Freesurfer

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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.

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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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Downloading v4.5.0
by Chester Kang 20 Dec '10

20 Dec '10

Hi, When I try to download v4.5.0 (Mac version) from the Archive, it seems like the file is missing/unavailable? http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/freesurfer-Darwi n-leopard-i686-stable-pub-v4.5.0-full.dmg Have also tried the mirrors link but that is down also. Could someone point me to an alternate location or correct URL? Thanks very much! Regards, Chester

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black screen when using tksurfer
by Amir Tahmasebi 20 Dec '10

20 Dec '10

Hi there, When I am using the "tksurfer" command for visualization, I only get a black screen: tksurfer $subject rh inflated There is no error reported at the command prompt except for a warning: No colortable found! Here is the version of the freesurfer I am using: freesurfer-Linux-centos4-stable-pub-v4.5.0 Any help is appreciated. Thank you, Amir -- ________________________________ Amir M. Tahmasebi, Ph.D. postdoctoral researcher Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA ________________________________ Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb

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Sulci segmentation
by FIDEL ALFARO ALMAGRO 20 Dec '10

20 Dec '10

Hi, I am pretty new in freesurfer and I do not know if this question has been answered before (It is difficult to search for 1 basic question), so I will post it anyways: - Is there any segmentation/labeling in freesurfer that allows the user to identify all the sulci of an MR image? I have done the recon-all, correctly, but I am not able to see any sulcus using tkmedit with the generated segmentations. Thanks in advance.

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ICV differs systematically in repeated measurements
by Diederick Stoffers 20 Dec '10

20 Dec '10

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

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tkmedit white matter editing
by Micheli, C. 20 Dec '10

20 Dec '10

Dear all I am using the tkmedit GUI to add/erase pixel in a slice-wise fashion in order to subsequently apply a tessellation on the white matter. I launch the command cd subject/mri tkmedit -f brain.mgz -aux wm.mgz from linux shell (64bit CentOS), where brain.mgz is the anatomical MRI and wm is the segmented white matter, both in the subject/mri folder Editing the voxels of the aux image works only when i want to insert pixels but not when i want to erase them (menu->EditVoxelsTool->right mouse click). I wonder if anybody uses this feature of tkmedit GUI and had the same problem. Appreciate any input Best, Cristiano

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[New release] - iSurf Brainview 2.0.0
by Pedro Paulo de Magalhães Oliveira Junior 19 Dec '10

19 Dec '10

Today it was released a major upgrade of iSurf Brainview. Major improvements could be noticed on the IPad. Now you can click the name of the brain structure and have a popup control with the definition and references for the area. As usual suggestions are welcome. Upcoming features include the use of Destrieux atlas and 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Cheers Pedro Paulo Jr. -- iOS 4.2

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