[Freesurfer] TIV estimation with FreeSurfer
Dear all, I am posting the questions I made to Bruce without going through the list along with his reply. **I would still like to be sure about question 1)***, as it is central to my conclusions. If anyone has any other ideas, please let me know. >There are still a couple of questions in my mind I would really like to > understand concerning this TIV estimation though: > 1) I first run FS without any visual inspection (-autorecon1 and 2) to get > the TIV estimate in the aseg.stats file. I then compared those values to the > ones obtained *after* adjusting the affine transf (in some cases using the > brain.mgz file, others manually) and the values changed. But is this the > correct procedure to adjust the TIV output, or am I looking at an artifact? > 2) Is it possible for me to build my own template for TIV estimation > purposes? If yes, which file should be replaced? > Thank you again for your help (btw, is there any chance I can obtain the > eTIV value without running -autorecon1 and 2 all the way?) Reply: >(1) We have very little experience with the eTIV, but I guess >the answer is yes, that would be the way to do it, and (2) the only way to >build your own atlas would be to use the aseg.mgz from a bunch of subjects >and mris_ca_train. Although 2) is possible in a practical way (ie, I can build my own atlas), I don't believe it would be valid for TIV estimation with FS, due to the bootstrap method you used to calculate the "scale factor". Am I right? Finally, could someone please explain me the point of trying to adjust the talairach output by using the T1.mgz and brain.mgz files? I know this works, but I don't understand why, especially with the brain.mgz: the reference atlas has skull... shouldn't using a skull stripped scan confound the process? Thank you all. Hope to hear from you soon. Joao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Head Points data files
Hi, What are the file format requirements for the 2 files called to load head points - *.hpts and *.trans into tkmedit or tksurfer? We have a whole-head neuromagnetometer (4-D Neuroimaging 3600 Magnes MEG system) with 248 sensor channels. I’d like to co-register my dipole locations with FreeSurfer’s aseg+aparc.mgz to efficiently localize dipoles x ROIs. I have already co-registered index points and headshape files to each subject’s aMRI within 4D’s software. Any advice is greatly appreciated! Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD Assistant Professor University of Texas MEG Lab 1333 Moursund St, Ste H114 Houston, TX 77030 Phone: 713.797.7574 Fax: 713.797.7590 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Aseg inforrmation
Hi Freesurfers, I have some questions about the aseg.stats file. What do the brainmask and brain segmentation volumes refer to? Is there a helpfile that defines these. Thanks Aju. ** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Aseg inforrmation
Hi Aju, The BrainMaskVOl in the aseg.stats file uses all of the voxels that are in the brainmask.mgz volume. the BrainSegVol uses all of the voxels that are labeled in the aseg.mgz segmentation. Jenni On Fri, 27 Oct 2006, Ajith Kumar U wrote: Hi Freesurfers, I have some questions about the aseg.stats file. What do the brainmask and brain segmentation volumes refer to? Is there a helpfile that defines these. Thanks Aju. ** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TIV estimation with FreeSurfer
yes, I agree that a new atlas might need a different scaling. And I also agree that the talairach_with_skull.lta should be adjusted relative to a volume with a skull on it, otherwise the eTIV wouldn't be right if there's atrophy. On Fri, 27 Oct 2006, Joao Pereira wrote: Dear all, I am posting the questions I made to Bruce without going through the list along with his reply. **I would still like to be sure about question 1)***, as it is central to my conclusions. If anyone has any other ideas, please let me know. There are still a couple of questions in my mind I would really like to understand concerning this TIV estimation though: 1) I first run FS without any visual inspection (-autorecon1 and 2) to get the TIV estimate in the aseg.stats file. I then compared those values to the ones obtained *after* adjusting the affine transf (in some cases using the brain.mgz file, others manually) and the values changed. But is this the correct procedure to adjust the TIV output, or am I looking at an artifact? 2) Is it possible for me to build my own template for TIV estimation purposes? If yes, which file should be replaced? Thank you again for your help (btw, is there any chance I can obtain the eTIV value without running -autorecon1 and 2 all the way?) Reply: (1) We have very little experience with the eTIV, but I guess the answer is yes, that would be the way to do it, and (2) the only way to build your own atlas would be to use the aseg.mgz from a bunch of subjects and mris_ca_train. Although 2) is possible in a practical way (ie, I can build my own atlas), I don't believe it would be valid for TIV estimation with FS, due to the bootstrap method you used to calculate the "scale factor". Am I right? Finally, could someone please explain me the point of trying to adjust the talairach output by using the T1.mgz and brain.mgz files? I know this works, but I don't understand why, especially with the brain.mgz: the reference atlas has skull... shouldn't using a skull stripped scan confound the process? Thank you all. Hope to hear from you soon. Joao ___ 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] Slice Time Correction Error
Hi all,
We are trying to implement a slice-time correction ('stc-sess -i fmc -o
fmcstc -so siemens -s FPPREW01 -d .') but we get the following error...
INFO: set hdr.hist.orient to -1 /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional
slicetimer -i
/net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/FPPREW01/bold/013/tmp.10997/in.img
-o /net/tucson/Raid/shart slicetimer:
/usr/lib/libstdc++.so.5: version `GLIBCPP_3.2.2' not found (required by slicetimer)
Is there a simple way to address this issue? Thanks, Dan Dillon
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