Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Can I mix different versions of freesurfer
by rong chen 23 Dec '10

23 Dec '10

Hi, I want to use FreeSurfer to analyze a longitudinal study. For each subject in my study, I already used FreeSurfer 4.2 to perform the cross-sectional analysis. However, FreeSurfer 4.2 did not have a longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for this purpose. My question is: A) Should I rerun the cross-sectional analysis using FreeSurfer 4.5 OR B) I just run 'recon-all -base' and 'recon-all -long' using FreeSurfer 4.5, based on the cross-sectional results from version 4.2. Thanks, Rong

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WM surface and Deep Brain nuclei
by Luke Bloy 23 Dec '10

23 Dec '10

Hello, I'm new to freeSurfer and just starting to look around so I apologize if this question is a bit naive. When I look at segmentation results, that include deep brain nuclei (thalamus etc) I see that they are all contained inside of the white matter surface. is there away to edit the surface so that these boundaries are represented? I imagine that this would change the topology of the WM region thus it might be difficult, Is there away to generate surfaces form these regions on there own? Thanks Luke

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Extract Hippocampal volume after manual editing?
by McLean John (NHS Greater Glasgow & Clyde) 23 Dec '10

23 Dec '10

Hi, I have ran recon-all and got the Hippocampal volumes I desire from the aseg.stats file. However, I have manually refined some of the volumes using the tkmedit segmentation tool brushes and I now need to extract the revised volume estimates. I believe I can run 'mri_segstats' to obtain the revised volume, this seems to run the full segmentation process again, would this be the recommended way of obtaining the revised volumes or if I'm only interested in the Hippocampal volume is there a more precise command I could run to extract only this from my revised aseg.mgz segmentation file? Many Thanks John McLean ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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volume - surface shift in tkmedit
by Micheli, C. 22 Dec '10

22 Dec '10

Dear all I would like to write an MRI anatomical volume and a surface in freesurfer format. The surface is correspondent to the white matter tessellation, while the volume represents T1 anatomical slices, both obtained from softwares external to FreeSurfer. Using the two functions save_mgh.m and write_surf.m from the freesurfer matlab interface files I am able to write the variables in the proper freesurfer folders. In the original nifti format volume and surface match both in voxel space and in millimiters space, but as soon as i visualize them in tkmedit the surface is shifted. Any clue why this happens? Is there any matrix that automatically translates the surface coordinates when it is read in tkmedit? I hope to get your feedback soon Best regards Cristiano

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Amygdala subregions
by Lin Nga 21 Dec '10

21 Dec '10

Hi all, Please excuse my naive question; I am new to FreeSurfer. I am trying to segment amygdala subregions and can't quite figure out how to do this. I didn't find anything in the tutorials or the freesurfer archives; if there is any documentation on how to do this, could someone point me in the right direction? Specifically, I'd like the regions listed below (copied from the FreeSurferColorLUT.txt): #No. Label Name: R G B A 7001 Lateral-nucleus 72 132 181 0 7002 Basolateral-nucleus 243 243 243 0 7003 Basal-nucleus 207 63 79 0 7004 Centromedial-nucleus 121 20 135 0 7005 Central-nucleus 197 60 248 0 7006 Medial-nucleus 2 149 2 0 7007 Cortical-nucleus 221 249 166 0 7008 Accessory-Basal-nucleus 232 146 35 0 7009 Corticoamygdaloid-transitio 20 60 120 0 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 7011 Fusion-amygdala-HP-FAH 122 187 222 0 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 7013 Endopiriform-nucleus 10 49 255 0 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 7015 Paralaminar-nucleus 45 205 165 0 7016 Intercalated-nucleus 117 160 175 0 7017 Prepiriform-cortex 221 217 21 0 7018 Periamygdaloid-cortex 20 60 120 0 7019 Envelope-Amygdala 141 21 100 0 7020 Extranuclear-Amydala 225 140 141 0 I've already ran recon-all and have aseg, aparc+aseg, and aparc.a2009+aseg available as outputs. Do I need aparc.a2005s+seg for the regions listed above? If so, how would I obtain it given the outputs of recon-all? Thanks for the help, Lin

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Freesurfer longitudinal analysis
by rong chen 21 Dec '10

21 Dec '10

Hi, I want to use FreeSurfer to analyze a longitudinal study. For each subject in my study, I already used FreeSurfer 4.2 to perform the cross-sectional analysis. However, FreeSurfer 4.2 did not have a longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for this purpose (in the FreeSurfer wiki, it said the longitudinal pipeline in 5.0 is broken). My question is: A) Should I redo the cross-sectional analysis using FreeSurfer 4.5 OR B) I just run 'recon-all -base' and 'recon-all -long' using FreeSurfer 4.5, based on the cross-sectional results from version 4.2. Thanks, Rong

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Re: [Freesurfer] ICV differs systematically in repeated measurements
by Martin Reuter 21 Dec '10

21 Dec '10

As I said, there are several talairach transforms. You need to look at the talairach.xfm. The wiki says: To check the quality of the registration file talairach.xfm file: cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk Martin On Tue, 2010-12-21 at 20:12 +0100, Diederick Stoffers wrote: > Hi Martin, > > > I read the wiki on eTIV after finding this outlier. I used > > > tkregister2 --mgz --s subject --fstal --surf orig > > > to check the registration, that looked pretty decent. Any other > pointers? > > > Thanks! > > > Diederick > > > > On 21 dec 2010, at 17:40, Martin Reuter wrote: > > > Hi Diederick, > > > > the ICV is computed from the linear talairach.xfm transform > > (including > > skull). There are all kinds of other talairach transforms produced > > by > > recon all, so make sure you are looking at the talairach.xfm > > (not ...lta > > or ..._with_skull.lta). > > > > You might want to read: > > http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV > > > > It is very likely that the clipping on your outlier image (missing > > cerebellum etc). produce an incorrect talairach.xfm and thus outlier > > ICV. > > > > Best, Martin > > > > On Tue, 2010-12-21 at 17:32 +0100, Diederick Stoffers wrote: > > > Hi Martin, > > > > > > > > > OK, I didn't expect different scanners/fieldstrengths to have that > > > big > > > an effect on ICV. Given that there is a systematic bias, one would > > > expect a very high correlation between ICV at timepoint one and > > > two. I > > > inspected a scatterplot and this was indeed the case, except for a > > > single outlier. The Tailairach registration looks fine for both > > > timepoints in this outlier. However, the scan at one timepoint > > > was > > > badly planned, part of the cerebellum and brainstem are missing. > > > Could > > > this explain the low ICV value in this subject? If not, what other > > > things should I check? > > > > > > > > > Cheers, > > > > > > > > > Diederick > > > > > > On 20 dec 2010, at 15:26, Martin Reuter wrote: > > > > > > > Hi Diederick, > > > > > > > > In a longitudinal study you need to ensure identical acquisition > > > > and > > > > processing, else you'll introduce a systematic bias. > > > > Some of my recent analyses indicate that even updating the > > > > software > > > > on the scanner can bias your results. Hardware changes are > > > > worse. > > > > > > > > Best Martin > > > > > > > > On Dec 20, 2010, at 6:48 AM, Diederick Stoffers > > > > <d.stoffers(a)gmail.com> wrote: > > > > > > > > > Hi all, > > > > > > > > > > I have a dataset with AD patients that were scanned twice, > > > > > once at > > > > > 1.5T and once at 3T at an interval of a few years. The ICV > > > > > values > > > > > are lower for almost all subjects at timepoint two (FS 5.0). > > > > > Isn't > > > > > ICV in the later FS versions supposed to be independent of > > > > > brain > > > > > volume as it is based on a scaling factor derived from the > > > > > Tailairach transform of the skull? Many thanks! > > > > > > > > > > Cheers, > > > > > > > > > > Diederick > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > >

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Re: [Freesurfer] ICV differs systematically in repeated measurements
by Martin Reuter 21 Dec '10

21 Dec '10

Hi Diederick, the ICV is computed from the linear talairach.xfm transform (including skull). There are all kinds of other talairach transforms produced by recon all, so make sure you are looking at the talairach.xfm (not ...lta or ..._with_skull.lta). You might want to read: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV It is very likely that the clipping on your outlier image (missing cerebellum etc). produce an incorrect talairach.xfm and thus outlier ICV. Best, Martin On Tue, 2010-12-21 at 17:32 +0100, Diederick Stoffers wrote: > Hi Martin, > > > OK, I didn't expect different scanners/fieldstrengths to have that big > an effect on ICV. Given that there is a systematic bias, one would > expect a very high correlation between ICV at timepoint one and two. I > inspected a scatterplot and this was indeed the case, except for a > single outlier. The Tailairach registration looks fine for both > timepoints in this outlier. However, the scan at one timepoint was > badly planned, part of the cerebellum and brainstem are missing. Could > this explain the low ICV value in this subject? If not, what other > things should I check? > > > Cheers, > > > Diederick > > On 20 dec 2010, at 15:26, Martin Reuter wrote: > > > Hi Diederick, > > > > In a longitudinal study you need to ensure identical acquisition and > > processing, else you'll introduce a systematic bias. > > Some of my recent analyses indicate that even updating the software > > on the scanner can bias your results. Hardware changes are worse. > > > > Best Martin > > > > On Dec 20, 2010, at 6:48 AM, Diederick Stoffers > > <d.stoffers(a)gmail.com> wrote: > > > > > Hi all, > > > > > > I have a dataset with AD patients that were scanned twice, once at > > > 1.5T and once at 3T at an interval of a few years. The ICV values > > > are lower for almost all subjects at timepoint two (FS 5.0). Isn't > > > ICV in the later FS versions supposed to be independent of brain > > > volume as it is based on a scaling factor derived from the > > > Tailairach transform of the skull? Many thanks! > > > > > > Cheers, > > > > > > Diederick > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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help
by subramanyam＠nbrc.ac.in 21 Dec '10

21 Dec '10

Dear Colleague, Following is the error we get upon running the mri_annotation2label command root@ubuntu:~# mri_annotation2label --subject one \ --h rh --labelbase ./label/aparc-rh ERROR: Option --h unknown root@ubuntu:~# mri_annotation2label --subject one \ --hemi rh --labelbase ./label/aparc-rh ERROR: Option --hemi unknown Kindly address this error and give a reply as soon as possible Many thanks V.P.Subramanyam Rallabandi Senior R&D Engineer National Brain Research Centre, Manesar, Gurgaon, Haryana-122050, INDIA.

2 1

problem with labels
by Irene Altarelli 21 Dec '10

21 Dec '10

Dear Freesurfers, I have a problem with labels. I select a given Talairach coordinate that interests me, draw an approximately circular label around it in tksurfer, and save it. When I open that same label in tkmedit, the central Talairach coordinate is changed and the whole label is somewhat shifted. Am I missing something? Should I use mri_label2vol or some other command? Thanks very much in advance! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23

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