Freesurfer

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30070 discussions

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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Templates in Freesurfer
by Juergen Haenggi 24 Oct '06

24 Oct '06

Dear Freesurfer users we use Freesurfer for analyzing patients with different dementias. Because the brains are very atrophic we deliberate whether the implemented templates (MNI 305) are OK for an analysis of atrophic brains with Freesurfer. Any suggestion? Thanks in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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TIV estimation using FreeSurfer
by Joao Pereira 24 Oct '06

24 Oct '06

Dear all, I have been trying to use the eTIV value FS outputs after the -autorecon1 and -autorecon2 stages, registering it in the aseg.stats file. The purpose would be to see how reliable that value is when compared to our own manual measurements. When reading the Buckner paper, I have noticed that a stringent requirement for optimal perfomance is the usage of an adequate template (i.e., age matched template), and I believe FS uses the MNI 305 template (at least in 2006 versions), which is not adequate for our population. My questions are: 1) Is it possible to build our own template and then introducing it in the FS package? If so, where? (please notice that I am not interested in surface templates) 2) If 1) is possible, is the TIV estimation hindered by such a procedure? I know you have adjusted the calculation of the eTIV using bootstrap, which means that you don't use a pure version of the atlas scale factor (ASF), but you scale it by a fixed number you've obtained with this adjustment. My guess is that this estimate will no longer be valid. 3) I have adjusted the initial transform outputs by using mri_total, T1.mgz, brain.mgz and, in some cases manual adjustments. This affected talairach.xfm. Is this the adequate approach for TIV estimation purposes? I remember reading something about talairach_with_skull.lta... Thank you very much for your patience and assistance! Regards, Joao Pereira

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Percent signal change: what stats to read
by raij＠nmr.mgh.harvard.edu 22 Oct '06

22 Oct '06

Hi, We have calculated a FIR group analysis with FS-FAST and have the corresponding ces, cesvar, f, fsig, iminsig, minsig, sig, and t maps in the contrast folders. Which one of these should I use for presenting % signal change? We want to do some further analyses of the group analysis results with matlab and would need to use % signal change as the input values for those analyses. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Freesurfer crash
by Wolf, Ingo 22 Oct '06

22 Oct '06

Hi everyone. I habe a rather obscure problem. After loading a volume with tkmedit, I tried to open the file menu via the file button in the menu bar and instanly freesurfer crashes. The software is installed on a Apple PowerMac OSX 10.4.6, Dual G5 2.5 GHz, Memory 2.5 GB. I wonder if this is a hardware problem? Thanks Ingo

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Re: [Freesurfer] posting a question again
by Joongnam Yang 20 Oct '06

20 Oct '06

Thanks, Doug, I never used mri_surf2surf, the latest version I downloaded. Would you be more specific on how to convert avg_thickness to the average subject? (I tried mri_surf2surf --srcsubject SUBJECT --tfmt avg_thickness, but it's asking a whole lot more variables...) Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/20/06 12:34 PM >>> Does it work if you don't use projfrac? We have a bug in the make_average_subject code that causes the average thickness (lh.avg_thickness) to be painted on the last subject in the list instead of the averaage subject. One work-around until we get this fixed is to convert the avg_thickness to the average subject with mri_surf2surf. This will require a new version of surf2surf, which you can get from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf Run it with --tfmt curv doug Joongnam Yang wrote: >Dear all, > >I've been waiting for an answer to the following question. > >I am trying to overlay group-averaged data (FSL) on an averaged anatomical >brain (Freesurfer). >I did the following, > >mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze >--srcreg register.dat --hemi lh --projfrac 0.5 --out >AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint > >and got the following error message, > >MRISreadCurvature: could not open >/home/nam/AVERAGE/average/surf/lh.thickness >No such file or directory > >In the surf directory, I DID find "lh.avg_thickness". >I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. >Would someone please let me know how to remedy this? > > > >>Nam. >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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