[Freesurfer] mris_preproc skips subjects
Dear Freesurfers, Sorry for this newbie question: I'm preparing my data for a group analysis using mris_preproc: mris_preproc --fsgd nocov.fsgd --target fsaverage --hemi lh --meas thickness --out lh.nocov.thickness.00.mgh I have 120 subjects in total and my FSGD file simply looks like this GroupDescriptorFile 1 Class Group1 Class Group2 Input pt01 Group1 Input pt02 Group1 [..rest of lines left out..] Input ct01 Group2 Input ct02 Group2 [..rest of lines left out..] When I run mris_preproc, the program only assembles the first two subjects in group 1 and the first subject in group 2, i.e. 3 subjects not 120. I have run -make all on all subjects and there is nothing to make. I'm running ver. 5.3.0 What is wrong? All the best, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_preproc skips subjects
Hi again, I'm still totally stuck here. Any idea what the problem might be? I tried running mris_preproc with the --s option instead of --fsgd and this apparently works for all subjects that I tried so far. Now, using --fsgd, mris_preproc only processes the first subject in group 2?! All the best, Anders 2015-02-21 14:42 GMT+01:00 Anders Hougaard : > Dear Freesurfers, > > Sorry for this newbie question: > I'm preparing my data for a group analysis using mris_preproc: > > mris_preproc --fsgd nocov.fsgd --target fsaverage --hemi lh --meas > thickness --out lh.nocov.thickness.00.mgh > > I have 120 subjects in total and my FSGD file simply looks like this > > GroupDescriptorFile 1 > Class Group1 > Class Group2 > Input pt01 Group1 > Input pt02 Group1 > [..rest of lines left out..] > Input ct01 Group2 > Input ct02 Group2 > [..rest of lines left out..] > > > When I run mris_preproc, the program only assembles the first two > subjects in group 1 and the first subject in group 2, i.e. 3 subjects > not 120. > > I have run -make all on all subjects and there is nothing to make. > I'm running ver. 5.3.0 > > What is wrong? > > All the best, > Anders ___ Freesurfer mailing list 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.
[Freesurfer] Bad design matrix
Dear all, I'm comparing cortical thickness of a group of patients to a group of controls. I want to regress out the effects of gender, age, disease severity and disease duration. For the controls, the last two parameters equals zero. When running mri_glmfit, i get ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 See the design matrix attached. My contrasts are set as 1 -1 0 0 0 0 0 0 0 0 and -1 1 0 0 0 0 0 0 0 0 What should I do to improve this? All the best, Anders 1.000 0.000 1.000 0.000 43.945 0.000 0.300 0.000 26.275 0.000; 1.000 0.000 0.000 0.000 47.622 0.000 0.100 0.000 21.101 0.000; 1.000 0.000 0.000 0.000 23.072 0.000 8.000 0.000 20.329 0.000; 1.000 0.000 0.000 0.000 51.751 0.000 1.700 0.000 39.874 0.000; 1.000 0.000 0.000 0.000 44.986 0.000 4.000 0.000 32.873 0.000; 1.000 0.000 0.000 0.000 42.067 0.000 1.000 0.000 30.259 0.000; 1.000 0.000 1.000 0.000 42.500 0.000 2.000 0.000 21.533 0.000; 1.000 0.000 0.000 0.000 46.661 0.000 3.000 0.000 34.051 0.000; 1.000 0.000 0.000 0.000 33.123 0.000 1.000 0.000 1.117 0.000; 1.000 0.000 1.000 0.000 26.272 0.000 0.300 0.000 18.015 0.000; 1.000 0.000 1.000 0.000 48.066 0.000 1.000 0.000 10.031 0.000; 1.000 0.000 0.000 0.000 49.251 0.000 8.000 0.000 38.987 0.000; 1.000 0.000 1.000 0.000 20.244 0.000 0.500 0.000 7.313 0.000; 1.000 0.000 0.000 0.000 30.949 0.000 3.000 0.000 23.499 0.000; 1.000 0.000 0.000 0.000 20.810 0.000 3.000 0.000 16.405 0.000; 1.000 0.000 1.000 0.000 53.106 0.000 1.000 0.000 43.307 0.000; 1.000 0.000 0.000 0.000 55.321 0.000 1.000 0.000 39.639 0.000; 1.000 0.000 1.000 0.000 24.583 0.000 2.000 0.000 18.357 0.000; 1.000 0.000 0.000 0.000 51.693 0.000 1.000 0.000 35.409 0.000; 1.000 0.000 0.000 0.000 26.497 0.000 2.000 0.000 11.458 0.000; 1.000 0.000 1.000 0.000 44.079 0.000 1.000 0.000 31.463 0.000; 1.000 0.000 0.000 0.000 33.114 0.000 1.000 0.000 22.461 0.000; 1.000 0.000 0.000 0.000 27.556 0.000 2.000 0.000 6.511 0.000; 1.000 0.000 0.000 0.000 25.730 0.000 8.000 0.000 21.517 0.000; 1.000 0.000 0.000 0.000 22.527 0.000 2.000 0.000 6.557 0.000; 1.000 0.000 1.000 0.000 20.413 0.000 1.000 0.000 4.646 0.000; 1.000 0.000 0.000 0.000 22.951 0.000 2.000 0.000 20.687 0.000; 1.000 0.000 1.000 0.000 41.218 0.000 1.000 0.000 0.726 0.000; 1.000 0.000 0.000 0.000 27.578 0.000 2.000 0.000 18.801 0.000; 1.000 0.000 0.000 0.000 27.389 0.000 2.000 0.000 17.793 0.000; 1.000 0.000 0.000 0.000 48.515 0.000 2.000 0.000 34.916 0.000; 1.000 0.000 0.000 0.000 21.878 0.000 4.000 0.000 11.877 0.000; 1.000 0.000 0.000 0.000 55.023 0.000 1.000 0.000 30.883 0.000; 1.000 0.000 1.000 0.000 30.138 0.000 0.500 0.000 3.376 0.000; 1.000 0.000 0.000 0.000 26.689 0.000 1.000 0.000 24.107 0.000; 1.000 0.000 0.000 0.000 29.906 0.000 1.000 0.000 12.674 0.000; 1.000 0.000 1.000 0.000 22.962 0.000 1.000 0.000 8.851 0.000; 1.000 0.000 0.000 0.000 20.178 0.000 2.000 0.000 6.856 0.000; 1.000 0.000 0.000 0.000 19.762 0.000 1.000 0.000 8.882 0.000; 1.000 0.000 1.000 0.000 22.968 0.000 1.000 0.000 7.932 0.000; 1.000 0.000 1.000 0.000 24.789 0.000 1.000 0.000 10.278 0.000; 1.000 0.000 0.000 0.000 27.190 0.000 1.500 0.000 4.309 0.000; 1.000 0.000 1.000 0.000 21.747 0.000 2.000 0.000 11.351 0.000; 1.000 0.000 0.000 0.000 27.650 0.000 1.000 0.000 11.641 0.000; 1.000 0.000 1.000 0.000 22.333 0.000 1.500 0.000 12.331 0.000; 1.000 0.000 0.000 0.000 29.525 0.000 1.000 0.000 19.499 0.000; 1.000 0.000 1.000 0.000 32.263 0.000 1.000 0.000 12.684 0.000; 1.000 0.000 0.000 0.000 28.906 0.000 7.500 0.000 21.670 0.000; 1.000 0.000 0.000 0.000 24.690 0.000 1.000 0.000 7.852 0.000; 1.000 0.000 0.000 0.000 18.639 0.000 1.000 0.000 3.710 0.000; 1.000 0.000 0.000 0.000 24.419 0.000 0.500 0.000 7.477 0.000; 1.000 0.000 0.000 0.000 53.821 0.000 0.167 0.000 30.582 0.000; 1.000 0.000 0.000 0.000 59.072 0.000 1.000 0.000 30.656 0.000; 1.000 0.000 0.000 0.000 31.844 0.000 0.333 0.000 17.654 0.000; 1.000 0.000 0.000 0.000 48.936 0.000 1.000
Re: [Freesurfer] Bad design matrix
0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. 2015-03-01 19:41 GMT+01:00 Douglas Greve : > > Try demeaning your covariates. By demeaning, I mean to compute the mean > across all subjects, then subtract the mean from all values (for each > covariate). > doug > > > > On 3/1/15 2:40 AM, Anders Hougaard wrote: > > Dear all, > > I'm comparing cortical thickness of a group of patients to a group of > controls. > I want to regress out the effects of gender, age, disease severity and > disease duration. > For the controls, the last two parameters equals zero. > > When running mri_glmfit, i get ERROR: matrix is ill-conditioned or > badly scaled, condno = 1e+08 > See the design matrix attached. My contrasts are set as > 1 -1 0 0 0 0 0 0 0 0 > and > -1 1 0 0 0 0 0 0 0 0 > > What should I do to improve this? > > All the best, > Anders > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Bad design matrix
Thanks Doug. Any suggestions for a more appropriate design? I guess this is a common situation where two or more parameters only apply to one group (in this case patients) and are zero or constant in the other. Best, Anders 2015-03-02 21:21 GMT+01:00 Douglas N Greve : > > It looks like the 4th column is always -0.9 and the 6th col is always > -9.138 which makes them redundant with column 2 and causes the error. > doug > > On 03/02/2015 03:16 PM, Anders Hougaard wrote: >> Dear Doug, >> >> Thanks for the answer. I deliberately chose not to demean. >> With demeaning I get the same error (see below). Any suggestions? >> >> Best, >> Anders >> >> Design matrix -- >> 1.000 0.000 -0.600 0.000 17.137 0.000; >> 1.000 0.000 -0.800 0.000 11.962 0.000; >> 1.000 0.000 7.100 0.000 11.190 0.000; >> 1.000 0.000 0.700 0.000 30.736 0.000; >> 1.000 0.000 3.100 0.000 23.735 0.000; >> 1.000 0.000 0.100 0.000 21.121 0.000; >> 1.000 0.000 1.100 0.000 12.395 0.000; >> 1.000 0.000 2.100 0.000 24.912 0.000; >> 1.000 0.000 0.100 0.000 -8.021 0.000; >> 1.000 0.000 -0.700 0.000 8.877 0.000; >> 1.000 0.000 0.100 0.000 0.893 0.000; >> 1.000 0.000 7.100 0.000 29.849 0.000; >> 1.000 0.000 -0.400 0.000 -1.825 0.000; >> 1.000 0.000 2.100 0.000 14.361 0.000; >> 1.000 0.000 2.100 0.000 7.267 0.000; >> 1.000 0.000 0.100 0.000 34.169 0.000; >> 1.000 0.000 0.100 0.000 30.500 0.000; >> 1.000 0.000 1.100 0.000 9.219 0.000; >> 1.000 0.000 0.100 0.000 26.270 0.000; >> 1.000 0.000 1.100 0.000 2.320 0.000; >> 1.000 0.000 0.100 0.000 22.325 0.000; >> 1.000 0.000 0.100 0.000 13.323 0.000; >> 1.000 0.000 1.100 0.000 -2.628 0.000; >> 1.000 0.000 7.100 0.000 12.379 0.000; >> 1.000 0.000 1.100 0.000 -2.581 0.000; >> 1.000 0.000 0.100 0.000 -4.492 0.000; >> 1.000 0.000 1.100 0.000 11.549 0.000; >> 1.000 0.000 0.100 0.000 -8.413 0.000; >> 1.000 0.000 1.100 0.000 9.663 0.000; >> 1.000 0.000 1.100 0.000 8.655 0.000; >> 1.000 0.000 1.100 0.000 25.778 0.000; >> 1.000 0.000 3.100 0.000 2.739 0.000; >> 1.000 0.000 0.100 0.000 21.745 0.000; >> 1.000 0.000 -0.400 0.000 -5.762 0.000; >> 1.000 0.000 0.100 0.000 14.969 0.000; >> 1.000 0.000 0.100 0.000 3.535 0.000; >> 1.000 0.000 0.100 0.000 -0.287 0.000; >> 1.000 0.000 1.100 0.000 -2.283 0.000; >> 1.000 0.000 0.100 0.000 -0.257 0.000; >> 1.000 0.000 0.100 0.000 -1.207 0.000; >> 1.000 0.000 0.100 0.000 1.140 0.000; >> 1.000 0.000 0.600 0.000 -4.829 0.000; >> 1.000 0.000 1.100 0.000 2.213 0.000; >> 1.000 0.000 0.100 0.000 2.503 0.000; >> 1.000 0.000 0.600 0.000 3.193 0.000; >> 1.000 0.000 0.100 0.000 10.361 0.000; >> 1.000 0.000 0.100 0.000 3.546 0.000; >> 1.000 0.000 6.600 0.000 12.532 0.000; >> 1.000 0.000 0.100 0.000 -1.286 0.000; >> 1.000 0.000 0.100 0.000 -5.428 0.000; >> 1.000 0.000 -0.400 0.000 -1.661 0.000; >> 1.000 0.000 -0.800 0.000 21.444 0.000; >> 1.000 0.000 0.100 0.000 21.517 0.000; >> 1.000 0.000 -0.600 0.000 8.515 0.000; >> 1.000 0.000 0.100 0.000 19.530 0.000; >> 1.000 0.000 1.100 0.000 1.824 0.000; >> 1.000 0.000 0.100 0.000 15.795 0.000; >> 1.000 0.000 0.600 0.000 -6.140 0.000; >> 1.000 0.000 2.600 0.000 0.803 0.000; >> 1.000 0.000 0.100 0.000 16.904 0.000; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000 -0.900 0.000 -9.138; >> 0.000 1.000 0.000
Re: [Freesurfer] flipping surface data
Dear Doug, I would like to the same thing that Kelsi (as I read the post) asked about: For patients with a lesion in one hemisphere, I want to compare the hemispheres with lesions to the contralateral hemispheres without lesions. I think that your answer below is a recipe for comparing right and left hemispheres within subjects. In my case half of the patients have a lesion in the right hemisphere and the other half have a lesion in the left hemisphere. I guess I should register all of the hemispheres to the left hemisphere of fsaverage_sym, but how do I set up the analysis for doing a paired comparison of hemispheres with lesion vs hemispheres without? All the best, Anders 2011/11/14 Douglas N Greve > > Try these instructions. You won't actually need to do the download and > install in you're local, but you will need to use the dev env. > > doug > > > > Download these files > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz > > # Copy surfreg and xhemireg into $FREESURFER_HOME/bin > # Copy mris_preproc into $FREESURFER_HOME/bin after making a backup > # Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR > cd $SUBJECTS_DIR > tar xvfz fsaverage_sym.tar.gz > > - > To apply an existing atlas (eg, fsaverage_sym) to an anatomical analysis > > # Reg to atlas (1-2 hours per subject) > # Creates $subject/xhemi > # Creates lh.fsaverage_sym.sphere.reg in $subject and $subject/xhemi > foreach subject (subjectlist) > surfreg --s $subject --t fsaverage_sym --lh > surfreg --s $subject --t fsaverage_sym --lh --xhemi > end > > # Create a stack of subjects > mris_preproc --target fsaverage_sym --hemi lh > --xhemi --paired-diff \ > --srcsurfreg fsaverage_sym.sphere.reg \ > --meas thickness \ > --out lh.lh-rh.thickness.sm00.mgh \ > --s subj1 --s subj2 ... > > # Smooth > mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5\ > --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm05.mgh > > # Analyze > mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir > glm.lh.lh-rh.thickness.sm05 \ > --osgm --surf fsaverage_sym lh > > # View > tksurfer fsaverage_sym lh inflated -aparc -overlay > glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh > > > kelsi wrote: > > Hi Freesurfers, > > > > Is there a tool to flip the orientation of surface data to the > > opposite hemisphere? We are working with stroke patients, and I would > > like to do analysis of the contralesional hemisphere of all the > > patients. However, this requires putting them on the same hemisphere > > for ttests, etc. I saw an earlier thread online about a program for > > flipping in the works, I was just wondering if this is now possible? > > Thank you! > > > > Kelsi > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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@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@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] Renaming subject directories
Dear Freesurfers, Is it ok to rename a subject directory, then run tkmedit and recon-all procedures and then rename the directory back again or will this cause problems? All the best, Anders ___ Freesurfer mailing list 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.
[Freesurfer] Radiological/neurological convention
Dear Freesurfers, Do the anatomical input images to recon-all have to be in the same orientation (neurological/radiological) or is it ok as long as the orientation labels are correct? All the best, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
Dear Freesurfers, I am now encountering a new error with the Hinds V1 procedure: I am still using the same version (5.1.0) and nothing has changed, except that I have been doing some cross-hemispheric registration for some of the subjects (not this one). using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 1.000 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /Applications/freesurfer/subjects/t05/surf/lh.sphere... reading template parameterization from /Applications/freesurfer/subjects/V1_average/label/lh.v1.invivo.tif... mrisReadTriangleFile(/Applications/freesurfer/subjects/t05/surf/lh.smoothwm): surface doesn't match /Applications/freesurfer/subjects/t05/surf/lh.sphere Any suggestions? All the best, Anders 2012/6/13 Anders Hougaard > Hi Bruce, > > That actually seems to do the trick. Thank you very much! > > Best, > Anders > > > 2012/6/12 Bruce Fischl > >> try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that >> solves your problem >> >> cheers >> Bruce >> >> On Tue, 12 Jun 2012, Anders Hougaard wrote: >> >> Dear Dr. Bock, >>> I get the same error in FS 5.1.0 when running recon-all -s >>> -label_v1. >>> >>> Did you find a solution? >>> >>> Best regards, >>> >>> Anders Hougaard, MD >>> Danish Headache Center >>> Dept. of Neurology >>> Glostrup Hospital >>> Copenhagen >>> Denmark >>> >>> 2011/11/11 Andrew Bock >>> Hello, >>> >>> I am having a similar problem to one described on the freesurfer >>> mail archive, where I receive the following error when trying to >>> identify V1 using the Hinds method (i.e. recon-all -s >>> -label_v1): >>> >>> processing subject V1_average... >>> MRISreadVertexPosition(white): could not open file >>> /usr/local/freesurfer/**subjects/V1_average/surf/rh.**white >>> No such file or directory >>> MRISreadOriginalProperties: could not read surface file white >>> No such file or directory >>> could not read surface positions from white >>> No such file or directory >>> >>> >>> As Prof. Krish Singh indicated in July, it appears the problem >>> occurs when trying to open rh.white (or lh.white) from the surf >>> subdirectory in V1_average, which doesn't exist. >>> >>> I have run recon-all -s -make all, but it returns >>> "make: Nothing to be done for `all'." >>> >>> Any help you can provide would be greatly appreciated! >>> >>> Thanks in advance, >>> >>> Andrew >>> >>> -- >>> Andrew Bock, Ph.D. >>> Department of Psychology >>> University of Washington >>> Seattle, WA 98195 >>> Tel: 206.543.3817 >>> Fax: 206.685.3157 >>> ab...@u.washington.edu >>> >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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@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] V3A ROI?
Dear experts, I am trying to find a probabilistic map of the visual cortical area V3A. I have not been able to find this particular area in the standard atlases in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but not V3A. Do any of you know have this ROI as a file or do you know of an atlas which contains it? An estimation based on an experiment, e.g. an average from retinotopic maps of healthy subjects would also be very helpful. All the best, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] V3A ROI?
Excellent, thank you. The link to the ROI files is this: http://www.princeton.edu/~napl/vtpm.htm Best, Anders 2016-07-11 12:26 GMT+02:00 Francesca Strappini : > Wang, Mruczek, Arcaro, Kastner (2014). > Probabilistic Maps of Visual Topography in Human Cortex. > Cerebral Cortex, Oct;25(10):3911-31 > > > 2016-07-11 12:13 GMT+02:00 Anders Hougaard : > >> Dear experts, >> >> I am trying to find a probabilistic map of the visual cortical area V3A. >> I have not been able to find this particular area in the standard atlases >> in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but >> not V3A. >> Do any of you know have this ROI as a file or do you know of an atlas >> which contains it? >> An estimation based on an experiment, e.g. an average from retinotopic >> maps of healthy subjects would also be very helpful. >> >> All the best, >> Anders >> >> >> ___ >> Freesurfer mailing list >> 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. >> >> > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > > ___ > Freesurfer mailing list > 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. > > ___ Freesurfer mailing list 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.
[Freesurfer] Extracting thickness values using labels
Dear Freesurfers, This is probably a very basic question, but I was unable to find an answer in the mailing list: I did a paired cortical thickness group analysis: mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas thickness --out lh.paired.00.mgh --paired-diff (smoothing) mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf fsaverage lh --cortex --glmdir lh.05_diff.glmdir I found an area of difference in cortical thickness and I would like to know the thickness values of this area for all of the input in paired.fsgd, not just the differences I get from the y.ocn.dat file. How do I extract thickness values from the lh.paired.00.mgh file using the label file of the significant cluster? All the best, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] Extracting thickness values using labels
Perfect, thanks Doug! 2016-10-06 17:34 GMT+02:00 Douglas Greve : > The easiest way to to re-run mris_preproc without the --paired-diff to get > a stack of all your data, then run > > mri_segstats --i stackwithalldata.smoothed.mgh --seg ocn.mgh --excludeid 0 > --avgwf ocn.dat > > ocn.mgh is the ocn file (output cluster number), and ocn.dat will be a > table with each input from diff.fsgd on the rows and each cluster on the > columns > > On 10/6/16 2:23 AM, Anders Hougaard wrote: > > Dear Freesurfers, > > This is probably a very basic question, but I was unable to find an answer > in the mailing list: > > I did a paired cortical thickness group analysis: > > mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas > thickness --out lh.paired.00.mgh --paired-diff > > (smoothing) > > mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf fsaverage > lh --cortex --glmdir lh.05_diff.glmdir > > I found an area of difference in cortical thickness and I would like to > know the thickness values of this area for all of the input in paired.fsgd, > not just the differences I get from the y.ocn.dat file. > > How do I extract thickness values from the lh.paired.00.mgh file using the > label file of the significant cluster? > > All the best, > Anders > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > 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. > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] Gamma / Histogram
Excellent, thanks!
2016-10-12 20:27 GMT+02:00 Douglas N Greve :
>
>
> On 10/08/2016 02:43 AM, Anders Hougaard wrote:
> > Dear Freesurfers,
> >
> > Please see the attached image.
> > It shows inflated fsaverage surface with gamma.mgh overlaid.
> > Gamma.mgh is from one contrast of a standard group analysis of
> > cortical thickness (two groups A and B, two contrasts A>B and B>A).
> >
> > 1) Is it correct to interpret the gamma values as between-group
> > difference of cortical thickness in mm?
> It depends on how you set up the contrast. If it is a simple A vs B,
> then yes, mm is correct.
> >
> > 2) I would like to reproduce the histogram in another software. Is it
> > possible to extract the gamma values for each vertex for this purpose?
> You can do it in matlab easily enough, eg,
> gamma = MRIread('gamma.mgh');
> gamma.vol will be the pixel values
> >
> > All the best,
> > Anders
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
> ___
> Freesurfer mailing list
> 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.
>
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[Freesurfer] Converting V1 labels to nifti
Dear Freesurfers, I would like to use V1 labels (created with the Hinds method) for a ROI-based analysis on data analyzed with FSL FEAT using FSL featquery. I have not run a full recon-all segmentation, only recon-all -s subjid -label-v1 I need to convert the labels to nifti volumes while registering to MNI standard space. I guess the right command would be something like mri_label2vol --label lh.v1.predict.label --reg register.dat --hemi lh --subject subject --o lh.v1.predict.label Is there a register.dat from the FSL feat directory that I could use for this? Anything else I need to add? Of course, I would like to keep the resulting volume probabilistic. All the best, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
Dear Dr. Bock, I get the same error in FS 5.1.0 when running recon-all -s -label_v1. Did you find a solution? Best regards, Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark 2011/11/11 Andrew Bock > Hello, > > I am having a similar problem to one described on the freesurfer mail > archive, where I receive the following error when trying to identify V1 > using the Hinds method (i.e. recon-all -s -label_v1): > > processing subject V1_average... > MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ > subjects/V1_average/surf/rh.white > No such file or directory > MRISreadOriginalProperties: could not read surface file white > No such file or directory > could not read surface positions from white > No such file or directory > > > As Prof. Krish Singh indicated in July, it appears the problem occurs when > trying to open rh.white (or lh.white) from the surf subdirectory in > V1_average, which doesn't exist. > > I have run recon-all -s -make all, but it returns "make: Nothing > to be done for `all'." > > Any help you can provide would be greatly appreciated! > > Thanks in advance, > > Andrew > > -- > Andrew Bock, Ph.D. > Department of Psychology > University of Washington > Seattle, WA 98195 > Tel: 206.543.3817 > Fax: 206.685.3157 > ab...@u.washington.edu > > ___ > Freesurfer mailing list > 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. > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
Hi Bruce, That actually seems to do the trick. Thank you very much! Best, Anders 2012/6/12 Bruce Fischl > try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that > solves your problem > > cheers > Bruce > > On Tue, 12 Jun 2012, Anders Hougaard wrote: > > Dear Dr. Bock, >> I get the same error in FS 5.1.0 when running recon-all -s >> -label_v1. >> >> Did you find a solution? >> >> Best regards, >> >> Anders Hougaard, MD >> Danish Headache Center >> Dept. of Neurology >> Glostrup Hospital >> Copenhagen >> Denmark >> >> 2011/11/11 Andrew Bock >> Hello, >> >> I am having a similar problem to one described on the freesurfer >> mail archive, where I receive the following error when trying to >> identify V1 using the Hinds method (i.e. recon-all -s >> -label_v1): >> >> processing subject V1_average... >> MRISreadVertexPosition(white): could not open file >> /usr/local/freesurfer/**subjects/V1_average/surf/rh.**white >> No such file or directory >> MRISreadOriginalProperties: could not read surface file white >> No such file or directory >> could not read surface positions from white >> No such file or directory >> >> >> As Prof. Krish Singh indicated in July, it appears the problem >> occurs when trying to open rh.white (or lh.white) from the surf >> subdirectory in V1_average, which doesn't exist. >> >> I have run recon-all -s -make all, but it returns >> "make: Nothing to be done for `all'." >> >> Any help you can provide would be greatly appreciated! >> >> Thanks in advance, >> >> Andrew >> >> -- >> Andrew Bock, Ph.D. >> Department of Psychology >> University of Washington >> Seattle, WA 98195 >> Tel: 206.543.3817 >> Fax: 206.685.3157 >> ab...@u.washington.edu >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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@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.
Re: [Freesurfer] label transformation to MNI space
Dear Doug, I have problem similar to this: I am trying to convert V1 labels from the Hinds method to volumes and transform them to MNI152 space for use in FSL. I tried using this command: mri_label2vol --label rh.v1.prob.label --reg $FREESURFER_HOME/average/mni152.register.dat --temp MNI152_T1_2mm.nii.gz --o rh_v1_prob.nii.gz --label-stat rh_v1_prob_stat.nii.gz ...but the output is not registered correctly. It seems to be shift downward as Linda described. Label conversion using the cmd mri_label2label --srclabel rh.v1.prob.label --s --regmethod surface --trglabel rh.v1.prob.new.label --hemi rh does not solve it. Any suggestions? Best regards, Anders Hougaard 2011/10/18 Douglas N Greve > The problem appears to be with the label itself. Try this conversion: > > mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod > surface --trglabel lh.entorhinal.new.label --hemi lh > > Also, you might want to use the entorhinal label define in the > aparc+aseg since it fills in the ribbon: > mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz > 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt > > doug > > > > > Linda Douw wrote: > > Hi Doug, > > Thanks for the reply. This cmd makes it slightly better I guess, but > still > > definetely off target. It seems to be shift downward, towards inferior, > > and therefore sometimes outside the skull. Any other ideas? > > Linda > > > > > >> The way the reg is set up, the targ is your mask. Try this cmd: > >> mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz > >> --o lh_entorhinal_MNI.nii.gz --reg > >> $FREESURFER_HOME/average/mni152.register.dat --inv > >> > >> doug > >> > >> Linda Douw wrote: > >> > >>> Hi all, > >>> > >>> I am trying to transform some labels from the aparc to masks in MNI > >>> space. > >>> Ideally, I would like to do this for each subject in my study > >>> individually > >>> (using their own rawavg.mgz and labels), but for now I started out with > >>> fsaverage. I first converted the label file into a nifti: > >>> > >>> mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject > >>> fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz > >>> --identity > >>> > >>> And then put the nifti file containing the label into MNI space: > >>> > >>> mri_vol2vol --mov lh_entorhinal.nii.gz --targ > MNI152_T1_2mm.brain.nii.gz > >>> --o lh_entorhinal_MNI.nii.gz --reg > >>> $FREESURFER_HOME/average/mni152.register.dat > >>> > >>> But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is > >>> completely wrong. I checked the location with tkregister as well: > >>> > >>> tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg > >>> /$FREESURFER_HOME/average/mni152.register.dat > >>> > >>> But here the entorhinal was also in the wrong place. > >>> > >>> Do you know how to fix this? > >>> > >>> Thanks, > >>> > >>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@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 > >> > >> > >> > >> > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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@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@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.
Re: [Freesurfer] label transformation to MNI space
Of course, you are right...It fits perfectly now. Thank you so much! Best, Anders 2012/7/4 Douglas Greve > Where did rh.v1.probl.label come from? The way you call mri_label2vol, it > should be in fsaverage space. If it is in an individual space, then the > registration is wrong. Try running mni152reg to create a registration from > the individual to mni152, then use that reg instead. > doug > > > On 7/4/12 5:32 AM, Anders Hougaard wrote: > > Dear Doug, > > > I have problem similar to this: > I am trying to convert V1 labels from the Hinds method to volumes and > transform them to MNI152 space for use in FSL. > I tried using this command: > mri_label2vol --label rh.v1.prob.label --reg > $FREESURFER_HOME/average/mni152.register.dat --temp MNI152_T1_2mm.nii.gz > --o rh_v1_prob.nii.gz --label-stat rh_v1_prob_stat.nii.gz > > ...but the output is not registered correctly. It seems to be shift > downward as Linda described. > > Label conversion using the cmd > mri_label2label --srclabel rh.v1.prob.label --s > --regmethod surface --trglabel rh.v1.prob.new.label --hemi rh > does not solve it. > > Any suggestions? > > Best regards, > Anders Hougaard > > > > 2011/10/18 Douglas N Greve > > The problem appears to be with the label itself. Try this conversion: > > mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod > surface --trglabel lh.entorhinal.new.label --hemi lh > > Also, you might want to use the entorhinal label define in the > aparc+aseg since it fills in the ribbon: > mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz > 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt > > doug > > > > > Linda Douw wrote: > > Hi Doug, > > Thanks for the reply. This cmd makes it slightly better I guess, but > still > > definetely off target. It seems to be shift downward, towards inferior, > > and therefore sometimes outside the skull. Any other ideas? > > Linda > > > > > >> The way the reg is set up, the targ is your mask. Try this cmd: > >> mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz > >> --o lh_entorhinal_MNI.nii.gz --reg > >> $FREESURFER_HOME/average/mni152.register.dat --inv > >> > >> doug > >> > >> Linda Douw wrote: > >> > >>> Hi all, > >>> > >>> I am trying to transform some labels from the aparc to masks in MNI > >>> space. > >>> Ideally, I would like to do this for each subject in my study > >>> individually > >>> (using their own rawavg.mgz and labels), but for now I started out with > >>> fsaverage. I first converted the label file into a nifti: > >>> > >>> mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject > >>> fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz > >>> --identity > >>> > >>> And then put the nifti file containing the label into MNI space: > >>> > >>> mri_vol2vol --mov lh_entorhinal.nii.gz --targ > MNI152_T1_2mm.brain.nii.gz > >>> --o lh_entorhinal_MNI.nii.gz --reg > >>> $FREESURFER_HOME/average/mni152.register.dat > >>> > >>> But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is > >>> completely wrong. I checked the location with tkregister as well: > >>> > >>> tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg > >>> /$FREESURFER_HOME/average/mni152.register.dat > >>> > >>> But here the entorhinal was also in the wrong place. > >>> > >>> Do you know how to fix this? > >>> > >>> Thanks, > >>> > >>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@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 > >> > >> > >> > >> > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > &
[Freesurfer] Error in preproc-sess in ver. 5
Hi all, While attempting to pre-process data for a retinotopy analysis with the following command: preproc-sess -surface song lhrh -fwhm 5 -sf sessid I get the following error when motion correction is started: Logfile is /Users/andershougaard/Programmer/freesurfer/retinotopy/log/mc-sess01-bold.log --- /Users/andershougaard/Programmer/freesurfer/retinotopy/sess01 RunList: 001 002 --- ** --- --- Motion Correcting Run 001 --- --- ** --- sess = sess01 Lør 2 Jul 2011 11:59:31 CEST mc-afni2 --i 001/f.nii --t 001/template.nii --o 001/fmcpr.nii --mcdat 001/fmcpr.mcdat ERROR: cannot find AFNI command 3dvolreg Any suggestions? Regards, Anders ___ Freesurfer mailing list 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.
[Freesurfer] Retinotopy stimuli
Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] Retinotopy stimuli
Hi all, Thank you very much! I did 2 runs of each of the stimuli I described in one session (I previously got some pretty decent maps from these data using the mrVista package from Stanford). I followed the retinotopy instructions from the FS wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) but the results did not make much sense. I guess I need to use some other commands or change some parameters in order to view reasonable eccentricity and polar angle maps. I have not managed to find any other documentation on how to do this. This is what my "raw angle" looks like: http://dl.dropbox.com/u/6981172/raw_angle.tif Best, Anders 2011/7/7 Jonathan Polimeni > > hi anders, > > the optimal set of stimulus parameters will depend somewhat on what > cortical area(s) you are trying to map and on the details of your > acquisition. in general, stimulating with both clockwise- and > counterclockwise-rotating wedges for polar angle mapping and with both > expanding and contracting rings for eccentricity mapping improves the > accuracy of the maps, and the proper analysis of this data is implemented > fsfast. the width of the wedge or the ring will depend on the cortical > area you are trying to stimulate, but you may want to consider a thinner > wedge. also, 8 Hz flickering has been shown to activate area V1 more > strongly than other frequencies, and smoothly moving stimuli can also > help. then, depending on your voxel size, field strength, coil array, > etc., you could include more cycles and may need to average together > multiple runs. > > marty, roger et al. have a few nice papers that i'd recommend that discuss > some of these details relating to phase-encoded retinotopic stimuli. > > Sereno & Tootell. Curr Opin Neurobiol. 2005;15(2):135-44. > Tootell et al. J Neurosci. 1997;17(18):7060-78. > Sereno et al. Science. 1995;268(5212):889-93. > > (the '97 paper discusses the ring/wedge thickness, the '95 paper discusses > the advantages of using both expanding + contracting stimuli, and the '05 > paper discusses the use of smoothly varying stimuli.) > > hope this helps. were you able to get reasonable looking maps with the > stimuli you described below? > > > -jon > > > > > On Thu, 7 Jul 2011, Anders Hougaard wrote: > > > Dear freesurfers, > > > > > > Which stimuli do you think provide the best retinotopic maps? > > > > I have done a retinotopy analysis using the following stimuli: > > > > Polar angle: > > > > - 45 deg counter-clockwise rotating wedge > > - 8 unique positions > > - flickering at 2 Hz > > - stimulation period: 36 sec > > - no. of cycles: 6 > > - TR = 3 > > > > Eccentricity: > > > > - expanding ring > > - 8 unique positions > > - flickering at 2 Hz > > - stimulation period: 36 sec > > - no. of cycles: 6 > > - TR = 3 > > > > Any suggestions on how to optimize this stimulation? > > E.g. different period length, more runs, bi-directional, different TR > > > > Thank you! > > > > Best regards, > > > > Anders > > > > > 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@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.
