[Freesurfer] Fwd: advise on generating individual standard deviation map
Hi Doug, I think I solved the registration issue. This is my command: mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval bert/surf/lh_av.thickness --trg_type curv Any objections? Thanks, Michael Begin forwarded message: From: Michael Scheel scheelmich...@googlemail.com Date: 10. Juni 2010 22:45:10 MESZ To: Doug Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] advise on generating individual standard deviation map Hi Doug, thanks for you reply. That is exactly what I want to do so many thanks for explaining that. However I have problems with the usage of mri_surf2surf michael$ mri_surf2surf --srcsubject bert --srcsurfval bert/surf/lh.thickness --trgsubject fsaverage --trgsurfval bert/surf/lh.thickness_average --hemi lh ERROR: could not determine type of bert/surf/lh.thickness_average Also when I run the example from the FS wiki site i get the following error (see below). Any idea what I'm doing wrong here? Thanks, Michael michael$ mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --trgsurfval bert-thickness-lh.img --trg_type analyze4d srcsubject = bert srcval = thickness srctype= curv trgsubject = ico trgval = bert-thickness-lh.img trgtype= analyze4d srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.sphere.reg Loading source data Reading curvature file /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.thickness Reading icosahedron /Applications/MriSoftware/freesurfer/lib/bem/ic7.tri Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (131122) Reverse Loop had 21908 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 146869, nTrgMulti = 16973, MnTrgMultiHits = 2.29076 nSrc121 = 89131, nSrcLost = 0, nSrcMulti = 41991, MnSrcMultiHits = 2.30095 Saving target data ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 On 10.06.2010, at 12:05, Doug Greve wrote: 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ERROR Could not determine file type during mri_vol2surf AND opening a talairach.xfm in tkmedit
Quick update: Removing the # character from the filename cleared up Problem Number 1. Duh! On 6/11/10 8:39 AM, Annelise Dickinson dickins...@mail.nih.gov wrote: Hi Sita, Thank you for your reply!! I was wondering if that # character in the movable file name could be creating any problems; I will definitely try it without and keep you updated! As for the second issue, I was trying to view Subject D10's talairach transformed brain in tkmedit. I followed the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to do so. My command line to open tkmedit was as follows: tkmedit D10 brainmask.mgz When the tkmedit GUI opened with the brainmask.mgz as the main volume, I went to File--Transforms--Load as Main volume and clicked OK At this point, a dialog box popped up with the error couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm and the transform did not open. ***HOWEVER the really strange thing is that I had done the exact same order of operations about five minutes earlier to open and view the same subject's talairach transformed volume and everything worked perfectly. I then closed tkmedit and when I tried it again five minutes later the above occurred.*** I know that temporal proximity and similar error messages do not necessarily mean that the two problems are related, but since they are both happening in the same subject's data, it got me wondering. Please let me know if you have any insights! Thanks so much again! -Elise From: Sita Kakunoori [s...@nmr.mgh.harvard.edu] Sent: Thursday, June 10, 2010 5:14 PM To: Dickinson, Annelise (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR Could not determine file type during mri_vol2surf AND opening a talairach.xfm in tkmedit Hi Elise, can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without the special character # and rerun mri_vol2surf. And regarding your second question, what was your command line. Were you trying to apply the transform talairach.xfm to a volume opened in tkmedit. Sita. On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: Hi all, Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error: mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file): mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm Has anyone seen such an error before and/or know how to fix it? Please let me know! Thank you!!! -Elise * 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer * 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
Re: [Freesurfer] ERROR Could not determine file type during mri_vol2surf AND opening a talairach.xfm in tkmedit
Hi Elise, After loading brainmask.mgz in tkmedit, apply the transform as 'File - Transforms - Load Transform for Main Volume' and select talairach.xfm. Sita. On Fri, 11 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: Hi Sita, Thank you for your reply!! I was wondering if that # character in the movable file name could be creating any problems; I will definitely try it without and keep you updated! As for the second issue, I was trying to view Subject D10's talairach transformed brain in tkmedit. I followed the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to do so. My command line to open tkmedit was as follows: tkmedit D10 brainmask.mgz When the tkmedit GUI opened with the brainmask.mgz as the main volume, I went to File--Transforms--Load as Main volume and clicked OK At this point, a dialog box popped up with the error couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm and the transform did not open. ***HOWEVER the really strange thing is that I had done the exact same order of operations about five minutes earlier to open and view the same subject's talairach transformed volume and everything worked perfectly. I then closed tkmedit and when I tried it again five minutes later the above occurred.*** I know that temporal proximity and similar error messages do not necessarily mean that the two problems are related, but since they are both happening in the same subject's data, it got me wondering. Please let me know if you have any insights! Thanks so much again! -Elise From: Sita Kakunoori [s...@nmr.mgh.harvard.edu] Sent: Thursday, June 10, 2010 5:14 PM To: Dickinson, Annelise (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR Could not determine file type during mri_vol2surf AND opening a talairach.xfm in tkmedit Hi Elise, can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without the special character # and rerun mri_vol2surf. And regarding your second question, what was your command line. Were you trying to apply the transform talairach.xfm to a volume opened in tkmedit. Sita. On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: Hi all, Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error: mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file): mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm Has anyone seen such an error before and/or know how to fix it? Please let me know! Thank you!!! -Elise * 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] are paired compairisons possible using QDEC
Hi, I have a group of siblings (one disorder, one unaffected). Is it possible for me to set up the group analysis in a way so that siblings are compared to their sibling, something analogous to a paired t-test, and if so do you have a tutorial or example to which you could direct me. Thank you, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] CT registration
Does FreeSurfer (or FSL) have any commands that support CT registration? -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how the -nonuintensitycor flag work?
Hi, there, I wan to use the -nonuintensitycor option of the recon-all command, my command line is: recon-all -s subjid -all -nonuintensitycor, But the process failed because in the following step, they can not find nu.mgz, so I need to create my own nu.mgz before running my recon-all command, is it correct? Thanks! Guang _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1___ 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.
