Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Re: [Freesurfer] matrix error
by Allie Rosen 07 May '12

07 May '12

Hi Doug, Is there a different number I can substitute into the fifth column so the numbers are not all zeroes? Thank you, Allie On Mon, May 7, 2012 at 12:39 PM, Allie Rosen <rosen.allie(a)gmail.com> wrote: > Hi Doug, > > Thanks for the help. The fifth column is all zeroes because the covariate > - length of disease - isn't applicable to control subjects. In the end, I > want to test the difference in thickness between the two groups, regressing > out the effect of both covariates (age and length of disease). I think this > means the difference in intercepts between the two groups. > > Thanks again, > Allie > > > > On Mon, May 7, 2012 at 12:29 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> Hi Allie, the 5th column of your design matrix is all 0s, which causes >> the ill conditioning. I don't think this design fits into our standard >> framework. You can still analyze and test, we'll just have to figure out >> exactly what needs to be done. In the end, what is it that you want to >> test? Just a difference in intercepts between the two groups? >> doug >> >> On 05/07/2012 09:38 AM, Allie Rosen wrote: >> > Hello, >> > >> > I am analyzing cortical thickness in a patient and control group. I >> > have two covariates: age and length of disease. I am using the model >> from: >> > >> > http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V >> > >> > However, for the control group I put length of disease as 0 in my FSGD >> > file. When I run the GLM, I get the following error message: >> > >> > matrix is ill-conditioned or badly scaled, condno = 1e+08 >> > >> > Can you please tell me what I am doing wrong? Below is the required >> > information. >> > >> > 1. Your command line: >> > >> > mri_glmfit --y lh.disease_length.thickness.20.mgz --fsgd >> > fsgd_disease_length.txt dods --glmdir >> > lh.disease_length.thickness.20.glmdir --surf fsaverage lh --C >> > groupdiff_length_disease.mat >> > >> > 2. The FSGD file >> > >> > GroupDescriptorFile 1 >> > Title Anorexia vs Controls >> > Class Control plus blue >> > Class Patient circle green >> > Variables Age Disease_Length >> > >> > Input C07 Control 37 0 >> > Input C28 Control 28 0 >> > Input C39 Control 37 0 >> > Input C54 Control 40 0 >> > Input C57 Control 32 0 >> > Input C10 Control 54 0 >> > Input C33 Control 31 0 >> > Input C29 Control 22 0 >> > Input A01 Patient 39 20 >> > Input A02 Patient 24 11 >> > Input A03 Patient 35 15 >> > Input A04 Patient 40 10 >> > Input A05 Patient 35 20 >> > Input A06 Patient 57 20 >> > Input A07 Patient 31 16 >> > Input A08 Patient 20 8 >> > >> > 3. And the design matrix >> > >> > Design matrix ------------------ >> > 1.000 0.000 37.000 0.000 0.000 0.000; >> > 1.000 0.000 28.000 0.000 0.000 0.000; >> > 1.000 0.000 37.000 0.000 0.000 0.000; >> > 1.000 0.000 40.000 0.000 0.000 0.000; >> > 1.000 0.000 32.000 0.000 0.000 0.000; >> > 1.000 0.000 54.000 0.000 0.000 0.000; >> > 1.000 0.000 31.000 0.000 0.000 0.000; >> > 1.000 0.000 22.000 0.000 0.000 0.000; >> > 0.000 1.000 0.000 39.000 0.000 20.000; >> > 0.000 1.000 0.000 24.000 0.000 11.000; >> > 0.000 1.000 0.000 35.000 0.000 15.000; >> > 0.000 1.000 0.000 40.000 0.000 10.000; >> > 0.000 1.000 0.000 35.000 0.000 20.000; >> > 0.000 1.000 0.000 57.000 0.000 20.000; >> > 0.000 1.000 0.000 31.000 0.000 16.000; >> > 0.000 1.000 0.000 20.000 0.000 8.000; >> > -------------------------------- >> > >> > Thank you, >> > Allie >> > >> > >> > >> > >> > _______________________________________________ >> > 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. >> >> >

2 2

trac-all -path error
by Chris Watson 07 May '12

07 May '12

Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. ------------------------------------------------------------------------ Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory: [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms

3 9

Re: [Freesurfer] problems with analysis after using fslmaths
by Douglas N Greve 07 May '12

07 May '12

Did you regenerate the seeds after filtering? On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote: > I have tried analyses with only one seed time course (either 1 voxel, > mean of a sphere of 1 voxel radius, or mean of a functionally defined > roi), as well as several seeds within the same design matrix, with the > same problem. > All of these analyses did yield higher pcc when done without filtering. > Caspar > > 2012/5/7 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > Is this doing all of those seeds simultaneously or one seed at a time? > > On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote: > > Hi, > > I am trying to use fslmaths to filter my data before I plug it > into a > > resting state analysis. However, once I obtain a pcc map, all > > correlation coefficients are <0.1, even the autocorrelation with the > > seed voxel. > > The data look fine when I open them in Matlab using MRIread; the > > correlations between individual voxel time courses obtained in > Matlab > > is about 0.6. > > > > My analysis stream is as follows: > > a) I filter the data using "fslmaths input -bptf highpass lowpass > > output"; from this I obtain a filtered nii.gz file > > b) I extract a seed timecourse from the filtered data in Matlab > > c) I run mkanalysis-sess with -notask > > d) I run selxavg3-sess > > e) I overlay the pcc.nii > > > > I have tried this with smoothed and unsmoothed data, with and > without > > nuisance regressors, with different seeds, with mri_convert > after step > > a. It is not a problem with the overlay since the max values in pcc > > are all <0.1. > > I noticed that there are some differences in the nifti header > (as read > > with MRIread) before and after filtering, but it seemed to me that > > they are gone after I used mri_convert. > > I do find much higher correlations with unfiltered data. > > Any advice what could be going wrong here? I am using Freesurfer 5.1 > > and FSL 4.1.9 on Linux. > > Thanks, Caspar > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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

1 0

problems with analysis after using fslmaths
by Caspar M. Schwiedrzik 07 May '12

07 May '12

Hi, I am trying to use fslmaths to filter my data before I plug it into a resting state analysis. However, once I obtain a pcc map, all correlation coefficients are <0.1, even the autocorrelation with the seed voxel. The data look fine when I open them in Matlab using MRIread; the correlations between individual voxel time courses obtained in Matlab is about 0.6. My analysis stream is as follows: a) I filter the data using "fslmaths input -bptf highpass lowpass output"; from this I obtain a filtered nii.gz file b) I extract a seed timecourse from the filtered data in Matlab c) I run mkanalysis-sess with -notask d) I run selxavg3-sess e) I overlay the pcc.nii I have tried this with smoothed and unsmoothed data, with and without nuisance regressors, with different seeds, with mri_convert after step a. It is not a problem with the overlay since the max values in pcc are all <0.1. I noticed that there are some differences in the nifti header (as read with MRIread) before and after filtering, but it seemed to me that they are gone after I used mri_convert. I do find much higher correlations with unfiltered data. Any advice what could be going wrong here? I am using Freesurfer 5.1 and FSL 4.1.9 on Linux. Thanks, Caspar

2 1

matrix error
by Allie Rosen 07 May '12

07 May '12

Hello, I am analyzing cortical thickness in a patient and control group. I have two covariates: age and length of disease. I am using the model from: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V However, for the control group I put length of disease as 0 in my FSGD file. When I run the GLM, I get the following error message: matrix is ill-conditioned or badly scaled, condno = 1e+08 Can you please tell me what I am doing wrong? Below is the required information. 1. Your command line: mri_glmfit --y lh.disease_length.thickness.20.mgz --fsgd fsgd_disease_length.txt dods --glmdir lh.disease_length.thickness.20.glmdir --surf fsaverage lh --C groupdiff_length_disease.mat 2. The FSGD file GroupDescriptorFile 1 Title Anorexia vs Controls Class Control plus blue Class Patient circle green Variables Age Disease_Length Input C07 Control 37 0 Input C28 Control 28 0 Input C39 Control 37 0 Input C54 Control 40 0 Input C57 Control 32 0 Input C10 Control 54 0 Input C33 Control 31 0 Input C29 Control 22 0 Input A01 Patient 39 20 Input A02 Patient 24 11 Input A03 Patient 35 15 Input A04 Patient 40 10 Input A05 Patient 35 20 Input A06 Patient 57 20 Input A07 Patient 31 16 Input A08 Patient 20 8 3. And the design matrix Design matrix ------------------ 1.000 0.000 37.000 0.000 0.000 0.000; 1.000 0.000 28.000 0.000 0.000 0.000; 1.000 0.000 37.000 0.000 0.000 0.000; 1.000 0.000 40.000 0.000 0.000 0.000; 1.000 0.000 32.000 0.000 0.000 0.000; 1.000 0.000 54.000 0.000 0.000 0.000; 1.000 0.000 31.000 0.000 0.000 0.000; 1.000 0.000 22.000 0.000 0.000 0.000; 0.000 1.000 0.000 39.000 0.000 20.000; 0.000 1.000 0.000 24.000 0.000 11.000; 0.000 1.000 0.000 35.000 0.000 15.000; 0.000 1.000 0.000 40.000 0.000 10.000; 0.000 1.000 0.000 35.000 0.000 20.000; 0.000 1.000 0.000 57.000 0.000 20.000; 0.000 1.000 0.000 31.000 0.000 16.000; 0.000 1.000 0.000 20.000 0.000 8.000; -------------------------------- Thank you, Allie

2 1

Volume to surface 2
by Gabriel Gonzalez Escamilla 07 May '12

07 May '12

1 0

Re: [Freesurfer] Difficulties in processing cortical thickness with 2 atrophic brains
by Bruce Fischl 06 May '12

06 May '12

thanks. So there looks to be a pretty dramatic failure in the aseg which is the root of man of your problems. If you upload one of your datasets I'll take a look Bruce On Mon, 7 May 2012, Zixuan Yang wrote: > Sorry Bruce! Please find the attachment here. > > Many thanks! > Kind regards, > > Zixuan > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Friday, 4 May 2012 10:28 PM > To: Zixuan Yang > Subject: RE: [Freesurfer] Difficulties in processing cortical thickness with 2 atrophic brains > > Hi Zixuan > > there was no attachment. Also, can you cc the list so others can answer? > > thanks > Bruce > On > Fri, 4 May 2012, Zixuan Yang wrote: > >> >> Hi Bruce, >> >> >> >> Please find the attached aseg images of participant A and B. Many thanks!!! >> >> >> >> Kind regards, >> >> Zixuan >> >> >> >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Friday, 4 May 2012 12:40 PM >> To: Zixuan Yang >> Cc: freesurfer(a)nmr.mgh.harvard.edu; mailman-owner(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Difficulties in processing cortical thickness with >> 2 atrophic brains >> >> >> >> What do the asegs look like? >> >> >> On May 2, 2012, at 8:18 PM, Zixuan Yang <zixuan.yang1(a)student.unsw.edu.au> >> wrote: >> >> Dear Freesurfer experts, >> >> >> >> I am processing some atrophic brains with Freesurfer. However >> considerable part of 2 participants? brains (WM+GM) is not >> recognized (especially for participant B, the posterior part is >> not processed at all). I have checked the Talairach registration >> of both, only the borderlines of the posterior brain regions >> are not exactly accurate. Then I have tried to add thousands of >> control points and run the <recon-all ?autorecon2-cp ?ssubject name> >> but that doesn?t help. >> >> >> >> Please find the attached slides of 2 participants. Could you >> please give me some suggestions for better processing or further >> editing? Many thanks!! >> >> >> >> Kind regards, >> >> Zixuan >> >> >> >> -- >> >> Zixuan YANG >> >> >> >> Ph.D student >> UNSW School of Psychiatry >> NPI - Euroa Centre, Prince of Wales Hospital Barker Street, >> RANDWICK NSW >> 2031 Australia >> Tel: 0405256313 >> >> Email: zixuan.yang1(a)unsw.edu.au >> >> >> >> <Participant A and B for cortical thickness.docx> >> >> _______________________________________________ >> 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. >> >> >> >

1 0

tracula
by carolina.mr 05 May '12

05 May '12

2 1

load multiple overlays with different colors
by keepmoon 05 May '12

05 May '12

Dear all, I search my question before I post it. I did find similar questions, but didn't find answer. I want to overlay two files with different colors. For example, one is sig1.mgh from cortical thickness, the other is sig2.mgh from area. I want to use tksurfer overlaying them with three colors: red is significant regions of thickness; blue is significant regions of area; green is overlap significant regions of thickness and area. I tried to use the following command: tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay sig1.mgh -overlay sig2.mgh It just can display sig1.mgh or sig2.mgh, but can't display two together. In addition, I don't know how to control overlap and other regions color. Anyone knows how to do this? Any help will be appreciated! Thanks in advance! Kathy

4 10

copy of pbsubmit
by Knut J Bjuland 05 May '12

05 May '12

Hi I am trying to setup a local pc as cluster to debug trac-all. Is it possible to get a copy of pbsubmit? I think I could use it as wrapper fro qsub on my pc. Best regards Knut J

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