I looked at the surface mask and it seems those 0-valued vertices are 0-valued in the mask as well (image attached). Is there a way to correct this? To reiterate we have already tried revising the registration.
Thanks again for your help!
Cesar
On Tue, May 6, 2014 at 2:41 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Is the cortex label 0 in the same locations where you have 0s in the surface mask?
On 05/06/2014 12:07 PM, Cesar Echavarria wrote:
Hi Doug,
Me and Shahin have looked at the registration and it looks fine. I know the activation is 0 because when I click on those vertices it tells me the tksconcat.nii value is "**0.000000**". I looked at the cortex.label file and found the 0-valued vertices within the file. We have scanned the same subject for different experiments but it is only for this session that we find the problem. Let me know if there's anything else we can check.
Thanks! Cesar
On Mon, May 5, 2014 at 6:04 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Have you checked the registration? If so, are you sure that the activation is exactly 0? Also, look at cortex.label to check whether somehow those vertices were not labeled. On 05/05/2014 04:08 PM, Cesar Echavarria wrote: I used the command below to check the brain mask relative to the subject's anatomy: tkmedit myla_anat orig.mgz -over Subjects/myla/bold/masks/brain.nii.gz The mask looked fine in that no portion of the brain appeared to lie outside the mask. Cesar On Mon, May 5, 2014 at 3:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: It could be that the brain mask is too aggressive. Try looking at Subjects/myla/bold/RRR/masks/brain.nii.gz doug On 05/05/2014 03:17 PM, Cesar Echavarria wrote: Hi Bruce, After unpacking the data, I simply run the selxavg command below and allow it to do the automatic pre-processing. selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh The analysis was generated with the following command: mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface fsaverage rh -fwhm 5 -paradigm LOC.par -event-related -polyfit 1 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 2 -refeventdur 16 -per-run -force -fsd bold After fixing up the registration I saved the registration file under :Subjects/myla/bold/014/register.dof6.dat" and ran bbregister for all the runs within the subject folder as below. bbregister --mov Subjects/myla/bold/015/f.nii --reg Subjects/myla/bold/015/register.dof6.dat --init-reg Subjects/myla/bold/014/register.dof6.dat --bold I then ran the selxavg3-sess again. Let me know if you need any more information to help. Thanks! Cesar On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: Hi Cesar what command lines did you run to register and sample? Bruce On Mon, 5 May 2014, Cesar Echavarria wrote: Hello freesurfer experts, The functional overlay for one of our subjects looks like the image attached. You'll notice the "holes" on the overlay that have a value of 0. I'm trying to get ride of these as I expect (as with other subjects) to have values for these vertices that are not 0. Myself and a colleague have tried improving the registration as much as we see possible, but the problem remains. Any tips on how to correct this issue would be greatly appreciated. Thanks in advance for your help! [cleardot.gif] Cesar Echavarria Research AssistantMartinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012 _______________________________________________ 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>> <mailto: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 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 sentto you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/