreshold=.05, then use 1.3 doug On 01/31/2013 07:37 AM, Richter, Julia wrote: > Dear Doug, > > thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it. > > Looking forward to your answer, > > Best, Julia > > -----Ursprüngliche Nachricht----- > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve > Gesendet: Mittwoch, 30. Januar 2013 17:16 > An: Richter, Julia; free surfer > Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec > > Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is the voxelwise threshold from FDR and sign is either abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report all clusters > > doug > > On 1/30/13 8:09 AM, Richter, Julia wrote: >> No it is not...or I just do not find it. >> >> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? >> >> Many thanks, Julia >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve >> Gesendet: Dienstag, 29. Januar 2013 18:46 >> An: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec >> >> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? >> doug >> >> >> On 01/29/2013 11:03 AM, Richter, Julia wrote: >>> Dear FreeSurfer experts, >>> >>> I did a group analysis in qdec, found several significant clusters and >>> would now like to extract the mean cortical thickness of each >>> significant cluster. I know that I have to run mri_glmfit-sim to do >>> this, but I do not understand which commands I need to get the >>> xxx.y.ocn.dat as output by running mri_glmfit-sim. >>> >>> Any ideas? Any help is appreciated. J >>> >>> Best wishes, Julia >>> >>> >>> >>> _______________________________________________ >>> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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