[Freesurfer] eTIV in qdec
Dear FreeSurfer experts, my idea was to put the eTIV as a variable in qdec. I have put this in my qdec.table.dat and when I run qdec and choose eTIV as variable I get the following error and qdec closes some seconds later automatically: Creating output directory /Users/dolphinede/Desktop/Probanden/qdec/Untitled Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat Normalized matrix condition is 389.695 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.00 Found 148142 voxels in mask Saving mask to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/mask.mgh Reshaping mriglm-mask... search space = 73700.662359 DOF = 77 Starting fit and test Fit completed in 0.0607667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995148, ar1std=0.005328, gstd=5.802773, fwhm=13.664487 Writing results lh-Avg-Intercept-thickness maxvox sig=35.9893 F=546.618 at index 1515 0 0seed=1319335878 lh-Avg-thickness-eTIV-Cor maxvox sig=6.48644 F=31.2833 at index 51144 0 0seed=1319335878 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 eTIV 1.45233e+06 147517 Class Means of each Continuous Variable 1 Main 1452332.4051 MatrixMultiply: m1 is null! No such file or directory I have no idea what is wrong. Best regards Daniel Klein ___ 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] pial surface voxel shift
Hi After running several subjects (using trio siemens dicomfiles) with recon-all -all -nowmsa, we have observed an apparent shift of approximately one voxel to the left of the pial surface as compared to the brainmask.mgz in the TkMedit coronal view. This was observed in all of our subjects. Do you have any explanation for this - are there any corrections we need to do to avoid this? Thanks, Pernille ___ 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] MCSRCH ERROR
Hello All, While processing a brain image data(.mgz) through ver5.0.0, I got the following errors. I have no idea how to resolve them. I need outputs in stats directory, there are only lh.aparc.a2009s.stats, lh.aparc.stats, and lh.curv.stats. What caused them? How should I resolve them? IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10318.1 tol 0.10 . . . inflating to sphere (rms error 2.00) 000: dt: 0., rms radial error=175.699, avgs=0 005/300: dt: 0.9000, rms radial error=175.446, avgs=0 010/300: dt: 0.9000, rms radial error=174.904, avgs=0 015/300: dt: 0.9000, rms radial error=174.193, avgs=0 020/300: dt: 0.9000, rms radial error=173.383, avgs=0 025/300: dt: 0.9000, rms radial error=172.518, avgs=0 030/300: dt: 0.9000, rms radial error=171.620, avgs=0 035/300: dt: 0.9000, rms radial error=170.706, avgs=0 040/300: dt: 0.9000, rms radial error=169.784, avgs=0 045/300: dt: 0.9000, rms radial error=168.860, avgs=0 050/300: dt: 0.9000, rms radial error=167.935, avgs=0 055/300: dt: 0.9000, rms radial error=167.012, avgs=0 060/300: dt: 0.9000, rms radial error=166.092, avgs=0 065/300: dt: 0.9000, rms radial error=165.175, avgs=0 070/300: dt: 0.9000, rms radial error=164.262, avgs=0 075/300: dt: 0.9000, rms radial error=163.352, avgs=0 080/300: dt: 0.9000, rms radial error=162.447, avgs=0 085/300: dt: 0.9000, rms radial error=161.547, avgs=0 090/300: dt: 0.9000, rms radial error=160.651, avgs=0 095/300: dt: 0.9000, rms radial error=159.759, avgs=0 100/300: dt: 0.9000, rms radial error=158.871, avgs=0 105/300: dt: 0.9000, rms radial error=157.989, avgs=0 110/300: dt: 0.9000, rms radial error=157.110, avgs=0 115/300: dt: 0.9000, rms radial error=156.236, avgs=0 120/300: dt: 0.9000, rms radial error=155.367, avgs=0 125/300: dt: 0.9000, rms radial error=154.502, avgs=0 130/300: dt: 0.9000, rms radial error=153.642, avgs=0 135/300: dt: 0.9000, rms radial error=152.786, avgs=0 140/300: dt: 0.9000, rms radial error=151.934, avgs=0 145/300: dt: 0.9000, rms radial error=151.087, avgs=0 150/300: dt: 0.9000, rms radial error=150.245, avgs=0 155/300: dt: 0.9000, rms radial error=149.407, avgs=0 160/300: dt: 0.9000, rms radial error=148.573, avgs=0 165/300: dt: 0.9000, rms radial error=147.744, avgs=0 170/300: dt: 0.9000, rms radial error=146.919, avgs=0 175/300: dt: 0.9000, rms radial error=146.098, avgs=0 180/300: dt: 0.9000, rms radial error=145.282, avgs=0 185/300: dt: 0.9000, rms radial error=144.470, avgs=0 190/300: dt: 0.9000, rms radial error=143.663, avgs=0 195/300: dt: 0.9000, rms radial error=142.860, avgs=0 200/300: dt: 0.9000, rms radial error=142.061, avgs=0 205/300: dt: 0.9000, rms radial error=141.266, avgs=0 210/300: dt: 0.9000, rms radial error=140.476, avgs=0 215/300: dt: 0.9000, rms radial error=139.693, avgs=0 220/300: dt: 0.9000, rms radial error=138.914, avgs=0 225/300: dt: 0.9000, rms radial error=138.140, avgs=0 230/300: dt: 0.9000, rms radial error=137.370, avgs=0 235/300: dt: 0.9000, rms radial error=136.604, avgs=0 240/300: dt: 0.9000, rms radial error=135.842, avgs=0 245/300: dt: 0.9000, rms radial error=135.085, avgs=0 250/300: dt: 0.9000, rms radial error=134.332, avgs=0 255/300: dt: 0.9000, rms radial error=133.583, avgs=0 260/300: dt: 0.9000, rms radial error=132.838, avgs=0 265/300: dt: 0.9000, rms radial error=132.098, avgs=0 270/300: dt: 0.9000, rms radial error=131.362, avgs=0 275/300: dt: 0.9000, rms radial error=130.629, avgs=0 280/300: dt: 0.9000, rms radial error=129.901, avgs=0 285/300: dt: 0.9000, rms radial error=129.177, avgs=0 290/300: dt: 0.9000, rms radial error=128.456, avgs=0 295/300: dt: 0.9000, rms radial error=127.740, avgs=0 300/300: dt: 0.9000, rms radial error=127.028, avgs=0 spherical inflation complete. . . . epoch 4 (K=1280.0), pass 1, starting sse = 541.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.32/19 = 0.01710 finalwriting spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %10.00 . . . pass 1: epoch 1 of 3 starting distance error %21.36 pass 1: epoch 2 of 3 starting distance error %21.04 unfolding complete - removing small folds... starting distance error %20.80 removing remaining folds... final distance error %20.81 364: 0 negative triangles . . . Thanks, Kenichiro Tanaka. ___ 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
Re: [Freesurfer] MCSRCH ERROR
Are you sure they are errors? We see this mysterious message sometimes, but I don't think it is really an error, and usually things are fine cheers Bruce On Tue, 18 Oct 2011, Kenichiro Tanaka wrote: Hello All, While processing a brain image data(.mgz) through ver5.0.0, I got the following errors. I have no idea how to resolve them. I need outputs in stats directory, there are only lh.aparc.a2009s.stats, lh.aparc.stats, and lh.curv.stats. What caused them? How should I resolve them? IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10318.1 tol 0.10 . . . inflating to sphere (rms error 2.00) 000: dt: 0., rms radial error=175.699, avgs=0 005/300: dt: 0.9000, rms radial error=175.446, avgs=0 010/300: dt: 0.9000, rms radial error=174.904, avgs=0 015/300: dt: 0.9000, rms radial error=174.193, avgs=0 020/300: dt: 0.9000, rms radial error=173.383, avgs=0 025/300: dt: 0.9000, rms radial error=172.518, avgs=0 030/300: dt: 0.9000, rms radial error=171.620, avgs=0 035/300: dt: 0.9000, rms radial error=170.706, avgs=0 040/300: dt: 0.9000, rms radial error=169.784, avgs=0 045/300: dt: 0.9000, rms radial error=168.860, avgs=0 050/300: dt: 0.9000, rms radial error=167.935, avgs=0 055/300: dt: 0.9000, rms radial error=167.012, avgs=0 060/300: dt: 0.9000, rms radial error=166.092, avgs=0 065/300: dt: 0.9000, rms radial error=165.175, avgs=0 070/300: dt: 0.9000, rms radial error=164.262, avgs=0 075/300: dt: 0.9000, rms radial error=163.352, avgs=0 080/300: dt: 0.9000, rms radial error=162.447, avgs=0 085/300: dt: 0.9000, rms radial error=161.547, avgs=0 090/300: dt: 0.9000, rms radial error=160.651, avgs=0 095/300: dt: 0.9000, rms radial error=159.759, avgs=0 100/300: dt: 0.9000, rms radial error=158.871, avgs=0 105/300: dt: 0.9000, rms radial error=157.989, avgs=0 110/300: dt: 0.9000, rms radial error=157.110, avgs=0 115/300: dt: 0.9000, rms radial error=156.236, avgs=0 120/300: dt: 0.9000, rms radial error=155.367, avgs=0 125/300: dt: 0.9000, rms radial error=154.502, avgs=0 130/300: dt: 0.9000, rms radial error=153.642, avgs=0 135/300: dt: 0.9000, rms radial error=152.786, avgs=0 140/300: dt: 0.9000, rms radial error=151.934, avgs=0 145/300: dt: 0.9000, rms radial error=151.087, avgs=0 150/300: dt: 0.9000, rms radial error=150.245, avgs=0 155/300: dt: 0.9000, rms radial error=149.407, avgs=0 160/300: dt: 0.9000, rms radial error=148.573, avgs=0 165/300: dt: 0.9000, rms radial error=147.744, avgs=0 170/300: dt: 0.9000, rms radial error=146.919, avgs=0 175/300: dt: 0.9000, rms radial error=146.098, avgs=0 180/300: dt: 0.9000, rms radial error=145.282, avgs=0 185/300: dt: 0.9000, rms radial error=144.470, avgs=0 190/300: dt: 0.9000, rms radial error=143.663, avgs=0 195/300: dt: 0.9000, rms radial error=142.860, avgs=0 200/300: dt: 0.9000, rms radial error=142.061, avgs=0 205/300: dt: 0.9000, rms radial error=141.266, avgs=0 210/300: dt: 0.9000, rms radial error=140.476, avgs=0 215/300: dt: 0.9000, rms radial error=139.693, avgs=0 220/300: dt: 0.9000, rms radial error=138.914, avgs=0 225/300: dt: 0.9000, rms radial error=138.140, avgs=0 230/300: dt: 0.9000, rms radial error=137.370, avgs=0 235/300: dt: 0.9000, rms radial error=136.604, avgs=0 240/300: dt: 0.9000, rms radial error=135.842, avgs=0 245/300: dt: 0.9000, rms radial error=135.085, avgs=0 250/300: dt: 0.9000, rms radial error=134.332, avgs=0 255/300: dt: 0.9000, rms radial error=133.583, avgs=0 260/300: dt: 0.9000, rms radial error=132.838, avgs=0 265/300: dt: 0.9000, rms radial error=132.098, avgs=0 270/300: dt: 0.9000, rms radial error=131.362, avgs=0 275/300: dt: 0.9000, rms radial error=130.629, avgs=0 280/300: dt: 0.9000, rms radial error=129.901, avgs=0 285/300: dt: 0.9000, rms radial error=129.177, avgs=0 290/300: dt: 0.9000, rms radial error=128.456, avgs=0 295/300: dt: 0.9000, rms radial error=127.740, avgs=0 300/300: dt: 0.9000, rms radial error=127.028, avgs=0 spherical inflation complete. . . . epoch 4 (K=1280.0), pass 1, starting sse = 541.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.32/19 = 0.01710 finalwriting spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %10.00 . . . pass 1: epoch 1 of 3 starting distance error %21.36 pass 1: epoch 2 of 3 starting distance error %21.04 unfolding complete - removing small folds... starting distance error %20.80 removing remaining folds... final distance error %20.81 364: 0 negative triangles . . . Thanks, Kenichiro Tanaka. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pial surface voxel shift
eek, no, we definitely don't see this. Can you upload the subject? Bruce On Tue, 18 Oct 2011, Pernille Iversen wrote: Hi After running several subjects (using trio siemens dicomfiles) with recon-all -all -nowmsa, we have observed an apparent shift of approximately one voxel to the left of the pial surface as compared to the brainmask.mgz in the TkMedit coronal view. This was observed in all of our subjects. Do you have any explanation for this - are there any corrections we need to do to avoid this? Thanks, Pernille ___ 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] mri_ca_register error
Hello , I am running recon-all with -cm switch and getting following error. Is there any workaround? Without -cm switch , recon-all completes all the processing just fine. Thank you. Hiroyuki mri_ca_register -invert-and-save transforms/talairach.m3z mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ 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] coregistration - FA to Freesurfer
Thanks Doug! It worked! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat. doug Joana Braga Pereira wrote: Hi Doug, Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects? Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug Joana Braga Pereira wrote: Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.**harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-request@**nmr.mgh.harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu
Re: [Freesurfer] mri_ca_register error
can you check to make sure that the partition is not full? If you have space, upload the dataset and we'll take a look cheers Bruce On Tue, 18 Oct 2011, Oya, Hiroyuki (UI Health Care) wrote: Hello , I am running recon-all with ?cm switch and getting following error. Is there any workaround? Without ?cm switch , recon-all completes all the processing just fine. Thank you. Hiroyuki mri_ca_register -invert-and-save transforms/talairach.m3z mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 ___ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ ___ 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] reg-feat2anat failure
The registration that should be used for all of these is anat2exf.register.dat found in feat/reg/freesurfer. Can you verify that that was the one that you manually changed? Look at the time stamp as compared to the other files in that folder. doug Michelle Umali wrote: Hi Doug, I am using reg-feat2anat on the feat directory of each run. reg-feat2anat --feat feadir.feat --subject XX Then I checked and adjusted the registration with: reg-feat2anat --feat featdir.feat --manual Next I checked and adjusted the registration to the standard with: reg-feat2anat --feat featdir.feat --manxfm func2std To generate cortical binary masks I used: aparc2feat --feat featdir.feat --annot BA fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz To generate subcortical binary masks I did: aseg2feat --feat featdir.feat --aseg aparc+aseg fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz When I looked at the masks in FSLview and checked the masks against the other atlases, everything was off even after painstakingly editing the registrations. Is there something I am doing wrong? Thanks. Michelle On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: How are you generating the masks? doug Michelle Umali wrote: Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Surface area measure
When I extract surface area data using the following commands, which measure of surface area am I getting, the pial surface, the WM surface, or the total of both combined? aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area --tablefile aparc_stats_rh.txt Thanks! Krista ___ 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] QDec questions
krista kelly wrote: Hi, just wondering if anyone has any advice on the following questions: I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) Unfortunately, you cannot use QDEC if you have three groups. You'll have to create an FSGD file and contrasts by hand, then run mri_glmfit. Do a search for FSGD on our wiki and go to the examples page. I think there is an example there for what you want to do. 2) If I use DODS, should I demean the ages if age is a nuisance variable? You should actually test whether there is an interaction between age and your group contrast of interest (using the DODS model). If there is not interaction, then switch to a DOSS where demeaning does not matter. 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? It depends on how you do the extraction. If you are using mris_anatomical_stats on each individual's unsmoothed data, then it will reflect the unsmoothed. doug Thanks! Krista ___ 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] Surface area measure
The white surface. doug krista kelly wrote: When I extract surface area data using the following commands, which measure of surface area am I getting, the pial surface, the WM surface, or the total of both combined? aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area --tablefile aparc_stats_rh.txt Thanks! Krista || ___ 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] label transformation to MNI space
The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] eTIV in qdec
i'm not able to replicate this error you are seeing. to attempt to replicate, i used the 40 subjects included in our tutorial, loaded into qdec, then clicked 'Generate Stats Data Tables', then selected 'aseg.volume' in Stats Data Import, then selected IntraCorticalVol (which is eTIV) and 'add selections to Data Table', then selected IntraCorticalVol as the continuous covariate in the design tab. the analysis completed successfully. which version of freesurfer are you using? n. On Tue, 2011-10-18 at 04:27 -0400, dolphin...@aol.com wrote: Dear FreeSurfer experts, my idea was to put the eTIV as a variable in qdec. I have put this in my qdec.table.dat and when I run qdec and choose eTIV as variable I get the following error and qdec closes some seconds later automatically: Creating output directory /Users/dolphinede/Desktop/Probanden/qdec/Untitled Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat Normalized matrix condition is 389.695 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.00 Found 148142 voxels in mask Saving mask to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/mask.mgh Reshaping mriglm-mask... search space = 73700.662359 DOF = 77 Starting fit and test Fit completed in 0.0607667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995148, ar1std=0.005328, gstd=5.802773, fwhm=13.664487 Writing results lh-Avg-Intercept-thickness maxvox sig=35.9893 F=546.618 at index 1515 0 0 seed=1319335878 lh-Avg-thickness-eTIV-Cor maxvox sig=6.48644 F=31.2833 at index 51144 0 0 seed=1319335878 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 eTIV 1.45233e+06 147517 Class Means of each Continuous Variable 1 Main 1452332.4051 MatrixMultiply: m1 is null! No such file or directory I have no idea what is wrong. Best regards Daniel Klein ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] label transformation to MNI space
Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely off target. It seems to be shift downward, towards inferior, and therefore sometimes outside the skull. Any other ideas? Linda The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Linda Douw, PhD. ___ 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] QDec questions
Sorry, I meant to say that you cannot use QDEC with more than 2 discrete variables (you have 3). You do not need to extract data from the smoothed thickness files, but the results you get from your ROI analysis may then differ a bit from that you get from the QDEC analysis. doug krista kelly wrote: Thanks Doug! Just a few more things: I only have two groups, so my contrast was wrong. Should it only be 1 -1, even if I have other variables I want to control for? Or should I have a contrast file for each discrete variable? How would I extract the smoothed data using mri_anatomical_stats? I realize the importance of smoothing data while doing a vertex-by-vertex analysis in QDec, but if I'm doing an ROI analysis by extracting the average thickness in a certain label (i.e. v1), is it necessary to do the stats on the smoothed data from each participant? Thanks! On Tue, Oct 18, 2011 at 2:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: krista kelly wrote: Hi, just wondering if anyone has any advice on the following questions: I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) Unfortunately, you cannot use QDEC if you have three groups. You'll have to create an FSGD file and contrasts by hand, then run mri_glmfit. Do a search for FSGD on our wiki and go to the examples page. I think there is an example there for what you want to do. 2) If I use DODS, should I demean the ages if age is a nuisance variable? You should actually test whether there is an interaction between age and your group contrast of interest (using the DODS model). If there is not interaction, then switch to a DOSS where demeaning does not matter. 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? It depends on how you do the extraction. If you are using mris_anatomical_stats on each individual's unsmoothed data, then it will reflect the unsmoothed. doug Thanks! Krista ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center 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
Re: [Freesurfer] Surface area measure
I don't know if that has ever been explored. doug krista kelly wrote: Great! Do you know if it is better to use one surface area (i.e. WM or pial) over the other when investigating differences between groups? On Tue, Oct 18, 2011 at 2:24 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The white surface. doug krista kelly wrote: When I extract surface area data using the following commands, which measure of surface area am I getting, the pial surface, the WM surface, or the total of both combined? aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area --tablefile aparc_stats_rh.txt Thanks! Krista || ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center 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] label transformation to MNI space
The problem appears to be with the label itself. Try this conversion: mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod surface --trglabel lh.entorhinal.new.label --hemi lh Also, you might want to use the entorhinal label define in the aparc+aseg since it fills in the ribbon: mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt doug Linda Douw wrote: Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely off target. It seems to be shift downward, towards inferior, and therefore sometimes outside the skull. Any other ideas? Linda The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] QDec questions
Yes, see the answer to your first question below. doug krista kelly wrote: Am I able to do vertex-by-vertex analyses using freesurfer if I have more than 2 discrete variables? If so, how? Is it also ok to use the unsmoothed data when doing surface area label analyses? Thanks! On Tue, Oct 18, 2011 at 3:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, I meant to say that you cannot use QDEC with more than 2 discrete variables (you have 3). You do not need to extract data from the smoothed thickness files, but the results you get from your ROI analysis may then differ a bit from that you get from the QDEC analysis. doug krista kelly wrote: Thanks Doug! Just a few more things: I only have two groups, so my contrast was wrong. Should it only be 1 -1, even if I have other variables I want to control for? Or should I have a contrast file for each discrete variable? How would I extract the smoothed data using mri_anatomical_stats? I realize the importance of smoothing data while doing a vertex-by-vertex analysis in QDec, but if I'm doing an ROI analysis by extracting the average thickness in a certain label (i.e. v1), is it necessary to do the stats on the smoothed data from each participant? Thanks! On Tue, Oct 18, 2011 at 2:23 PM, 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: krista kelly wrote: Hi, just wondering if anyone has any advice on the following questions: I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) Unfortunately, you cannot use QDEC if you have three groups. You'll have to create an FSGD file and contrasts by hand, then run mri_glmfit. Do a search for FSGD on our wiki and go to the examples page. I think there is an example there for what you want to do. 2) If I use DODS, should I demean the ages if age is a nuisance variable? You should actually test whether there is an interaction between age and your group contrast of interest (using the DODS model). If there is not interaction, then switch to a DOSS where demeaning does not matter. 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? It depends on how you do the extraction. If you are using mris_anatomical_stats on each individual's unsmoothed data, then it will reflect the unsmoothed. doug Thanks! Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.
Re: [Freesurfer] label transformation to MNI space
This fixed the problem, thanks! The problem appears to be with the label itself. Try this conversion: mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod surface --trglabel lh.entorhinal.new.label --hemi lh Also, you might want to use the entorhinal label define in the aparc+aseg since it fills in the ribbon: mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt doug Linda Douw wrote: Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely off target. It seems to be shift downward, towards inferior, and therefore sometimes outside the skull. Any other ideas? Linda The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Linda Douw, PhD. ___ 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 Average of Retinotopy Results
Hi Doug and the Freesurfers, Thanks for your help. I have 2 questions.: 1) I did the retinotopy analysis on the fsaverage surface as you suggested below and then ran isxconcat-sess for my eccen and polar data: e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf sessid -o group_polar_lh but how do you do this for the fieldsign analysis, since the cess.nii and other files don't exist? 2) So when trying to run a group mri_glmfit on the polar and eccen maps with: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir group_eccen_lh.wls --nii.gz I got an error, because I have two ces.nii.gz and cesvar.nii.gz files each. I am not sure how this happened. I only have one run each of polar and wedge data. What may have generated these two files and which one do I use? Thanks. Michelle On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: When you run preproc-sess use -surface fsaverage lhrh instead of -surface self lhrh. Then create a new analysis with the same parameters, except use -surface fsaverage lh instead of -surface self lh. doug Michelle Umali wrote: Hi Doug, I'm a little confused as to how to assign functional data to the fsaverage space. 1) Do you mean just change each subject's subjectname file to fsaverage and then do the same thing as before for each person? 2) Also, when I specify the analysis do I change -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name? e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force then the same for selxavg3-sess and fieldsign-sess and then isxconcat-sess would be: isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh Thanks. Michelle On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: If you want to combine across subjects, then you need to run the analysis on fsaverage (ie, rerun preproc-sess, create a new analysis, run selxavg3-sess, and then isxconcat-sess). doug Michelle Umali wrote: Dear Freesurfers, I've generated individual polar, eccentricity, and fieldsign maps for each of my subjects. I would like to generate group average maps of these that I can visualize on the fsaverage brain. When I ran: isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh I got: ERROR: analysis space is self surface, not supported How do I do a group average for the 3 different maps? Thanks. Michelle For each person I ran recon-all and flattened occipital patches. Then: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sjXX -force selxavg3-sess -a rtopy.self.rh -s sjXX -force fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to
