Re: [Freesurfer] Creating aparc.a2009s+aseg.mgz for the averaged data
You can create a ribbon volume with the command below: mris_volmask \ --label_left_white 2 --label_left_ribbon 3 \ --label_right_white 41 --label_right_ribbon 42 \ --save_ribbon --save_distance youraveragesubject Note this when you make the aparc+aseg in this way, it should only be used when visualizing data on the mni305 brain. Don't extract volumes, etc. If you want to use one of the surface parcellations, do a surface-based analysis. doug On Sat, 17 Jul 2010, liang wang wrote: Hi, When I use make_average_subject to generate an average data, I can't find aparc.a2009s+aseg.mgz within the new average/mri. To get common parcellation to all subjects, I need to create this file. I understand that mri_aparc2aseg --s average --a2009s enable to perform what I want. However, when running this command, a error message shows up ERROR: cannot find /drive3/Stammer/Thickness/average/mri/ribbon.mgz. As displayed by this message, I did not find the ribbon.mgz file. I don't konw how to figure out this problem. Any suggestions? By the way, my make_average_surface file is updated by Nick's new one. And it does not include ribbon.mgz before updating. Liang -- 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.
Re: [Freesurfer] Extracting fMRI time course and computing correlations among them
definitely use the individuals. Use mri_vol2surf to convert the motion corrected (and otherwise unsmoothed) fmri time courses to the surface. Then use mri_segstats with the --avgwf and --annot options to compute the mean time course over the parcellations. doug On Sat, 17 Jul 2010, liang wang wrote: Hi, Does anyone know one of studies which uses the parcellations (aparc or aparc.a2009s) Freesurfer provides to extract fMRI time course from each subject's fMRI data. Reading the instructions in Freesurfer Wiki, I know how to do that. However, I am not sure whether I should use the parcellations from the average output (obtained from make_average_subject), or the parcellations based on each subject. I would next compute functional connectivity between these regions. I am appreciated for any suggestions. Liang -- 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.
Re: [Freesurfer] different rotation matrix from same DICOM
Probably the AA matlab file is using dicom coordinates which are LPS whereas my software uses RAS. On Thu, 15 Jul 2010, Xu, Jun wrote: Hi, I found out something that I do not understand when I was trying to create rotation matrix from scratch. I have used two methods and hope they will give me the same results. 1st method---form matrix from cross product as described in http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/quatern.html for example: -0.9994 00.0343 0.0153 -0.89530.4451 0.03070.44540.8948 I use formed rotation matrix * D (voxel size) --- I got exactly same affine matrix (1:3) as the one in nifti header. However, I tried another method since I would like to use normal vector if there is no row and col vector directly available in DICOM header. 2nd method --- form matrix from vox2ras_rsolveAA.m I got the matrix has the wrong signs although the numbers are exactly same. It cannot be simply apply some (making sensed) unity matrix for the correction (I have already correct normal vector for the sake of the requirement in 1st method reverse the sign for the first 2 row in normal vector, if I do not correct it, the matrix is still not same). For example: 0.9994 -0.0.0343 -0.0153 -0.89530.4451 -0.03070.44540.8948 I was wondering if you would know the reason for it. Thanks, Jun ___ 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.
Re: [Freesurfer] question: gray matter segmentation
The stats files are computed with partial volume correction. doug On Thu, 15 Jul 2010, Yunjo Lee wrote: Hi, I am a new user of FreeSurfer and trying to figure out gray matter segmentation. A volume that I extracted from aparc+aseg.mgz using mri_segstats did not match the volume reported in /stats/ text files (for example, aseg.stats, rh.aparc.stats). Even without specifying a mask in mri_segstats, there's always a discrepancy of 100 voxels or something. Where do the numbers in /stats/ files come from? Aren't they from aparc+aseg.mgz? Thanks! Yunjo -- 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.
Re: [Freesurfer] problem converting .ima files
wow, I have no clue. You can tar up the data and drop it to me at the file drop. But I just want to warn you that it might take me a while to get to. doug On Thu, 15 Jul 2010, Scott Hayes wrote: Hi, I am trying to convert .ima files, and my command seems to work fine for some series: mri_convert -it siemens -ot nii 523-2-4.ima ../srs2.nii but not others: mri_convert -it siemens -ot nii 523-3-132.ima ../srs3.nii These are series collected from the same scan session. The data were reportedly collected at MGH: Siemens Allegra, around the fall of 2001 (if that helps at all). I'm running freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 I don't receive any error messages. The problem seems to be similar to one previously described in the archives, although I was not able to find the final solution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00890.html Any guidance would be appreciated. Thanks, Scott -- 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.
Re: [Freesurfer] FDR Calculations
It computes the p-values first. doug On Thu, 15 Jul 2010, James Porter wrote: Hello- Does the built-in FDR function in tksurfer and QDEC run the calculations upon the actual values in the .mgh files, or does it take the exponent of those -log10(p) values first? -- 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.
Re: [Freesurfer] ERROR selxavg-sess
Hi Keta, this is a pretty old version. Are you sure you don't want to upgrade? The ipr is the in-plane resolution stored in the seq.info file in the bold directory. Newer versions don't use this anymore. doug On Thu, 8 Jul 2010, ±¬Ìî¸ÂÀ wrote: Hi,Freesurfers I'm going to analyze the functional data. By now I finished reconstruction of anatomical data and maiking hierarchy, mc-sess,spatialsmooth-sess,inorm-sess,mkanalysis-sess and fslregister. But selxavg-sess output following ERROR. please tell me about -ipr. Keta ke...@localhost[retino1] % mkanalysis-sess.new -analysis retino -TR 2 -paradigm para.para -designtype blocked -funcstem fmcs -nconditions 4 -timewindow 34 -motioncor -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force Completed successfully ke...@localhost[retino1] % selxavg-sess -analysis retino -s sekiguchi001 -df sessdirfile -noomnibus INFO: WhitenFlag = 0 -- selxavg-sess logfile is /home/kenta/data/sessions/retino1/log/selxavg-sess-bold-retino-100708112251.log -- --- /home/kenta/data/sessions/retino1/sekiguchi001 2010ǯ 7·î 8Æü ÌÚÍËÆü 11:22:51 JST INFO (sekiguchi001): RunList = 001 002 003 004 /home/kenta/data/sessions/retino1/sekiguchi001/bold selxavg2 -TR 2 -parname para.para -o retino/h -i 001/fmcs -i 002/fmcs -i 003/fmcs -i 004/fmcs -cfg /home/kenta/data/sessions/retino1/retino/analysis.cfg -ipr here --- Parsing Config File: /home/kenta/data/sessions/retino1/retino/analysis.cfg -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: flag -ipr requires one argument ERROR (/home/kenta/data/sessions/retino1/sekiguchi001): selxavg failed -- 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.
Re: [Freesurfer] RAS to talairach transform
The auto is what is automatically created. The other will be the same as the auto unless you have made manual adjustments. doug On Wed, 23 Jun 2010, Corey Keller wrote: Hi freesurfers, I am trying to convert electrode coordinates from RAS to talairach space. I have 128 electrodes sitting directly on the pial surface which was created from recon-all. I see that the output of each reconstruction has two transforms, talairach.xfm and talairach.auto.xfm. There seems to be a difference between the two - could you explain the difference and which one I should be using? I cannot seem to find this online. Thanks. Best, Corey ___ 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.
Re: [Freesurfer] extracting anatomical ROI in native space
Try using nifti output, ie, --o label1.nii doug On Sat, 19 Jun 2010, Hwee Ling Lee wrote: Dear all, Apologies for my ignorance. I'm trying to extract the transverse gyrus, transverse sulcus, planum temporale and temporal pole from the inflated surface created by freesurfer. What I intend to do, is to convert these labels into spm analyze format files in native space, and apply the deformation parameters from DARTEL into standard space. Until now, I have created new labels for these regions, and using the mri_label2vol command line: mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz -fillthresh .5 -o label1.bshort However, it prompted me for a register.dat file and I do not have this. Using the advice from Dr. Doug Greve, I have tried to use the -identity: mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz -identity -fillthresh .5 -o label1.bshort When I did this, I get 256 files for label1. So I think I might have done something wrong here. Could someone please advise me how to do this? I'm lost here. Thank you very much in advance! Best regards, HweeLing -- 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.
Re: [Freesurfer] Registration of talairach and original space?
You need a registration between the space in which your label is defined and the fmri. The problem is that there are many definitions of what Talairach space means. Can you get your label into the fsaverage space? Ie, look at it with tkmedit using fsaverage as the subject? doug On Wed, 9 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: Hi all, We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this registration. However, we are stuck because as far as we know bbregister only works in one direction, fmri to anatomical. We have a region of interest defined as a sphere around a coordinate in Talairach space. What we need to do is to translate that region of interest into the space of an individual subject's fmri data. How can Freesurfer do this? Any suggestions would be greatly appreciated!! Best, Elise and Kathleen * Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 * Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickins...@mail.nih.gov ___ 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.
Re: [Freesurfer] Registration of talairach and original space?
You can use mri_label2vol. It takes the same registration matrix that you used to get to the surface. doug On Wed, 9 Jun 2010, Hansen, Kathleen (NIH/NIMH) [F] wrote: We have another question that is very related, so I will ask that at the same time: We have a region of interest defined on an individual subject's surface. How can Freesurfer translate that ROI into the coordinates of the original fmri data? It's clear to us how to get from fmri to the surface, but not the other way around. Thanks, Kathleen and Elise On 6/9/10 12:49 PM, Dickinson, Annelise (NIH/NIMH) [F] dickins...@mail.nih.gov wrote: Hi all, We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this registration. However, we are stuck because as far as we know bbregister only works in one direction, fmri to anatomical. We have a region of interest defined as a sphere around a coordinate in Talairach space. What we need to do is to translate that region of interest into the space of an individual subject's fmri data. How can Freesurfer do this? Any suggestions would be greatly appreciated!! Best, Elise and Kathleen * Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 * Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickins...@mail.nih.gov ___ 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.
Re: [Freesurfer] retinotopy: MGH vs UCSD
What do you mean by the UCSD freesurfer? A long time ago I re-wrote a stream that Anders was using, and it gave similar results. I've just re-written it again and it will be released with version 5. doug On Wed, 9 Jun 2010, francesca strappini wrote: Hi all, I would ask you about freesurfer and retinotopy. I'm going to begin the analysis of some retinotopic data. I would ask if you know if the retinotopic analysis made by MGH freesurfer is qualitatively comparable to, or it's good as, that made by USCD freesurfer (old freesurfer). Thank you kindly in advance. Francesca -- 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.
Re: [Freesurfer] advise on generating individual standard deviation map
I don't have anything explicitly that will compute a map of z-scores, but you could do a two group analysis with your subject as the only one in one group and then do a group analysis. Alternatively, you can transform you individual to the fsaverage space (mri_surf2surf), then compute the z using fscalc.fsl. You'd have to compute the group mean and stddev using mri_concat (--mean and --std), then use fscalc.fsl, something like fscalc.fsl --surf fsaverage lh lh.thickness.fsaverage.mgh -sub groupmean.mgh -div groupstd.mgh zscore.mgh doug On Wed, 9 Jun 2010, Michael Scheel wrote: Dear FS experts, could someone advise on how to create from an individual thickness file (?h.thickness) a standard deviation or z-score map of the thickness with respect to a control group. Thanks, Michael ___ 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.
Re: [Freesurfer] Question about getting fusiform stats
look in the subject/stats/?h.aparc.stats file doug On Tue, 8 Jun 2010, Weisinger, Brian (NIH/OD) [E] wrote: Hello I am trying to retrieve the fusiform volumes of a sample. I looked in the subject output files but didn't see any mention of the fusiform and when I searched the website so far all I could find involved fsl and functional data which mine is not. If it is possible to do could you please point me in the right direction to figure this out. Thank you for your help ___ 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.
Re: [Freesurfer] fsaverage aseg
It was created by mapping all the individual asegs of the input subjects to mni305, then detertermining the most frequently occuring label. It should only be used for display purposes. doug On Tue, 8 Jun 2010, Michael Waskom wrote: Hi all, How was the fsaverage aseg.mgz (in the 4.5 distribution, if it differs) created? I can't seem to find this information anywhere on the Freesurfer website. Thanks! Mike -- 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.
Re: [Freesurfer] Label files for the Cortical Ribbon
How did you create the .label files? mri_label2vol (your last step) does not produce them. Maybe with mri_cor2label run on the output of mri_label2vol? doug On Mon, 7 Jun 2010, Tina Jeon wrote: Hello freesurfers! After creating some labeling files from aparc.a2005s.annot, I noticed that my sulci and gyri volumes generated from the .label files (i.e., after running mri_annotation2label and mri_label2vol) were only representing the outer layer of the white surface. Is there any way to generate .label files that include the entire cortical ribbon? Thanks, any help would be appreciated. Tina Jeon ___ 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.
Re: [Freesurfer] brain regions
The corpus collosum is labeld in the auotmatic volume segmenation (aseg.mgz). The prefrontal cortex is subdivided into a number of regions in the auotmatic surface parcellation (lh.aparc.annot or rh.aparc.annot) doug On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote: Hello FS experts, A quick question, I'm looking for specific brain regions, but I can't seem to find them in the files once processing has been completed, I'm just wondering if FS does processing for areas including prefrontal cortex and corpus collosum? Thanks, Fatima -- 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.
Re: [Freesurfer] brain regions
How did you look at it (what was your command-line)? You should load it as a segmentation in tkmedit. What version of FS are you using? Older versions did not have CC defined, but it would have to be pretty old. doug On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote: Thank you for that Doug, I just had a look in the aseg.mgz file, but unless I'm blind, I can't seem to see it...could you tell me what it's labelled as please? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: 08 June 2010 10:53 To: Ahmed, F, Me fah...@sun.ac.za Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] brain regions The corpus collosum is labeld in the auotmatic volume segmenation (aseg.mgz). The prefrontal cortex is subdivided into a number of regions in the auotmatic surface parcellation (lh.aparc.annot or rh.aparc.annot) doug On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote: Hello FS experts, A quick question, I'm looking for specific brain regions, but I can't seem to find them in the files once processing has been completed, I'm just wondering if FS does processing for areas including prefrontal cortex and corpus collosum? Thanks, Fatima -- 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.
Re: [Freesurfer] brain regions
cmd line? On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote: I'm running version 4.3.1 -Original Message- From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 08 June 2010 11:01 To: Ahmed, F, Me fah...@sun.ac.za Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] brain regions How did you look at it (what was your command-line)? You should load it as a segmentation in tkmedit. What version of FS are you using? Older versions did not have CC defined, but it would have to be pretty old. doug On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote: Thank you for that Doug, I just had a look in the aseg.mgz file, but unless I'm blind, I can't seem to see it...could you tell me what it's labelled as please? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: 08 June 2010 10:53 To: Ahmed, F, Me fah...@sun.ac.za Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] brain regions The corpus collosum is labeld in the auotmatic volume segmenation (aseg.mgz). The prefrontal cortex is subdivided into a number of regions in the auotmatic surface parcellation (lh.aparc.annot or rh.aparc.annot) doug On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote: Hello FS experts, A quick question, I'm looking for specific brain regions, but I can't seem to find them in the files once processing has been completed, I'm just wondering if FS does processing for areas including prefrontal cortex and corpus collosum? Thanks, Fatima -- 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.
Re: [Freesurfer] Different slices number for control group
Is there total overlap between group and number of slices? Sounds not very good. I don't have a feel for what the MR on this and whether changing the number of slices would create systematic differences in SNR or contrast. Maybe Andre would like to weih in. doug On Tue, 8 Jun 2010, pik...@tin.it wrote: Hi freesurfers! We want to estimate the differences of cortical thickness between two groups. The images of the control group are taken from a different acquisition session. the only differences would be the number of slices (200 vs 128). It is still possible to compare the two groups? Images were acquired on the sagittal plane on a 3T Phillips scanner, SENSE coil, voxels 1x1x1, matrix 256x256, T1 MPR. Thanks so much for your time Laura -- 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.
Re: [Freesurfer] Group analysis---qdec questions
This tests whether the quantity = (controls-patients)-(males-females) is different than 0. Note the order of the inputs may be different (making the final sign different). The order depends on the order that you specfied in the levels file you passed to qdec. doug On Thu, 3 Jun 2010, liyari5018 wrote: Hi FS experts, when i use qdec to analysis my data: 45 norms and 45 patients, what does this means: Is there a diagnosis--gender interaction in the mean thickness? (PS: I got a corrected results in this item, but i don't know how to report it) Thanks for you reply! LJ -- 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.
Re: [Freesurfer] Exporting volumes from freesurfer subject folder
Do you just mean the volume in mm^3 of the caudate, etc? These numbers are in the aseg.stats files in each subject. You can create a spread sheet using asegstats2table (including just specifying the segs you want). doug On Tue, 1 Jun 2010, Weisinger, Brian (NIH/OD) [E] wrote: Is there any fast way to take out a specific volume from a group of subjects so as to where I could pull out the caudate and hippocampus volumes for each person to analyze statistically between groups? Thank you, Brian Weisinger ___ 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.
Re: [Freesurfer] converting label files
Hey Libby, try using mri_label2vol. It will ask for a template volume and registration. If you are mapping it to each functional run use example_func as the template and the register.dat created by reg-feat2anat as the registration. If you are mapping it to a gfeat of the combined runs of each subject, then use the standard space (eg, avg152T1) as the template and the anat2std.register.dat from one of the functional runs (should not matter which one). doug On Tue, 1 Jun 2010, Elizabeth O'Hare wrote: hello, i'm trying to take a label that i drew on each subject's surface into volumetric space so that i can extract fMRI parameters within this anatomically defined ROI. i am able to see the label within each subject's orig.mgz volume with tkmedit. however, i'm not sure how to convert this label file into a format that FSL will recognize, given that neither mri_surf2vol, not mri_convert recognize labels as valid input files. any advice is most appreciated! thanks, libby Elizabeth O'Hare, Ph.D. Postdoctoral Fellow Helen Wills Neuroscience Institute University of California, Berkeley 132 Barker Hall, MC #3190 Berkeley, CA 94720 510-642-5554 edoh...@berkeley.edu ___ 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.
Re: [Freesurfer] Reporting coordinates from Group analysis
You can do a cluster-based correction for multiple comparisons to compute the p-value of the cluster. Is that what you mean? doug On Thu, 20 May 2010, Rajagopalan, Venkateswaran wrote: Thanks Doug, but for instance in my result the inferiorparietal region is significantly different in some areas but not in the entire region, so in this case it will difficult because i have to move the cursor to regions where it is significant and other vertex where it is not significant this means that i will have two or more coordinates to report a single region, i am wondering is there a way to identify in this map which cluster is significant and report its center coordinate. Thanks in advance venkat From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thu 5/20/2010 1:33 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Reporting coordinates from Group analysis If you click on a point, it should tell you in the control window what the talairach coordinates are doug Rajagopalan, Venkateswaran wrote: Dear All, I checked the archives but couldn't get a complete answer. I performed group analysis of cortical thickness using mri_glmfit. I am wondering how to report the coordinates of regions where cortical thickness is significantly different, i used FDR for multiple comparisons in tksurfer. So how to get these coordinates after FDR where is this file stored. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org http://www.clevelandclinic.org/ for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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 === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -- 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.
Re: [Freesurfer] Creating annotation file for lobar regions...
Try running mri_annotation2label with --lobes lh.lobes.annot doug On Thu, 20 May 2010, Rudolph Pienaar wrote: Hi all -- Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab. Apologies if this question has come up before... a quick google didn't reveal anything. Many thanks -=R -- 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.
Re: [Freesurfer] convert/reconstructing with mrdc
Just run mri_convert dicom-from-series.dcm 001.mgz where dicom-from-series.dcm is a single file from the T1 series (it will find the rest). doug On Sun, 29 Nov 2009, Jesse Bledsoe wrote: I have all of the dicoms - what is the best way to run mri_convert on all of the dicoms in the t1 directory? Thank you, Jesse On Sun, Nov 29, 2009 at 5:29 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Yes, though you may need to be careful about the orientation. I'm not sure if BRIKs have orientation info, but I'm sure that mri_convert does not read it. If you can go back to the dicoms, that is best. doug Jesse Bledsoe wrote: I have T1volume+org.BRIK - should I use those with mri_convert? Thanks again, Jesse On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] sa...@mail.nih.gov mailto:sa...@mail.nih.gov wrote: mri_convert usually work with BRIK files. Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format which FreeSurfer can read fine. cheers, ziad On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote: These are not the standard .BRIK files? Ziad (ccd) will know. Bruce On Tue, 24 Nov 2009, Jesse Bledsoe wrote: Hello, So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC). There are 120 MRDC files in the T1 directory. I believe I need to run mri_convert on these MRDC files but am unsure of what the correct command would be? Thanks in advance, Jesse -- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. ___ 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
Re: [Freesurfer] FDR correction (fwd)
Here's Tom Nichols explanation. He points out that you use the maximum i, not the minimum, so you don't have to get past i=1. Thanks Tom! -- Forwarded message -- Date: Fri, 16 Oct 2009 23:11:09 +0100 From: Thomas Nichols t.e.nich...@warwick.ac.uk To: Doug Greve gr...@nmr.mgh.harvard.edu Cc: Donna Dierker do...@brainvis.wustl.edu Subject: Re: [Freesurfer] FDR correction (fwd) Dear Doug, Great discussion! But I think it misses the point. Can you forward the following to the list? The Benjamini-Hochberg (BH) FDR procedure uses the inequality P(i) = i / V * q for the ordered P-values P(1)=P(2)=...=P(V) and desired level-q FDR control, which suggests that one will never get significance unless P(1)q/V, just like Bonferroni. HOWEVER, the key element of BH-FDR is that you get to search over i and find the *largest* P-value that satisfies the inequality and use that P-value as a threshold. Hence when considering changing resolutions (i.e. increasing V, but increasing resolution/smoothness and roughly keeping the information content of the images the same) the magic of BH-FDR is that if the 5-th %ile of uncorrected P-values is FDR-significant at one resolution, i.e. i' = 0.05*V satisfies P( i' / V ) = i' / V * q then one would expect that the 5-th %ile of P-values after up-sampling would have a similar value, and thus would also satisfy the inequality even though V has changed. That is the motivation that FDR is resilient to changes in resolution. However, I should note that in my own experience, leaving V fixed but changing smoothness, often changes the distribution of P-values dramatically, and thus changes the FDR result. But that should be a different beast that up-interpolation. Hope this helps! -Tom On Fri, Oct 16, 2009 at 5:43 PM, Doug Greve gr...@nmr.mgh.harvard.eduwrote: Tom, here's an FDR question for you. It appears that the FDR correction is dependent on the number of voxels (need p fdr/N just to get past i=1). Meaning that as N grows, the min p-value must also shrink to get past i=1. Any way to get around this? thanks doug -- Forwarded message -- Date: Fri, 16 Oct 2009 11:30:59 -0500 From: Donna Dierker do...@brainvis.wustl.edu To: Michael Harms mha...@conte.wustl.edu Cc: freesurfer@nmr.mgh.harvard.edu, Yulia WORBE yulia.wo...@upmc.fr Subject: Re: [Freesurfer] FDR correction Regardless: FDR's sensitivity appears resolution-dependent to me. On 10/16/2009 10:39 AM, Michael Harms wrote: Interesting post Donna, but my understanding of FDR is that it sets the p-value threshold based on the LARGEST p-value that satisfies the FDR relationship. That is, steps 3 and 4 in Genovese et al. (2002) are: 3) Let r be the largest i for which p = i/V*q (assuming c=1) 4) Threshold the image at the p-value p(r). So, it isn't the case that you require the most significant p-value to satisfy p = 0.05/V just to get past i=1 as you put it in your post. Rather, you pick the largest p-value that satisfies the relationship, meaning that lower (more-significant) p-values may not have necessarily satisfied p = i/V*q for their particular position in the sorted list of p-values. cheers, Mike H. On Fri, 2009-10-16 at 10:13 -0500, Donna Dierker wrote: I never heard anything on my post here, but it might just be high surface resolution: http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html On 10/16/2009 09:58 AM, Michael Harms wrote: Your FDR analysis sounds correct. You probably have a rather small number of marginally significant vertices, which is why none survive FDR. You could try increasing the q value from say 0.05 to 0.1, in which case 10% of the surviving vertices would be expected to be false positives. cheers, Mike H. On Fri, 2009-10-16 at 12:03 +0200, Yulia WORBE wrote: Dear Freesurfer team, We are currently doing a cortical thickness studies between a group of psychiatric patients (n=60) and controls (n=30). We tested several smoothing levels (15mm, 20mm, 25mm) When setting an uncorrected threshold (such as p0.005), we obtained several regions of decreased thickness, which are consistent with the pathology. However, when trying to correct for multiple comparisons using FDR (Set Using FDR button in qdec), the computed threshold is very high (e.g. 4.3 for 20mm smoothing) and, obviously, no significant regions are left. Did we do anything wrong in the analysis ? Thank you very much for your help, Yulia ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
Re: [Freesurfer] FDR correction
Good point (meaning that I don't know the answer). I'll see if I can find out. doug On Fri, 16 Oct 2009, Donna Dierker wrote: Regardless: FDR's sensitivity appears resolution-dependent to me. On 10/16/2009 10:39 AM, Michael Harms wrote: Interesting post Donna, but my understanding of FDR is that it sets the p-value threshold based on the LARGEST p-value that satisfies the FDR relationship. That is, steps 3 and 4 in Genovese et al. (2002) are: 3) Let r be the largest i for which p = i/V*q (assuming c=1) 4) Threshold the image at the p-value p(r). So, it isn't the case that you require the most significant p-value to satisfy p = 0.05/V just to get past i=1 as you put it in your post. Rather, you pick the largest p-value that satisfies the relationship, meaning that lower (more-significant) p-values may not have necessarily satisfied p = i/V*q for their particular position in the sorted list of p-values. cheers, Mike H. On Fri, 2009-10-16 at 10:13 -0500, Donna Dierker wrote: I never heard anything on my post here, but it might just be high surface resolution: http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html On 10/16/2009 09:58 AM, Michael Harms wrote: Your FDR analysis sounds correct. You probably have a rather small number of marginally significant vertices, which is why none survive FDR. You could try increasing the q value from say 0.05 to 0.1, in which case 10% of the surviving vertices would be expected to be false positives. cheers, Mike H. On Fri, 2009-10-16 at 12:03 +0200, Yulia WORBE wrote: Dear Freesurfer team, We are currently doing a cortical thickness studies between a group of psychiatric patients (n=60) and controls (n=30). We tested several smoothing levels (15mm, 20mm, 25mm) When setting an uncorrected threshold (such as p0.005), we obtained several regions of decreased thickness, which are consistent with the pathology. However, when trying to correct for multiple comparisons using FDR (Set Using FDR button in qdec), the computed threshold is very high (e.g. 4.3 for 20mm smoothing) and, obviously, no significant regions are left. Did we do anything wrong in the analysis ? Thank you very much for your help, Yulia ___ 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 ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] generate mask
you might try mris_volmask. It expects two surfaces (usually white and pial), so you might have to generate a 2nd surface with mri_surf2surf with --surf-xyz, --targ-xyz, and --projabs XXX (XXX =? 1mm). doug On Fri, 16 Oct 2009, Daniel G. Wakeman wrote: Hi, I need to generate a mask from a 'BEM' surface (10242 vertices). I have tried doing this utililzing mri_surf2vol; however, this doesn't produce a good mask as only the vertices are utilized creating a speckled volume. Is there any way to create a proper mask utilizing all of the surfaces of a surface? Thanks Dan ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess
isxconcat-sess creates the files that you pass to mri_glmfit (ie, multi-frame volumes and/or surfaces where each frame is a subject). Something like: AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii You can then use this as input to mri_glmfit passing it with the --y option. You can get more help from the FS FAST tutorial. Go to the wiki, type isxconcat-sess in the Search field, then hit the Text button. doug On Wed, 14 Oct 2009, Maximilien Chaumon wrote: Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find error in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess
What does your matlab script do? Your glmfit cmd looks fine. On Thu, 15 Oct 2009, Maximilien Chaumon wrote: Thanks Doug, I was just a bit confused because I thought the help for mri_glmfit mentioned an osgm directory that wasn't there. I was given a matlab script that does that now. I'm using a command like this: mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask ../tal.mask.nii Thanks Mx 2009/10/15 Doug Greve gr...@nmr.mgh.harvard.edu isxconcat-sess creates the files that you pass to mri_glmfit (ie, multi-frame volumes and/or surfaces where each frame is a subject). Something like: AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii You can then use this as input to mri_glmfit passing it with the --y option. You can get more help from the FS FAST tutorial. Go to the wiki, type isxconcat-sess in the Search field, then hit the Text button. doug On Wed, 14 Oct 2009, Maximilien Chaumon wrote: Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find error in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] optseq2 help: DPSD and jitter
On Sat, 26 Sep 2009, Asaf Kaftory wrote: Hello list, I'm new to optseq, and would like your help with the following issues: 1. What exactly does DPSD mean? and why does the TR has to be an integer of it? Delta Post-Stimulus Delay. The time between samples in the FIR. Usually, it is just the TR. If you want to do sub-TR estimation, you can make it less than the TR. It has to be an integer divisor of the TR because it forms the basic tick of the clock. 2. My experiment design uses jitter - both ITI (i.e., between trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event? That is right. Sorry, don't know of anything that will give you with-in event jitter. 3. Is it true that jitter in optseq is made by inserting NULLS, and that the DPSD determines the steps of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right? Yes. doug hope to hear from you soon, Asaf. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to extract segmented hippocampus
You can just use tksurfer, something like tksurfer subject lh hippocampus assuming you called it lh.hippocampus There will be a lot of warnings/errors printed to the terminal. These just have to do with the fact that the number of vertices will be different than the cortical surfaces. You can also load them into tkmedit: tkmedit subject orig.mgz lh.hippocampus -aseg to check how good the surface is. doug On Thu, 17 Sep 2009, Gonzalo Rojas Costa wrote: Dear Douglas: And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz with the mri_binarize command ?... Sincerely, Gonzalo Rojas Costa mri_binarize with --match 17 or --match 53 will do it doug Guang Zeng wrote: Hi, there, I'd like to extract the left and right hippocampus from aseg.mgz, so basically what I want is a volume where left hippocampus have value (or label) 17 and right hippocampus have value (or label) 53, all the other place are zero. How can I do it? Using mri_threshold or mri_label2vol? Thanks a lot! Guang Hotmail: Free, trusted and rich email service. Get it now. http://clk.atdmt.com/GBL/go/171222984/direct/01/ ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness map
Yes, this is what our group analysis tools do. You can find tutorials on the wiki. You'll probably start with mris_preproc. doug On Thu, 20 Aug 2009, Feng-Xian Yan wrote: Hi, Thank you for your responses before. I have another problem want to solve. I check the number of vertex for all subjects, but I found that the number of vertex for each subjects and each hemispheres is different. Because I want to compare cortical thickness using vertex-by-vertex, I would to obtain the same vertex number. Therefore, have something to do to obtain the same vertex number, i.e. template the cortical thickness at each vertex for each subject on the fsaverage surface, or other methods? How can I do? Would you get me a hand? Thank you in advance! Feng-Xian 2009/8/18 Feng-Xian Yan mimigi...@gmail.com Thank s for your response. So, the coordinates are MNI coordinates, not Talairach coordinates. Thank you in advance. Feng-Xian 2009/8/18 Douglas N Greve gr...@nmr.mgh.harvard.edu The values in the asc file are in MNI305 space. You can see this in tksurfer with View-Configure-Information and select the mni305 button. Feng-Xian Yan wrote: Thank you for your response. So, you mean that I have to do mris_convert two times. One for lh.white.tal.asc, another for lh.thickness.asc. And the Tal coordinates in lh.white.tal.asc file corresponds to the cortical thickness value in lh.thickness.asc file. But, the Tal coordinates in lh.white.tal.asc is difference from the result in the tksurfer tool box. That is to say, when I open this subject by tksurfer, I look at the coordinate of the vertex Tal in the tksurfer tool box, and the coordinate is difference from the coordinates that obtain from the command ?mris_convert ?c lh.thickness lh.white lh.thickness.asc?. What do have some problems? Thank you in advance! Feng-Xian 2009/8/18 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.edu You have convert the thickness file (lh.thickness) to ascii like you did with the surface (with mris_convert). You will then have two files, and the second file will have the thickness values. doug Feng-Xian Yan wrote: Hi, Sorry, I don't know what you mean. I know each lines is a vertex and represent a Tal coordinate, but each lines only contain xyz, but not contain cortical thickness value of these coordinates. That is to say, the following is Tal x Tal y Tal z -13.424789 -125.068245 12.671550 0 What?s wrong do I think? Thank you in advance. Feng-Xian 2009/8/18 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Just convert the lh.thickness to ascii as well. Each line of the xyz coords corresponds to a line in the thickness ascii (each line is a vertex). doug Feng-Xian Yan wrote: Hi, I try it again with you recommend me, but the produced asc file (lh.white.tal.asc) only contain x, y, z coordinates. (The following shows that.) #!ascii version of lh.white.tal 155006 310008 -13.424789 -125.068245 12.671550 0 -13.939213 -125.063232 12.714314 0 -14.861158 -125.268639 12.404987 0 But, I want to have cortical thickness value with Tal coordinates. This file doesn?t satisfy our demand. Our demand should contain two points. 1) Each vertex across the mantle was represented with an estimated value of cortical thickness and these estimated values of cortical thickness should have their coordinates. 2) We want to analysis the cortical thickness difference of three groups, so we want to the cortical thickness value of each vertex across each subjects should be matched. That is to say, the cortical thickness should superimposed on a template surface like fsaverage. Therefore, how do we do to obtain the asc file matching our demands? Thank you in advance. Feng-Xian 2009/8/14 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Try these commands: mri_surf2surf --s subject --hemi lh --sval-tal-xyz white --tval-xyz --tval lh.white.tal mris_convert lh.white.tal
Re: [Freesurfer] from dicom to mgz
we often have problems reading philips dicoms, not sure why. doug On Fri, 17 Jul 2009, Jose Luis Cantero Lorente wrote: Hi, I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line? Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcan...@upo.es http://www.upo.es/neuroaging/en/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [Fwd: fsaverage to average7]
This cmd is not going to work. I don't think we have a way to convert between the two. Sorry, doug On Wed, 17 Jun 2009, Yigal Agam wrote: Hi all, Is there a way to convert results that I have on fsaverage to average7? I need to do that to be compatible with some average7 results that go into the same paper. When I use mri_surf2surf, activation is displaced. Any advice would be appreciated. This is what I've done: mri_surf2surf --srcsubject fsaverage --trgsubject average7 --sval [fsaverage file]--hemi lh --tval [average7 file] Thanks, Yigal ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] label2vol
You can mri_convert the output specifying the output type as -odt short. Sorry, don't have any easy way to change the slicing. doug On Wed, 10 Jun 2009, xfore...@ucla.edu wrote: Dear Freesurfer experts, I'm trying to convert the annotation file into (binary Analyze file), I tried the command mri_label2vol and it seems to worked fine, but I find out that the output file is in 32bit/vox resolution, and the program I want to use to open the file doesn't support that and crashes everytime I try to open it. I was wondering if there's anyway to make the output file 16 bit/vox instead? also the output file is in COR, is there anyway I can make it Axial? Best, Andy ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Partial Volume Correction and wmparc.stats
yes, it is On Thu, 11 Jun 2009, Nasim Maleki wrote: Dear Freesurfer developers, I'm wondering whether the wmparc.stats is computed with a partial volume correction at the boundaries of the structures. Thank you, Nasim ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Questions on ROI Comparisons
(1) probably using mri_segstats with --annot fsaverage lh aparc and specifying the --y input to mri_glmfit as the --i invol and specify a --avgwf output to get all the subjects. (2) Yes, you would expected it. I'm not sure what it means if you don't see it. Maybe a bug somewhere. (3) You can smooth it with mri_surf2surf or mris_fwhm and specify a label to smooth in. This will be similar to the full-brain smoothing except at the edges. doug On Fri, 12 Jun 2009, Bruce Fischl wrote: I'll leave 1-3 for Doug and Nick. As for 4, this is a QA step to make sure nothing failed in the spherical registration, or the segmentation/surface reconstruction in that region. cheers Bruce On Thu, 11 Jun 2009 nmal...@mclean.harvard.edu wrote: Dear all, 1-Is there a way to use mris_anatomical_stats to calculate mean ROI values on the re-sampled and smoothed individual subject data that is produced in the pre-processing step, rather than mapping the ROI back to each subjectsrsquo; space? If so what is the command? 2-If you define a ROI where there is statistically significant difference (between 2 groups) at the group level on your average subject and then map the ROI back to each subjectrsquo;s space and measure the mean value of say thickness in that ROI, should you expect to find the same significant difference between the groups that you are comparing? What does it mean if you donrsquo;t for some ROIs? 3- Is there a way to smooth the vertices in a ROI similar to what is done at the preprocessing level? 4- There is a comment on wiki (qdec, ROI analysis) that indicates the usefulness of mapping the ROI back to each ubject's space to 'check the integirty of your reults'. Could you please elaborate more on this? Thank you, Nasim -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Co-vary
In this case you would have six regressors: 1. control-offset 2. hiv-offset 3. control-age 4. hiv-age 5. control-ed 6. hiv-ed If you want to test group thickness regressing out the effect of age and ed, then you would just set the contrast to: 1 -1 0 0 0 0 0 Note that this will test it at age=0 and ed=0, which you may or may not want to do. Ideally, you would test them at some age/ed in the range of your sample. A lot of people simply demean each covariate, but this can bias the results depending upon who you add or remove. Better to choose an age/ed level independent of your sample. doug On Sat, 13 Jun 2009, Jeff Sadino wrote: Hello Freesurfers, My apologies for this very basic question more about statistics than freesurfer, but I have not found an answer anywhere on the wikis, or the web (maybe it is too basic :-) ) I am interested in age-related effects of hiv and I wanted to covary for age and education in mri_glmfit. For example, if my fsgd file is: class control class hiv variables age ed input subj1 control 40 13 input subj2 hiv 35 12 ... ... and I use dods, is my contrast matrix the place where I would tell it to covary? Something like: 0 0-1 1 1 11 1 (y-int) (age slope) (covary for age) (covary for ed) As always, thank you for your help, Jeff _ Hotmail® has ever-growing storage! Don?t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: 'Max' in sig.cluster.summary
The sig.mgh is the input that creates the sig.cluster.mgh (and the summary table). doug On Thu, 4 Jun 2009, Judith Segall wrote: Doug. Again, I am only asking about the sig.cluster.summary. This was a thickness study, where monte-carlo simulations where used to correct for multiple comparisons. Why would the *max in column 2 of the sig.cluster.summary* be derived from the sig.mgh and not the sig.cluster.mgh? Since, this report is generated at the same time as the sig.cluster.mgh. (ClusterNo *Max* VtxMax Size(mm^2) TalX TalY TalZCWP CWPLowCWPHiNVtxs Annot) I only used the scatter plot as example as to why I has a question about how to interpret the sig.cluster.summary. - Judith On Thu, Jun 4, 2009 at 11:51 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you load the FSGD and look at the scatter plot, the y-axis will be the thickness value (assuming you're doing a thickness study:). doug Judith Segall wrote: Doug and freesufer list. When I load the sig map in tksurfer i know that the CWP is displayed as the -log(10)p; however, I am not asking about visualization or the CWP. The newest version of the wiki does a great job in explaining the p values. I am only asking about the sig.cluster.summary report. It makes since that The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold. But then what units is it in? When I was not sure what the second column was I turned to visualization. After, loading both the sig.cluster.mgh and the group descriptor file in tksurfer and then selecting a vertex in the region with the most significance, which is based off of the CWP, it displays a scatter plot. The scatter plot does not have a label for the y-axis; however, the highest point on the y-axis is similar to the max, in column 2, of the sig.cluster.summary report. On the older wiki, there was a paragraph describing how the y was thickness. But, the sig.cluster.summary report does not have any labels for the second column. But, since the value was similar to the y-axis I began to interpret it as thickness, but wanted to clarify with the freesurfer team. - Judith On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is the maximum vertex-wise -log10(p) found in the cluster. Why do you think otherwise? You should be able to load the sig map into tksurfer and go to that vertex to find out. doug Judith Segall wrote: Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'. Doug: I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLowCWPHiNVtxs Annot 1 -4.310 40526376.78-12.0 -66.1 5.40.01920 0.01750 0.02100 706 lingual In Pratap's email his answer to my question of what is the max in the CWP is, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh. So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness? Thanks, Judith S. On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value). doug Pratap Kunwar wrote: Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the Max in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the
Re: [Freesurfer] export skull stripped images
just mri_convert brainmask.mgz brainmask.nii doug On Thu, 4 Jun 2009, Jose Luis Cantero Lorente wrote: Dear Freesurfers, is it feasible to save to nii the MR images after stripping the skull in Freesurfer? If so, please let me know how to do it. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcan...@upo.es http://www.upo.es/neuroaging/es/ ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_glmfit-sim bug?
Is this for a permutation test? Sorry, this is my fault. I've put a new version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim that should fix the problem. Can you test it out? thanks doug On Mon, 1 Jun 2009, Georg Homola wrote: Hi All (and especially Doug, again)! As one of the final steps I run mri_glmfit-sim for clusterwise correction (of my random effects analysis btw.). It always worked well and I also didn't change the command line recently, but since I updated Freesurfer to the latest version (4.3.1) it quits with: ERROR: you must supply --fwhm with --sim, even if it is 0 There is no flag like --fwhm for mri_glmfit-sim and when I try --fwhm-override it won't change anything. Am I missing something? Thanks Georg ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] tksurfer Load Group Descriptor File error
Are you loading the one created by mri_glmfit (in the output directory)? doug On Mon, 6 Apr 2009, Jeff Sadino wrote: Thank you for the advice Sid. I added those lines, and now my errors disappear, but I still get a blank screen where there should be a scatterplot. Is this a graphics issue with my hardware, or do I need to do something differently? This is my fsgd file: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class nc circle red Variables Age Input 060017_HG01 nc .5 Input 060023_F01 nc .8 Input 060024_HG01 nc .1 Input 060025_HG01 nc .5 ... ... The screen that pops up has thickness on the y-axis, but a range of only 0-1 and Age on x-axis with range 0-1. My ages were real (50.8, 40.8, 50.1, etc.), but I changed them to between 0 and 1 to see if that helped, but no good. Thanks in advance for your help, Jeff Sadino Date: Thu, 12 Mar 2009 18:52:45 -0700 Subject: Re: [Freesurfer] tksurfer Load Group Descriptor File error From: sid...@gmail.com To: jsad...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Class ctrl should be followed by marker and color specification (Class ctrl circle red, for e.g). ditto for cd . sid. On Thu, Mar 12, 2009 at 6:37 PM, Jeff Sadino jsad...@hotmail.com wrote: Hello, Can someone help me get scatterplots of my data? I am using freesurfer 3.0.5. I have ran these commands: mris_preproc --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness --out lh.try1.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval lh.try1.fw.mgh mri_glmfit --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf fsaverage lh --glmdir lh.try1.dir tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay lh.try1.dir/try1.mtx/sig.mgh Then selected a vertex, then File-Load Group Descriptor File and selected try1.fsgd, but I get this error: WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. This is try1.fsgd: GroupDescriptorFile 1 Title try1 MeasurementName thickness Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 I also tried with lh.try1.dir/y.fsgd, but get a similar error: INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: gdfRead: reshaping WARNING: Marker for class ctrl was invalid. WARNING: Color for class ctrl was invalid. WARNING: Marker for class cd was invalid. WARNING: Color for class cd was invalid. y.fsgd looks like this: GroupDescriptorFile 1 Title try1 MeasurementName external Tessellation surface PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh DesignMatFile fsgd.X.mat dods ResidualFWHM 22.331472 Class ctrl Class cd Variables Age Input 040004_P02 ctrl 55.18 Input 050046_S02 ctrl 37.45 ... ... Input 070073_S01 cd 20.54 Input 070114_OGM01 cd 46.03 Creator mri_glmfit SUBJECTS_DIR /share/apps/freesurfer/subjects SynthSeed1237057379 In both cases, a graph pops up, but it is blank. Thank you in advance for your suggestions, Jeff Sadino Hotmail® is up to 70% faster. Now good news travels really fast. Find out more. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Windows Live?: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_allup_1a_explore_042009 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Measuring cortical thickness with high resolution data
Falk, it looks like that file was somehow converted to DOS. try: dos2unix recon-all chmod a+x recon-all then re-run doug On Mon, 6 Apr 2009, Falk Lüsebrink wrote: Hi Nick, I tried using your modified recon-all today but as soon as I try to process any data I receive following error message: 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...]. Also it doesn't matter at all which flags I add to recon-all or if I don't use any flags at all, the error is the same. The unmodified recon-all performs well. Regards, Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, April 02, 2009 3:28 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data Falk, There are no plans in the near future, but in the long term we'd like to remove the dependence on conforming the data. It just occurred to me that you could have the best of both worlds: first run your data through the normal stream (conforming) up through autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same resolution as that created using the -hires stream, and copy it over. At least that would eliminate having to edit the original hires brainmask, which would save hours of work. If i get few minutes i will try this. You can copy that recon-all over top your existing v4.x freesurfer installation (attached again for the list). Nick On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote: Hi Nick, Thank you very much. I'll have to look into that and try to process some other volumes which might work a bit better, with less manual intervention. Are there any plans to improve Freesurfer in the (near) future so that hires data can be processed within the currently available stream? Regards, Falk -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Wednesday, April 01, 2009 7:53 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data Falk, Attached is a modified recon-all script where I've added a -hires switch to force the stream to not conform the data to 1mm^3, and to not use the atlases. Note that you should add the -clean flag to delete any work that had been done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz). However, in working with the .8mm data that you sent me, working with hires data will require quite a bit of manual intervention due to the fact that the atlases normally used cannot be used. The first problem occurs in skull-stripping, where quite a bit of dura and skull remains, and seems to have intensity values close to gray matter. This would have to be manually erased on each of the slices. If it is not erased (I did not do this because of the amount of time required), then the wm.mgz file, which is what is tessellated to create the initial surface, will be very wrong (it tessellates the garbage surrounding the gray matter). See also Bruce's prior posting on the problems of working with hires data in freesurfer. Nick On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote: Hi Freesurfers, Iÿÿm trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an issue anymore. My problem is that Freesurfer usually conforms the voxel size to 1mm which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for the recon-all process to avoid the conformation and to skip the subcortical segmentation, but another problem arises while using these flags. The error I receive is occurring after the WM Segmentation and states as follows: # #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 cp wm.mgz wm.seg.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.9 +- 5.8 [80.0 -- 125.0] GM (69.0) : 66.3 +- 11.6 [30.0 -- 96.0] setting bottom of white matter range to 77.9 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... thickening thin strands 20 segments, 4813 filled 10270 bright non-wm voxels segmented. 5589 diagonally connected voxels added...
Re: [Freesurfer] Masking brainmask based on surfaces
I thought it was 4.0.3, so maybe that's not it. Can you look at the ribbon.mgz file? You can load it as a segmentation, ie, tkmedit subject orig.mgz -seg ribbon.mgz aparc+aseg is suppossed to inherit the cortex from ribbon.mgz doug On Mon, 6 Apr 2009, Martin Kavec wrote: Hi Dough, this data were analyzed using 4.0.4. So indeed it not the latest, which I am running normally. From which version has this been fixed, so I can check, before re-runing. From which point should I rerun the analysis. Thanks, Martin On Monday 06 April 2009 18:42:36 Douglas N Greve wrote: This looks like a problem we had with an older version. What version of freesurfer are you running? Martin Kavec wrote: Hi, I am trying to mask a non-brain tissue left by watershed based on the cortical surfaces. I found that all what I need to be left is in aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz and used FSL to binarize aparc+aseg and mask the brainmask. I found that at many places the results is too conservative and too much of the GM is missing, see the attached images, and particularly the temporal lobes. Is there a better approach to what I am trying to do and what could be the explanation to the results I get. Thanks, Martin -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Masking brainmask based on surfaces
but you are using aparc+aseg to generate the mask, so if aparc+aseg is perfect, the mask should be as well. Do the mask and aparc+aseg match? On Mon, 6 Apr 2009, Martin Kavec wrote: Doug, ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces ?h.white. Thanks, Martin On Monday 06 April 2009 22:17:18 Doug Greve wrote: I thought it was 4.0.3, so maybe that's not it. Can you look at the ribbon.mgz file? You can load it as a segmentation, ie, tkmedit subject orig.mgz -seg ribbon.mgz aparc+aseg is suppossed to inherit the cortex from ribbon.mgz doug On Mon, 6 Apr 2009, Martin Kavec wrote: Hi Dough, this data were analyzed using 4.0.4. So indeed it not the latest, which I am running normally. From which version has this been fixed, so I can check, before re-runing. From which point should I rerun the analysis. Thanks, Martin On Monday 06 April 2009 18:42:36 Douglas N Greve wrote: This looks like a problem we had with an older version. What version of freesurfer are you running? Martin Kavec wrote: Hi, I am trying to mask a non-brain tissue left by watershed based on the cortical surfaces. I found that all what I need to be left is in aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz and used FSL to binarize aparc+aseg and mask the brainmask. I found that at many places the results is too conservative and too much of the GM is missing, see the attached images, and particularly the temporal lobes. Is there a better approach to what I am trying to do and what could be the explanation to the results I get. Thanks, Martin -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] determining sizes of clusters on surface data
Sorry, I have not used this toolbox much. Maybe Don can chime in.
doug
On Fri, 3 Apr 2009, Zhong Jidan wrote:
Hi,
I was trying to figure out if there is any way to determine the exact
size at which clusters becomes significant given a specified
significance on the surface data.
Then i found there is a subject talking about this:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.html
In that talk,Don Hagler mentioned Keith Worsley's Random Field
Theory method
(http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m)
can be used to directly (in seconds) estimate the cluster size
thresholds given:
..total surface area
..number of vertices
..fwhm smoothness.
function [cluster_threshold,peak_threshold] =
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval);
* % alpha: corrected p-value
** % {default = 0.05}
** % pval: uncorrected p-value
** % {default = 0.001}
*I tried this function, and it does give me a cluster size with mm^2,
say 100 mm^2. But I don't know whether this is the right thing to do.
As I'm doing some statistical analysis using GLM, so I also try the
method from Keith Worsley's statistical toolbox, then I can get the
cluster's No. of vertices and the corrected p-value(alpha=0.05) for
the cluster.
Here is one example:
clusid nverts resels P
---
1 2205 18.2781 2.1299e-06
2 208 1.421050.013359
3 127 1.155330.026747
458 1.04430.036658
5 5 0.519762 0.20884
6 105 0.464429 0.2571
The thing I don't understand is , if we are looking for a cluster size
threshold, then we can say that, the clusters above that threshold
size is what we want to keep. And also, the p-value of the clusters
above that threshold size should
be below alpha we set, say 0.05. But when checking the tale above, the
first four clusters' p- value is smaller than 0.05, then we should
keep it. But according to the no. of vertices, we can caculate the
cluster size in mm^2. Then the 4th
cluster size is obviously below 100mm^2, the threshold we found using
the function fs_calc_cluster_thresh. Oppositely, the 6th cluster has a
large no. of vertices and its cluster size is above 100mm^2, while
it's
not kept because its p value is above 0.05.
I know what happened here is because of the 'resels', but it really
confuse me which one is the right one. Since you said we can use the
function, then why is the result conflicted with each other?
Could you tell me what's wrong here or what did I miss ?
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.htmlThanks
a lot,
Jidan
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How can I convert an individual subject's mask to the group average space
On Sun, 22 Mar 2009, Avram Holmes wrote: All, I have generated a mask of the cingulate regions for each of my participants from their aparc+aseg.mgz files (see attached image) and I would like see how these masks overlay with the group average brain I have generated for my study. Is there a simple way to transform a mask from an individual subjects space to the group average volume space? I made my group average with the make_average_subject command. You can create a mask of the cingulate with mri_binarize --match XXX, then convert that into the average space with mri_vol2vol (for command-line ops see how the aseg is done in make_average_subject), then concatenate all of your masks together with mri_concat, adding --mean to compute the mean. The value at each voxel will then be the fraction of your subjects that had a cingualte mask at that voxel. You can display this as an overlay, or you can threshold it to turn it back into a mask. In a related question is it possible to generate a group average aparc+aseg.mgz file? I can see the surface labels in the average and the aseg.mgz cortical labels. However, I don't know of a way to generate the aparc+aseg.mgz file. I did write software to do this, but it turned into a real mess. Cortex is so thin and the location of the indivdual cortical regions so variable, that the final map ended up with all kinds of strange holes (a good advertisement against talairach!). If you just want it for display, you should be able to run mri_aparc2aseg --s avgsubject --volmask, but this won't reflect the actual labels from your group of subjects. doug Thanks for any help you can offer, Avram -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] merging rh and lh surfaces
you can get something like what you want with cd $SUBJECTS_DIR/subject mri_binarize --i mri/ribbon.mgz --min .0001 --o mri/tmp.mgh mri_tessellate mri/tmp.mgh 1 surf/lh.both mris_smooth -nw surf/lh.both surf/lh.smboth tksurfer subject lh smboth Note that eventhough you call it lh it has both hemis. lh is just to fool freesurfer into thinking it is a hemi. doug On Sun, 22 Mar 2009, Bruce Fischl wrote: I see. Sorry, we don't have any easy-to-use tools for creating a single pial surface. You could change the value in the filled.mgz so that lh and rh are the same and try tesselating/deforming it. I've done this in the past, but you have to mess around a bit to get it to work. cheers, Bruce On Fri, 20 Mar 2009 s...@nmr.mgh.harvard.edu wrote: Hi Bruce, I am trying to create a volume conductor of human brain for FEM based source reconstruction. A nice surface of full pial (and other compartments like WM) layer is supposed to generate 3D FEM mesh by means of a meshing tool. Cheers, Seok can you tell us why you want such a thing? I have generated them before, but mostly for special-purpose applications. It's not something we routinely do On Fri, 20 Mar 2009 p...@netfilter.com.br wrote: I think Bruce or Douglas can explain better. However, the reason for both hemispheres being separated is that you need to mantain an S2 topological space. Sent from my Nokia phone @E71 -Original Message- From: s...@nmr.mgh.harvard.edu Sent: 19/03/2009 19:07:48 Subject: [Freesurfer] merging rh and lh surfaces Hi, I would like to have a single surf file that composed of both right and left pial surf. Is there a way to do it in freesurfer? Best. seok ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] reg-feat2anat failed
Hi Xin, I'm not sure what's going wrong here, I think I need more info. Can you follow the steps in surfer.nmr.mgh.harvard.edu/fswiki/BugReporting? doug Wang, Xin wrote: hello, Freesurfer group, I try to use registration.mat files of FSL/FEAT routines, instead of anat2example_func.bat, to register the orig.mgz and example_func.nii.gz with the thinking that using initial_highres in FEAT may improve the reg. However, tkregister2 catastrophically failed to register two brains when I use --fsl flag. Modifying header of example_func with mri_convert does not solve the problem. I will appreciate any suggestion on using .mat file for registration. second question: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use? Thank you in advance for any suggestion. Xin wang -Original Message- From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:26 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files that can be read into any program. doug Wang, Xin wrote: Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further suggestion on how to do the registration without the information on qform and sform in case I can not get them. Does convert to ANALYZE format or manually correct in tkregister2 work? Thank you again, Xin -Original Message- From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:09 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit? WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented Fix that, and everything will work fine. doug Wang, Xin wrote: Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now? Thank you in advance, Xin ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?
You can use feat2surf (or mri_vol2surf directly), this will create
something like lh.zstat1.mgh. You can then use
lhz1 = MRIread('lh.zstat1.mgh');
doug
Yunjie Tong wrote:
Hi
I was able to view the statistical maps (from FSL) on the subject's
surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I would
like to see the same image in Matlab. I could show the subject's
surface as well as the the cortical parcellation in Matlab by
modifying the functions freesurfer_read_surf.m and read_annotation.m.
I do not know how to overlap the statistical map onto the surface
then. Is there any Matlab function I can use? Thanks.
Best,
Yunjie
___
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
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with post-spm registered data
There is no gold standard. Mainly just visualizing it with the surfaces and making sure the surfaces line up with the bright and dark folds in the EPI, as it says in the tutorial. doug Wang, Xin wrote: Sorry for asking same question here again. I asked Dung before holiday about the criteria of good registration of fMRI and thickness map. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html I paste my question again: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use? I will appreciate if Dave could give more explanation or references of beautiful match between functional and structural images. Thank you in advance. Xin Wang From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:03 PM To: Dave Brohawn Cc: jroff...@partners.org; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with post-spm registered data Hi Dave, I'm not sure where to begin with this. Can you give more info? In particular, you might look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues efficiently. doug Dave Brohawn wrote: Hello, Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold. When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present. After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view. We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever. Please let me know if you have an answer to how this could have happened. Dave Brohawn ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?
you'll only get the vertices. If you multiple those dims together,
you'll get the number of vertices in the subject's surface, so just
reshape it to 1d
doug
Yunjie Tong wrote:
Thanks Doug,
However, I do not know how to interpret the data. For example, my
lhz1.vol has dimensions of 1x9022x17. What does that mean? I am
looking for the vertex and faces, with which I could display them in
Matlab using patch. Do I miss something? Thanks.
Best,
YJ
On Jan 6, 2009, at 12:44 PM, Doug Greve wrote:
You can use feat2surf (or mri_vol2surf directly), this will create
something like lh.zstat1.mgh. You can then use
lhz1 = MRIread('lh.zstat1.mgh');
doug
Yunjie Tong wrote:
Hi
I was able to view the statistical maps (from FSL) on the subject's
surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I
would like to see the same image in Matlab. I could show the
subject's surface as well as the the cortical parcellation in Matlab
by modifying the functions freesurfer_read_surf.m
and read_annotation.m. I do not know how to overlap the statistical
map onto the surface then. Is there any Matlab function I can use?
Thanks.
Best,
Yunjie
___
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
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parameter comparison in native vs. template space
Christine Ecker wrote: I would like to export cortical thickness measures and compare the data across subjects in a vertex-by-vertex fashion. Please could you confirm that similar functions such as mri_glmfit are based on the parameters in template space e.g. lh.thickness.fsaverage.mgh and not on the parameters in native space e.g. lh.thickness. yes So for a group comparison I would have to export the files in template space (e.g. lh.thickness.fsaverage.mgh) and could then map the output back onto the template? not sure what you mean, the thickness.fsaverage.mgh is already in the template space Also, why are the parameters not the same in native and template space? Not sure what you mean. Can you give an example? Finally, in order to compare groups on the basis of the parcellated regions (e.g. lh.aparc.stats). Are parameters such as area, volume, curvature etc comparable across groups or would they still have to be corrected for whole-brain volume? If you are going to correct for brain or head size, then you'd do it for volume, thickness, and surface area measures, but not necessarily curvature. doug I would be very grateful if you could help me further. Thank you! ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unpacking err runs
Try adding -unpackerr Adrienne McCallister wrote: Hello, I am unpacking recent functional data and during a function run we needed to stop it early and so now when I view it in unpacksdcmdir, it has a err next to the run. Since those runs are typically skipped when unpacking, is it possible to override that and download the file anyway? Any help would be appreciated. Sincerely, Adrienne ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with post-spm registered data
Hi Dave, I'm not sure where to begin with this. Can you give more info? In particular, you might look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues efficiently. doug Dave Brohawn wrote: Hello, Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold. When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present. After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view. We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever. Please let me know if you have an answer to how this could have happened. Dave Brohawn ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] vertex/talairach coordinates
yes, it is Bruce Fischl wrote: actually Doug can confirm, but I think the average surface RAS are already Talairach coords On Wed, 24 Dec 2008, Nick Schmansky wrote: Corey, I'm not 100% sure how to do this but a starting point is to use mris_info on the surface file you are getting coordinates from, like: mris_info rh.inflated and get the surfaceRAS to talaraiched surfaceRAS matrix, and use that in matlab to do your conversions. Of course I'd check a few of them against what you see in tksurfer. Nick On Tue, 2008-12-23 at 12:34 -0500, Keller, Corey J. wrote: Hi Freesurfers, I have a list of 50 vertices picked from an average subject's inflated brain in mne_analyze and would like to find the talairach coordinates for each of these vertices. Is there a more efficient way to do this than to load tksurfer and find these vertices by hand? Thanks again. -Corey ___ 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 ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote: Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should average contain? should it point to the average of the population, of fsaverage, or is it just a flag? This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage. 2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files. Just the hemisphere If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters? The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately. Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning? Can't say without the cmd line, but I'm guessing you have a rouge space in your script best regards, sid. On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu wrote: Sid, A group analysis can be performed from the command-line using mri_glmfit directly. See this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis You can use a different average subject, other than fsaverage, although it doesnt improve an analysis to use a subject from your group. Also, you can create a symlink from $FREESURFER_HOME/subjects/fsaverage to your SUBJECTS_DIRS, to spare having to copy the data. Nick On Sun, 2008-12-28 at 12:01 -0800, Siddharth Srivastava wrote: Hi Nick, Thanks, It was my mistake. It works exactly as you say. I still have to look at qdec documentation, but could i ask if it is possible to perform the group analysis in a batch mode, without the GUI, i.e ? regarding the movement of data, the first time i did it, i got a screen full of memory addresses and corresponding routines, followed by a crash ( exit from wish, back to shell). I am not able to replicate it, seems to work now. Also, is it possible to register everything to a different surface, other that fsaverage.. for example to one of the subjects? Can this be located outside the relative paths reachable via $SUBJECTS_DIR ? In fact, can fsaverage be located outside? For the processing i did, i had to copy the fsaverage as one of the subjects, so that it can be located within the current context of $SUBJECTS_DIR . Thanks again, for the timely help. sid. On Sun, Dec 28, 2008 at 9:17 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu mailto:ni...@nmr.mgh.harvard.edu wrote: Sid, The .mgh files, in the case of the commands you ran, store surface data corresponding to the 'fsaverage' subject. So you would first load the inflated surface for fsaverage (tksurfer fsaverage lh inflated), then you would use the Load Overlay menu option to load the .mgh file(s) you created. You probably will have to adjust the color thresholds (View- Configure-Overlay). For the lgi data, you can use: recon-all -s subj -qcache -measure pial_lgi which will sample the subjects lgi data to the fsaverage surface, at which point you could average that (although typically a statistical analysis is performed on the set of subjects sampled to fsaverage, see out group analysis slides and tutorial pages). You should be able to move subject data around to other directories without any problems. Does tksurfer really halt after that 'not in scripts dir' message? That is a common message and not an error. Can you open tksurfer for the sample bert subject? Nick On Sat, 2008-12-27 at 19:14 -0800, Siddharth Srivastava wrote: Hi Nick, I finally got a chance to use the sequence of command that you had provided below. In continuation of this thread: a) The output of using the command mentioned in reply 2) below is an MGH file (and not faces/vertices combination)? How is it possible to get a smoothed surface that i can load as an overlay in tksurfer? I would
Re: [Freesurfer] Thanks for the answers
make sure you're not using a 0-based index with matlab
Yunjie Tong wrote:
Hi Doug and Bruce,
Thanks for your answers. One more question, why the vertex RAS of the
same spot on the brain given in TkSurfer is not the ones I read by
Matlab program freesurfer_read_surf?
The commands I am using are:
[vertex_coords, faces] =
freesurfer_read_surf('tutorial_subjs/subject/surf/lh.inflated');
tksurfer subject lh inflated
Thanks,
YJ
if you have the voxel index (col, row, slice) then you can:
V2R = [
-1.00.00.0 128.0
0.00.01.0 -128.0
0.0 -1.00.0 128.0
0.00.00.01.0 ]
crs = [col row slice]';
xyz = V2R[crs+1; 1];
then find the vertex whose xyz coors are closest to xyz
Yunjie Tong wrote:
Hi freesurfer experts,
I have a single subject anatomical data in freesurfer. If I know the
volume index of a point on the surface of the cortex ( from T1.mgz
in TkMedit), how can I find out the corresponding vertex index or
the vertex RAS in TkSurfer. Thanks. BTW, I am using matlab.
Thanks,
Yunjie
___
Freesurfer mailing list
Freesurfer@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
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
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
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
how are you defining your ROI? Below is some info Im putting together on segmentations, parcellations, and labels. It's still pretty raw, but it might be useful to you. Segmentation - each voxel has an index - index into lookup table (LUT), eg FreeSurferColorLUT.txt - only one index per voxel - surface or volume - binary segmentation (mask) - 0 and 1 Parcellation/Annotation - surface only (surface annotation is redundant) - each vertex has a name - inconvenient - cross-reference to FreeSurferColorLUT.txt Label - a single segmentation/parcellation - surface or volume - text file with a list of 5 numbers for each vertex/voxel - 1. VertexNo (0-based, ignored for volume labels) 2. X coordinate of voxel/vertex in tkreg space 3. Y coordinate of voxel/vertex in tkreg space 4. Z coordinate of voxel/vertex in tkreg space 5. Statistic (not used by all programs) Color Table: - List of segmentations/parcellations - Each row has 6 columns: 1. Index 2. Name (no spaces) 3. Red (0-255) 4. Green (0-255) 5. Blue (0-255) 6. Statistic Convert a set of labels into an annotation/parcellation: mris_label2annot Convert an annotation/parcellation to a set of surface labels: mri_annotation2label Convert an annotation/parcellation to a surface segmentation: mri_annotation2label (name misleading) Convert a single ROI in a volume or surface segmentation into a volume or surface label: mri_cor2label (surface or volume labels, name misleading) Convert a set of volume labels into a volume segmentation: mri_label2vol Convert a set of surface labels to a surface segmentation: No single program. Use mri_label2annot, then mri_annotation2label Convert a label on one subject to a label on another subject: mri_label2label (surface or volume labels) Convert a surface segmentation to an annotation: mris_seg2annot Merge two or more labels together: mri_mergelabels Create a label from a bounding box: bblabel Merge an annotation/parcellation with a volume segmentation to create a new volume segmentation: mri_aparc2aseg Create a binary segmentation (mask) from a segmentation: mri_binarize (use --match) Create surface labels from thresholded surface activation maps: mri_surfcluster Create an annotation/parcellation from thresholded surface activation maps: mri_surfcluster Create a surface segmentation from thresholded surface activation maps: mri_surfcluster Create volume labels from thresholded volume activation maps: mri_volcluster Create a volume segmentation of activation clusters: mri_volcluster Gabriel GLZ wrote: hello in the case that i have a ROI and i don't know wich voxeles are in there, or the coordenates of those voxeles, i want to create a specific label that only contains those voxeles, how can i do that??' Acceso muy fácil al uso compartido de fotos con Fotos de Windows Live™. Arrastrar y colocar http://www.microsoft.com/windows/windowslive/photos.aspx ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surface cluster area bug
Hi Y'all, I've recently found an error in the way that mri_surfcluster reports the area of a cluster when using a group surface such as fsaverage. The bottom line is that the area reported is about 25% too big. However, the cluster-wise p-values reported by mri_surfcluster based on simulations from mri_glmfit ARE NOT AFFECTED. Volume clustering is unaffected. I have fixed this bug in the Martinos Center dev environment. Part of this fix is to make old versions of mri_glmfit simulation incompatible with new versions of mri_surfcluster (and vice versa) for surfaces (ie, mri_surfcluster will exit with an error or will crash -- either way, it will not complete), as this could generate erroneous p-values. We will be propagating the fix to our stable version after the holidays, and make new distributions available. More info and updates can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface As always, sorry for the bug. doug ps. On the brighter side, I discovered this bug while implementing gaussian random field (GRF) corrections for multiple comparisons, so soon you will be able to run GRF in seconds instead of running monte carlo simulations over a weekend. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transformation from volume index to vertex index
if you have the voxel index (col, row, slice) then you can: V2R = [ -1.00.00.0 128.0 0.00.01.0 -128.0 0.0 -1.00.0 128.0 0.00.00.01.0 ] crs = [col row slice]'; xyz = V2R[crs+1; 1]; then find the vertex whose xyz coors are closest to xyz Yunjie Tong wrote: Hi freesurfer experts, I have a single subject anatomical data in freesurfer. If I know the volume index of a point on the surface of the cortex ( from T1.mgz in TkMedit), how can I find out the corresponding vertex index or the vertex RAS in TkSurfer. Thanks. BTW, I am using matlab. Thanks, Yunjie ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2 error
it wants the number of dimensions to be either 3 or 4, even if the size of those dims is only 1. You'll probably have to edit the header, though I'm not sure how to do that. Susie Heo wrote: Hello, When I try to use the Freesurfer command 'tkregister2' (or 'mri_convert', or any Freesurfer command for that matter) to read in my nifti files created using SPM, I receive the error message: niiRead(): 2 dimensions in ../rsH794_1.nii; unsupported ERROR: could not read ../rsH794_1.nii as 24 Does anyone know what the problem is and how to fix it? Susie ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] .mat/.hdr and orientation
I would have thought that that mri_convert cmd (with .img) would have worked. what went wrong? Susie Heo wrote: Hello, I am hoping that someone can help me to solve my orientation/angle acquisition problem: 1) I have an EPI oblique slice in Analyze format with incorrect orientation/angle acquisition information in the .hdr file (no .mat file) 2) I have a distorted image of the same slice in Analyze format with the correct orientation/angle information in the .hdr/.mat files 3) I would like to change the .hdr/(.mat?) file of 1) to conform to the orientation/angle specs of 2). I have tried: 1) Replacing 1).hdr w/ 2).hdr--incorrect orientation; image off center; same as if kept 1).hdr 2) Replacing 1).hdr w/ 2).hdr and 2).mat--correct slice angle, image flipped -y and possibly -x? 3) mri_convert input output --iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 where input = 1).img, 2).hdr, 2).mat --lost slice angle, correct orientation Any tips? What exactly do the .hdr and .mat files contain? Susie ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average
Hi Petr, when you list your subjects, just use the subject's name. It looks like you put path specifiers in there, ie, ./1013 shoudl be simply 1013 doug p.s.bjer...@studmed.uio.no wrote: Hi, Trying to make an average of about 60 subjects. The problem is that the proper files are not produced. In average/mri/ I only have the mni305.cor.mgz and the folder transforms. There should more. During processing I can see the following repeating at some point: tail: cannot open `+3´ for reading: No such file or directory. Not sure what +3 means... Further, in the end of output (also in the make_average_volume.log, attached) we have the ERROR: failure writing /./..//.mgh where is the first of the subjects in the list. If I try to remove it and rerun, it only complain about the next in line... Don´t know what to do here...:) Petr ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] reg-feat2anat failed
Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit? WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented Fix that, and everything will work fine. doug Wang, Xin wrote: Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now? Thank you in advance, Xin ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert 3D set to a single 4D ?
There are two things you can do, mri_concat spm_*.img --o 4d.img you can also do it with mri_convert, but I don't think it buys you anything over using mri_concat. doug Siddharth Srivastava wrote: hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid. ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert 3D set to a single 4D ?
mri_convert will fail in the same way. But it should have worked. Can you point me to the dir and give me read perms? Siddharth Srivastava wrote: Hi Doug, Thanks for the reply. I tried mri_concat as you suggested, and got the following: WARNING: analyzeRead(): matfile usual path tospmfile1-0003.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. - INFO: could not find usual path tospmfile1-0003.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in usual path tospmfile1-0003.mat file - These files are the outputs from spm_reslice command, and i looked at the contents of the mat files: they have 2 entries: M and mat, and store the same matrix. Do you think mri_concat may be getting confused by 2 entries in the mat file? Is there any flag i can use (eg --it analyze ) to make it run? I would also be interested in using the mri_convert option as an alternative. can you (or anyone) help me with the command line flags? regards, sid. On Mon, Dec 15, 2008 at 12:11 PM, Doug Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: There are two things you can do, mri_concat spm_*.img --o 4d.img you can also do it with mri_convert, but I don't think it buys you anything over using mri_concat. doug Siddharth Srivastava wrote: hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid. ___ Freesurfer mailing list Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] func2roi-sess command issue
it's only positive for the contrast that you have specified. the roi summary reports the HRF amplitudes for each condition. When you compute the contrast of those, you should get the right sign. doug Dave Brohawn wrote: Hello, In the stable 3 environment, I ran the func2roi-sess command. This is what was included: func2roi-sess -roidef dACC99_rh -analysis EMerror -anatlabel dACC-rh -maskcontrast ASevfix -maskframe 5 -maskthresh 0.0043648054 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR I then ran this summary generating command: roisummary-sess -roidef dACC99_rh -analysis EMerror -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR -sumfile $SUBJECTS_DIR/dACC999_rh.txt I've viewed the summary file, and found that there are negative values listed for some of the conditions time points (e.g conditon 1, 2 sec after stimulus onset). How can this be if I included the masktail pos flag? I thought that only captured positive activation. If there is a way to solve this issue and capture only positive activation, please post when you can. Thank you, Dave Brohawn ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Discrepancy between sig.nii and .w files
I just noticed this about a week ago and have not been able to track it down. The w file (or anything created by mri_vol2surf, which is run by paint-sess) is the gold standard. When tksurfer loads in a volume/registration, it is slightly off. I'm working on why. doug Jesse Friedman wrote: Hi, I'm using paint-sess to create .w files from a contrast's sig map (I need the .w files for use with MNE). When I view the sig.nii file in tksurfer, the activation differs subtly but noticeably from the .w files. For example, I'll run a command like: paint-sess -analysis EC -contrast eVc -offset 5 -s subjects/RMCON005 When I load RMCON005/bold/EC/eVc/sig-5-lh.w into tksurfer, the activation is slightly different than when I load RMCON005/bold/EC/eVc/sig.nii and view that hemisphere at that offset. Is this discrepancy to be expected? If so, is there a way to create .w files that have identical activation to the sig.nii file? -- Jesse Friedman, B.A. Massachusetts General Hospital Martinos Center, Manoach Lab Psychiatric Neuroimaging 149 13th Street #2613 Charlestown, MA 02129 Phone: (617) 726-1908 Fax: (617) 726-4078 jes...@nmr.mgh.harvard.edu ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Some questions about my analysis
Christian Scheel wrote: Dear all, I have got several questions about the analysis of my data. Maybe you can help me out: 1) Regarding the different levels of smoothing (FWHM) in Qdec are there already some 'standards' that one should usually stick to? My results look better when I set the smoothing level to 15 or even 20, but is it really appropriate to use such high levels of smoothing? As with all smoothing, there is no real standard, but it is not unusual to use 15 or 20. Surface smoothing is much more forgiving that volume smoothing in terms of mis-localization of activation. In fMRI volumetric analysis, it is not unusual to see 10-20mm smoothing. 2) In Qdec is there a possibilty to set something like an 'Extent threshold' in order to display only clusters of a certain size and hide all clusters that are smaller? This is not possible in Qdec yet. Outside of qdec, there is mri_surfcluster which will do this. We will be adding it into qdec. 3) Am I correct that the best way to get the total gray and white matter volume is a) for the gray matter volume: mris_volume ?h.pial minus mris_volume ?h.white b) for the white matter volume: mris_wm_volume subject ?h I'll leave this for others. I read that the values for white and gray matter in the aseg.stats are not that accurate, but what about the GrayVol value in the ?h.aparc.stats files? I was a bit surprised that the sum of these GrayVol values is not the same as the total gray matter volume calculated with mris_volume (although it comes quite close) 4) All of recon-all has been run with Freesurfer 4.02 for all subjects - is it OK to use Freesurfer 4.05 or 4.10 for the analysis? I'll leave this for others. 5) I have tried loading my data into the qdec version shipped with Freesurfer 4.05 and noticed that now there is an option to chose between DODS and DOSS. In my study I wish to compare the thickness of a group of patients and a group of controls accounting for gender and age. Did I understand Dougs freshly updated wiki page correctly and can I use DOSS in case I assume that age has the same effect on patients and controls (so same slope) and they are only starting at different thickness levels? And when chosing DOSS is age really still in the calculation as a covariate? I was surprised to see that I can only chose the question 'Does the average thickness, accounting for gender, differ between patient and control' but not 'accounting for gender and age'. Yes, if you believe that the slope is the same for patients and controls, you can use DOSS. Age is used as a covariate, and the question text should be changed to reflect this. 6) I would like to have a look at the local gyrification index aswell but still need to buy Matlab for it. Do I also need some extra toolboxes to run the lgi calculation - or do I just need the core programm? I'll leave this for others. doug Any help is greatly appreciated. Best wishes, Christian Scheel --- University of Cologne Department of Psychiatry ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Paired Analysis with FreeSurfer
I just created another wiki page to document how to perform a paired statistical analysis in FreeSurfer (someone was asking me about it, but I lost the email). The page is here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis It is admittedly a little rough, so let me know if you find typos or have questions. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] I cannot get tutorial data
Sorry, try it now. doug wrote: Hi, Mr. and Mrs I want Tutorial file of fsfast. But I didin't get it from the following pass. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast-tutorial/fsfast-tutorial.subjects.tar.gz If you know about that please let me know. Thank you for your help. Best regards, Kenta ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] register.dat
Try looking at the docs on
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
esp the fscoords.{pdf,ppt}
doug
Julien Dubois wrote:
Hi
I need one piece of info that I can't seem to find anywhere (after 1h
of searching).
What exactly do the numbers in register.dat correspond to (I know for
the first four rows, but the last four rows are still a mystery)?
Can I manually temper with that info (if I know I translated an image
by hand before coregistration, for example)?
Thank you very much in advance
- Julien Dubois
___
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Docs for FSGD Files
Hi Y'all, I've completed some new documentation on the FreeSurfer Group Descriptor (FSGD) files. They can be found in these locations: https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss Please let me know if you have questions (or find typos:). doug -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Statistic analysing for a mask
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines. doug Alexandru Hanganu wrote: Dear Freesurfer users, We have an MNI mask and we want to apply this mask on a group of subjects for small volume correction. so we did the following steps: 1. cd $SUBJECTS_DIR/fsaverage/surf fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat 2. cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh 3. cd $SUBJECTS_DIR/subjid/surf mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh . . . Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits = 2.31875 Saving target data 4. Next step was just for verifying, but we received an error (maybe it's not so important): cd $SUBJECTS_DIR/subjid/surf mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg We want to determine the statistics only for this mask for the whole group of subjects (qdec, or mri_glmfit). If the mapping of our subjects thickness data was good, what should we do next in order to achieve our goal ? Thank you. Best regards, Dr. Alexandru Hanganu ___ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany. ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_volcluster
I would probably use --ocn with mri_volcluster to create a single volume in which each voxel value is the cluster number it belongs to. Then split them out like: mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh doug Gregory Dierksen wrote: Hi, I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). The commands I've been using are: mri_volcluster --in microbleeds-reslice.mgz --allowdiag --thmin .5 --labelbase ../scripts/clusters/testing/cluster mri_label2vol --label ../scripts/clusters/testing/cluster-0001.label --temp orig-flip-reslice.mgz --o cluster-0001.mgz (NOTE: the -reslice is because these volumes have been resliced from 0.4492, 0.4492, 6. sized voxels to conform to 1 mm^3 sized voxels; the dimensions of the image were altered as well, from 384 x 512 x 23 voxels to 173 x 230 x 138 voxels) When I view cluster-0001.mgz with tkmedit the result is a 3D checkerboard like pattern with no two voxels having common edges (despite the original cluster in microbleeds-reslice.mgz being a solid cluster of 90 mm^3). What I wanted to see was that each cluster could be reconstructed in a single volume (i.e. cluster-0001.mgz, cluster-0002.mgz, etc with each volume containing only one cluster). Also, when I use mri_cor2label and then mri_label2vol to switch between label files and volumes files, the clusters (despite not being split up like I want) are solid and do not display this checkerboard effect...leading me to think that its an issue with mri_volcluster. Any help you can offer would be great. Thanks. Greg -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Statistic analysing for a mask
what's your cmd? You need to make sure to add --in lh.thickness to get thickness in the summary file Alexandru Hanganu wrote: Thank you Nick, and Doug for your answers. I used both --reshape flag and --noreshape flag and the results after mri_segstats were in both cases: . . . Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation 0 0 134504 134504 1 1 29338 29338 Reporting on 2 segmentations So I understand that these are the thickness data of the mask I used. Are these data in mm ? Because when using mris_anatomical_stats command line to see the thickness - the data is in mm, and is very different. Sincerely, Alex. ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] missing information in volume headers
It was likely converted thru an intermediate format that did not retain those values (eg, nifti or analyze) before being imported into freesurfer. Jared Price wrote: Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_info was run on some of the orig.mgz volumes the values listed for echo time and flip angle in some of the scans were 0.00, even though there was a listing for repetition time. What could have caused this? Could misinformation in the header cause variation in the freesurfer processing of that scan? Cheers, Jared ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] vertex wise correction for multiple comparisons using permutation
Yes, the max stat is stored in the CSD, and it's purpose is to enable voxel-wise correction, but I've never gotten around to it (and this is the 1st request:). You might be able to program something in matlab pretty quickly. You can use FS's load_csd.m to load the CSD file, and MRIread() to load the overlay. doug Lúcia Garrido wrote: Dear Freesurfers, I'd like to correct for multiple comparisons vertex-wise instead of cluster-wise. Is it possible to do this using permutation (and not FDR)? I've seen in an e-mail from last year that the values of maximum statistic stored in the CSD file could be used for this purpose, and I'd be very grateful if you could let me know how. Many thanks, Lucia ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question on tksurfer tcl
try just running tksurfer with the -label-outline option. j janssen wrote: Hi, using version 4.0.5 my goal: to display in tksurfer an inflated brain with curvature and an *outlined* label, using a tcl-script. there are probably numerous ways, i did: tksurfer subject rh inflated -gray -tcl tksurf.tcl where tksurf.tcl contains: make_lateral_view rotate_brain_x -90 redraw labl_load label-file set gaLinkedVars(redrawlockflag) 0 SendLinkedVarGroup redrawlock set gaLinkedVars(labelstyle) 1 SendLinkedVarGroup view save_tiff tiff_file.tiff all works except for the label to be outlined. any suggestions? thanks! -joost ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to compare left vs right hemi (flip RL)
We don't have a good way to do this yet. I've have been working on one but have dropped the ball. Some people will analyzed both the correctly-oriented data and left-right reversed for each subject, but this is not the best way to do it. doug Frederic Andersson wrote: Hi, Is there any way to compare left vs right hemisphere (surface morpho. and functional data). I mean, is there any function to flip one hemisphere in order to compare it with the other one? Thanks, Frederic Andersson ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using qdec to compare groups of twins?
Do you just want to do a paired analysis? Do you want to include other covariates? Burmicz, Ryzarda wrote: Hello, Could you please advise as to whether or not the following analysis is suitable? I would like to compare groups of monozygotic twins (MZ concordant vs. MZ control ; MZ discordant affected twin vs. unaffected twin) using qdec. This is not as straightforward as group comparisons usually are because I cannot make the assumption of all data being independent as twin pairs are, obviously, related to one another. To get around this issue I have started a qdec analysis and added a category 'pair' in which twin pairs share a category as follows (qdec.table.dat), in order to indicate that they have shared genetic and environmental influence: subject no subjid pairdiagnosis age gender 1 a MZ_Discord_Well ... ... 2 a MZ_Discord_Ill 3 b MZ_Discord_Ill 4 b MZ_Discord_Well 5 c MZ_Discord_Well 6 c MZ_Discord_Ill 7 h MZ_Discord_Well 8 h MZ_Discord_Ill 9 l MZ_Discord_Well 10 l MZ_Discord_Ill 11 m MZ_Discord_Well 12 m MZ_Discord_Ill 13 n MZ_Discord_Well 14 n MZ_Discord_Ill 15 p MZ_Discord_Well 16 p MZ_Discord_Ill 17 s MZ_Discord_Well 18 s MZ_Discord_Ill 19 t MZ_Discord_Well 20 t MZ_Discord_Ill I would appreciate if you could suggest a more robust way around this. Many thanks, Rysia ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error with motion-correction session(ms-sess)
Looks like matlab is having trouble running from the shell. I have no idea what causes this, you may have to ask your system administrator for help. doug wrote: Hi, Mr or Ms My name is Kenta in Japan. I'm undergraduate student. Please help me! I've tried some things to solve the error with mc-sess. But I could not solve this error. The mc-sess processing didn't completely run and following message showed up. I'm using matlab R2007a, macOS10.5.5, and freesurfer ver4.0.5. If you want some information about this error or another things, let me know. == - INFO: northog = 6, pct = 100 2008-12-02 20:08:06.237 MATLAB[1256:60b] Process manager already initialized -- can't fully enable headless mode. == Yours sincerely. Kenta ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Possible to constrain FDR to a label in the volume?
Yea, there's not a mask to label. There is a mask to brain, but I'm not sure if you can substitute your own mask for it. I just tried to run it, and could not get FDR to work at all in tkmedit. Is it working for you at all? doug Dan Dillon wrote: Dear FreeSurfers, I've created a basal ganglia label and am wondering if it's possible to constrain the FDR calculation to that label? Based on earlier messages it seems like tksurfer has a marked label only option for FDR, but I haven't been able to find something similar in tkmedit. Any help greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_label2vol
what is your command line? On Fri, 28 Nov 2008, Steinmann, Iris wrote: Hi Freesurfers, there is a little problem: I load fsaverage in tkmedit and marked with tools-'Configure-Brush-Info...' an area in the volume, then I saved it as a label (newarea.label). I want to create a binary mask with this newarea.label and used mri_label2vol, to have 1 where the label is and 0 where it is not. But it doesnt work...I just get a file (I tried it with nii and bfloat) with only 0 everywere. Is something wrong in my workflow? I hope somebody have an idea... best greetings Iris -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 2D to 3D registration
Hi Susie, I have a tool that works very well on this type of thing, but I am not quite ready to release it (a few more weeks). It will be greatly facilitated if you acquired a whole-brain image during your scan (this can include the MPRAGE itself). If not, then you'll have to do some hand registration to get it close (if you collect more data of this type, make sure to get a whole-brain scan -- virtually anything will do, including a single time point from an epi). doug Susie Heo wrote: Hello, I would like to register a 2D EPI oblique axial slice to a 3D MPRAGE and am hoping that Freesurfer will help me do this. I have not had any luck with other fMRI software packages. Caveat: Each subject's EPI axial slice was taken parallel to his/her specific hippocampal longitudinal axis and the angle is unknown. Therefore, I have a low-res 2D axial slice at an unknown angle and a high-res 3D MPRAGE. Is Freesurfer capable of finding and applying the appropriate transformation? Specific suggestions would be greatly appreciated. Best, Susie ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fs-fast smoothing
Hi Scott, you should skip steps 2-6 (that is the old stream). Instead, run isxconcat-sess after #1, then smooth on the surface either in isxconcat-sess or with mri_surf2surf before running mri_glmfit. doug Scott Gorlin wrote: Hi, I'd like some clarification on the recommended procedure for smoothing functional data across the cortical surface in FS-FAST. I've managed to get it working using the following procedure: 1) analyze my data using selxavg3-sess in the native space, without smoothing 2) resample the averages into the spherical space using func2sph-sess 3) smooth these averages using sphsmooth-sess (which required several edits to work with .nii files) 4) recreate the contrasts in the smoothed sph space with stxgrinder-sess 5) paint the analysis onto the surface with paint-sess (which also required edits for .niis) 6) view with surf-sess (which I had to edit to read the subject properly) Surely there's a simpler way to accomplish this? I'm particularly confused because the online documentation says that selxavg3 replaces stxgrinder, but it seems stxgrinder has to be called to make contrasts in non-native space (and uses different code to produce the contrasts than selxavg). Plus, the revision date for stxgrinder is more recent! Then, it seems odd that isxconcat will reproject the data for a group analysis if it's already sampled on the surface via func2sph. Thanks, Scott ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Segmentation Volume Data
The aseg.stats is computed with a partial volume correction at the boundaries of the structures, tkmedit just counts voxels. Yuan Xu wrote: Hi FreeSurfer: when I compare a brain structure volume count on the aseg.stats files with a volume of same structure measured using tkmedit Segmentation Label Volume Count feature to display on TkMedit Tools window. They are closer but not the same, usually about 3 to 10% difference. Why? Thanks, Yuan ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fs-fast smoothing
Oh, in that case the easiest thing to do is to smooth the raw data on the surface. If you have a development version of freesurfer, you can do this with preproc-sess using the -surf-fwhm option doug Scott Gorlin wrote: Thanks Doug, though I'm still a bit confused: I'd like to see the smoothed results on the individuals, not just the group - so it seems isxconcat-sess wouldn't be appropriate. Are you suggesting running mri_surf2surf directly on the contrast sig.nii files? Is smoothing a significance map the equivalent of smoothing the data, then recreating the significance in the sphere space? This didn't seem true to me, which is why I tried to recreate the significance maps as below. Thanks, -S Doug Greve wrote: Hi Scott, you should skip steps 2-6 (that is the old stream). Instead, run isxconcat-sess after #1, then smooth on the surface either in isxconcat-sess or with mri_surf2surf before running mri_glmfit. doug Scott Gorlin wrote: Hi, I'd like some clarification on the recommended procedure for smoothing functional data across the cortical surface in FS-FAST. I've managed to get it working using the following procedure: 1) analyze my data using selxavg3-sess in the native space, without smoothing 2) resample the averages into the spherical space using func2sph-sess 3) smooth these averages using sphsmooth-sess (which required several edits to work with .nii files) 4) recreate the contrasts in the smoothed sph space with stxgrinder-sess 5) paint the analysis onto the surface with paint-sess (which also required edits for .niis) 6) view with surf-sess (which I had to edit to read the subject properly) Surely there's a simpler way to accomplish this? I'm particularly confused because the online documentation says that selxavg3 replaces stxgrinder, but it seems stxgrinder has to be called to make contrasts in non-native space (and uses different code to produce the contrasts than selxavg). Plus, the revision date for stxgrinder is more recent! Then, it seems odd that isxconcat will reproject the data for a group analysis if it's already sampled on the surface via func2sph. Thanks, Scott ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical labeling issue
The cortical segmentation from the aseg does not often line up very well as it is only based on a voxel/volume analysis. The aseg is not informed by the surface analysis. doug [EMAIL PROTECTED] wrote: Hello all- I'm having some trouble with sessions in which the pial surface is not matching up with the cortical segmentation. Subjects were run on a 1.5T Vision scanner and we're using an average of 3 MPRAGEs. Does anyone have any suggestions on how to troubleshoot this issue? I've attached a snapshot illustrating this problem. Thanks, Tessa These materials are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return email. ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] stats in freesurfer
Lúcia Garrido wrote: Dear all, I have a few questions about stats in freesurfer that I'd be very grateful if you could answer. 1. Is it possible to reduce the search from the whole brain to a smaller region of interest to apply corrections for multiple comparisons? For example, if I'm interested in differences in the fusiform gyrus, can I restrict the FDR correction to the fusiform? Yes, click in the fusiform, click on the Mark Label button (or tools-Labels-Mark Selected Label), then check the Only Marked button next to the FDR, then Set Threshold Using FDR, the Apply. Not sure about the others. 2. Is it important to control for any global measure when comparing cortical thickness? For example when comparing grey matter volume, it's good practice to control for the intracranial volume. In case of cortical thickness (and other dependent measures in freesurfer), do you know how these are affected by the intracranial volume (or other measures) and how these could be controlled? 3. Finally, I posted a question a few days ago about comparing volume using freesurfer. I'm sorry for insisting on this but I still haven't found any response. My question was whether it's possible to compare volume maps in freesurfer. I'm using an older version (4.0.4) and my impression is that the most recent version might have this feature, but this is unclear to me. I'd be very grateful if you could let me know if this is the case. And if there's any way in which I can compare volumes usig data pre-processed using the version I have. Thank you very much! Best wishes, Lucia ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Issues with FreeSurfer and Slicer3
from a freesurfer standpoint, it looks like you've done the right thing. Sorry, can't help out much on slicer. It is possible that slicer is expecting an integer data set, so you can try mri_convert FSParcel_FSorient.mgz FSParcel_FSorient.int.mgz --out_data_type int doug joel bruss wrote: I must have posted this to an incorrect address before so I'll try this again: Hello- I'm running freesurfer-Linux-centos4- stable-pub-v4.0.5 on Suse 11. I've used the output of FreeSurfer, specifically wmparc.mgz to create a 32-bit volume to which I've applied edits. The two commands I used were: mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o wmparc-in-native.mgz --regheader --interp nearest mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz wmparc_in_native_analyze (The new Analzye set was renamed FSParcel.hdr/img) After making the appropriate edits, I wanted to put this file back into mgz format/freesurfer space so I ran: mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o FSParcel_FSorient.mgz --regheader --interp nearest (I assumed that a target of wmparc would be most appropriate sinc that's what I started with but I've tried aseg as well) I've been playing around with Slicer and trying load the file as a label file to which I create (I believe) vtk models. If I convert wmparc to an Analyze set and then back to FreeSurfer mgz without any edits, I get an exact copy, as would be expected. If I make any alterations to the file and follow my steps, Slicer gripes that it can't parse the header. No matter what dims I use, I get pixels scattered across the screen and it appears that the volume is scrunched to 1 slice. If I run tkregister (as mri_vol2vol suggests) tkregister2 --mov FSParcel_FSorient.mgz --targ $SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg everything looks fine. I find the Slicer documentation a bit lacking and don't know who to turn to. Is there something inherently wrong with my commands or is there a way to write header params to the mgz file so that Slicer will just work? -Joel ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Configure thresholds in overlay options
In general, this is a bit of a mess. The way that I do it is to use piecewise and set the min and mid to the same thing (this is what linear opaque was supposed to do). This way, anything that is over threshold has color, everything else is transparent. BTW, everything over the mid will be opaque. Values between min and mid will be semi-transparent. Some people like to much around with the min and mid to improve the look of the image, but really you want anything over threshold to be opaque. doug Juranek, Jenifer wrote: Hi, Running FSv405 on RHEL5. Is any descriptive information available for threshold options in the configure overlay display gui? Specifically the bases for linear, linear opaque, and piecewise thresholds? Visually, the three options appear dramatically different. Are there specific datatypes each overlay option is designed to handle? Many thanks for any information you can provide, Jenifer ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_surf2surf - Error
did you create a subject called average? This is done with make_average_subject. Alternatively, we distribute an average subject called fsaverage, so you can just use that instead if you want. doug Alexandru Hanganu wrote: Dear Freesurfer Users, We have a little problem with mri_surf2surf. Our goal is to determine the statistical data - t-test, ANOVA, for a group of subjects. So initially we made the recon-all, autorecon1,2,3 and -qcache for all subjects. After that we created the FSGD file and mris_preproc - in order to create ?h.thickness.mgh file. Now in order to initiate the mri_glmfit step we have to create the ?h.thickness.sm10..mgh file with the mri_surf2surf command. We used this command line: mri_surf2surf --hemi lh \ --s average \ --sval lh.thickness.mgh \ --fwhm 10 \ --tval lh.thickness.sm10.mgh and we receive the Error: – /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open file Could you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help. Best regards, Dr. Alexandru Hanganu ___ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany. ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
All those commands will do the same thing. When you pass mri_convert a single dicom file, it looks at all the files in that directory and finds all the dicoms that have the same series number, and puts them into one volume. Alexa Nardelli wrote: Hi, I have a question regarding converting files to mgz format from siemens (dicom). Per each image I have 144 IMA files (i.e. for one subject I have files from .001.IMA to .144.IMA) and I am wondering how to convert those into 1 mgz file. The only way I seem to find is to use the command: mri_convert filename.001.ima subjectname/mri/orig/001.mgz mri_convert filename.002.ima subjectname/mri/orig/002.mgz ... mri_convert filename.144.ima subjectname/mri/orig/144.mgz While this is painful and time consuming I also worry that in my quest to find the hippocampal volumes, Freesurfer will not read these files as one volume. Is this the correct way to convert these files? Or is there another easier way? Thanks Alexa ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] optseq2 question
Hongchuan Zhang wrote: Hi, list, I am new to optseq2 so I really need advices to my questions. We have an experiment of 2 factors with36 trials for each factor, and another 24 null trials. So in total we have 96 trials. We also have 3 random jitters which make our trials could last for either 4.6, 5 or 5.4 seconds. The total session time is thus 480 seconds. Since our TR is 2 seconds, the ntp = 240. My questions are: (1) How can I set the psdwin? My intuition is that dPSD should be divided by both TR and trial duration. That means we can only have a dPSD = 0.2. Would that be too small? I observed that by doing this the largest psdmaxis only 2 seconds. That is not too small, but if you are going to analyze your data with an FIR model, then it will kill your power. If you are going to assume a shape (eg, gamma function or diff of gammas), then it is fine. (2) What should I do if I want to break the session into two parts? The previous optseq version seems to allow one specify the runs for each sesssion. But I did not find this option in optseq2. Can I just use half the trials to get two sequences and use themfor thetwo parts? Yes, spec --nkeep 2 doug Thanks! Your suggestionis appreciated. Hongchuan 2008-11-03 Hongchuan Zhang, Ph.D. Postdoctoral Research Associate Developmental Cognitive Neuroscience Laboratory Northwestern University 2240 North Campus Drive Frances Searle Building, Room 2-356 Evanston, Illinois, 60208 phone: (847)467-1549 e-mail: hongchuan-zhang at northwestern.edu ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec problem?
There are two things you can do here. One is to create your own design matrix in a text file and pass it to mri_glmfit with the --X (instead of using an fsgd file). If you want to stay with the fsgd, then you can spec DODS (this will set up one regressor for MMSE instead of two). doug Martin Kavec wrote: Hi, I am trying to run a group analysis on cortical thickness between patients and controls. In the qdec.dat I set a MMSE for all the controls 0.0. Now, whenever I try to covariate thickness against age and MMSE, the qdec complains that there is no spectrum in MMSE values. I tried to set MMSE for one of controls to 0.1 and the analysis goes fine. After thinking for a while, I started to wonder whether I shouldn't calculate thickness difference first, but I am not finding the receipt on the web anymore. Thanks in advance, Martin ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation region export
They are in aseg.mgz, you can extract them into a nifti file with mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii 251 is the code for CC Posterior (found in $FREESURFER_HOME/FreeSurferColorLUT.txt) doug vin wrote: hi, I am trying to export segmented regions as NIFTI, and it works for the regions like Thalamus whole. But when freesurfer finished autorecon, than it showed lot of sub regions for example : Thalamic sub regions and also CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum) and...Mid anterior and Anterior. How I can get these sub regions. In which files they are stored, and How I can extract them as NIFTI format. any suggestion would be great !! thank you very much , vin ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
