Freesurfer October 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
61 discussions

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sub-cortical segmentation
by Durastanti, Valentina (NIH/NINDS) [F] 30 Oct '06

30 Oct '06

Hi, I'd like to know where I can find a detailed description of the sub-cortical segmentation stages thanks Valentina

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mri_annotation2label
by Dahlia Sharon 30 Oct '06

30 Oct '06

Hi, I have two annotations, ?h.aparc.annot and ?h.aparc.a2005s.annot, created by recon-all with the -cortparc and -cortparc2 command options. I would like to convert each of these to a set of labels. For aparc.a2005s.annot I run (hopefully this is correct): mri_annotation2label --subject subj04_bay2 --hemi rh --annotation aparc.a2005s --labelbase $SUBJECTS_DIR/subj04_bay2/label/aparc2005-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt But for aparc.annot I don't know what table file I should specify (there are two other files in the $FREESURFER_HOME folder that could potentially be correct: Simple_surface_labels200s.txt and surface_labels.txt). Could you tell me which table to use for aparc.annot? Thanks, Dahlia.

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average T1's before correcting for inhomogeneity?
by Stephen Towler 30 Oct '06

30 Oct '06

Greetings all, I'm new to freesurfer, so apologies if this has been covered. Two questions about early processing: 1) It looks like the recon-all script averages multiple T1's prior to correcting inhomogeneity. If processing T1's acquired on different days, and/or on different scanners, might it be advantageous to manually run mri_nu_correct.mni on each individually before averaging? Other than CPU time, why average first and then correct for inhomogeneity? 2) Is freesurfer's use of MNI_N3 over FSL's fast inhomogeneity correction algorithmic, empirical, historical, or other? Thanks! Stephen -- Stephen Towler stowler(a)mbi.ufl.edu 352-294-0048 office 352-258-6409 mobile 352-392-8347 fax Leonard Lab Department of Neuroscience PO Box 100244 University of Florida HSC Gainesville, FL 32610

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Head Points data files
by Juranek, Jenifer 30 Oct '06

30 Oct '06

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

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Slice Time Correction Error
by Dan Dillon 28 Oct '06

28 Oct '06

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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TIV estimation with FreeSurfer
by Joao Pereira 27 Oct '06

27 Oct '06

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

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Aseg inforrmation
by Ajith Kumar U 27 Oct '06

27 Oct '06

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. **************************************************

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tables for mri_annotation2label (fwd)
by Dahlia Sharon 26 Oct '06

26 Oct '06

In the same vein of mri_annotation2label: When I ran mri_annotation2label --subject subj25_bay2 --hemi rh --labelbase $SUBJECTS_DIR/subj25_bay2/label/aparc-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt (where $SUBJECTS_DIR is ~dahlia/structurals/) on mirabai in the nmr-std-env, 11 of 35 labels were created, and for the rest it said 'skipping' (e.g. the snippet below). How can I get all the labels to be created from the annotation file? Thanks! Dahlia. 0 0 --- skipping 1 0 --- skipping 2 0 --- skipping 3 0 --- skipping 4 0 --- skipping 5 0 --- skipping 6 2479 /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-006.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-006.label 7 0 --- skipping 8 6499 /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label 9 0 --- skipping 10 0 --- skipping ---------- Forwarded message ---------- Date: Thu, 26 Oct 2006 16:13:05 -0400 (EDT) From: Dahlia Sharon <dahlia(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Subject: tables for mri_annotation2label Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia.

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Total Cerebral Volume
by Anil Roy 26 Oct '06

26 Oct '06

Hello everyone, Can someone please point out where freesurfer outputs the total cerebral volume (white + gray). Thanks, Anil.

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tables for mri_annotation2label
by Dahlia Sharon 26 Oct '06

26 Oct '06

Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia.

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Freesurfer October 2006