Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

Question about reorienting images
by Timour Al-Khindi 09 Nov '10

09 Nov '10

Hello, We are looking for a way to reorient the orig.mgz files and the segmentation (aseg.mgz) into a different plane, and we have a couple of questions. We've used tkregister2 to reorient the orig image: tkregister2 –mov orig.mgz –tar orig.mgz –regheader –reg myregister.dat myregister.dat is created by this command line. We rotate the brain in the tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol command line to rotate the orig and the aseg images. For aseg.mgz: mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp nearest --o rotaseg.mgz For orig.mgz: mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o rotorig.mgz This seems to look decent when we load it up in tkmedit, but we have two questions about the use of mri_vol2vol 1) Why does the algorithm need a target (won't run without it), since the transformation info is saved in myregister.dat? Also, how does it manage to work (which it does), given than neither of the targets entered are in the reoriented space? Should we use a different target? What is the role of the target? 2) A previous post specifies that "interp nearest" should be used to rotate the aseg.mgz file. What is the function played by that command? Should we also use it when rotating the orig.mgz file? It works without it, but do we risk distorting the image? Thanks in advance! Tim Al-Khindi

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longitudinal base error
by Guang Zeng 09 Nov '10

09 Nov '10

Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs %%%%%%%%%% Any one can help me? Thanks a lot!uang

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Talairach registration
by Leatherday, Chris 08 Nov '10

08 Nov '10

Hello, I am a new freesurfer user and am interested in the subcortical volumetric segmentation procedure that is used, particularly relating to the hippocampus. I am finding it difficult to decipher exactly what freesurfer does in relation to Talairach registration, I've read that there is an affine registration and a detailed non-linear warping procedure, as well as registration to a brain atlas template. Could you please point me in the right direction so that I can understand the exact procedure that the program follows in terms of warping to a standard space? Thank you Chris Leatherday

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How to get the Talairach coordinate of labels
by Jin Li 08 Nov '10

08 Nov '10

Hi, Freesurfers, As the *.label file provide the vertex number and R,A,S positions. How could I get the corresponding position in Talairach coordinates for each vertex? That is, how could I convert the label in a subject's space into that in talairach space, considering the label is generated from a surface, like shown in the attachment? I tried to use mri_label2label to convert the label into fsaverage space, but when shown in tksurfer, the RAS position was not similar to Talairach position in fsaverage. Any help would be appreciated. Best! Jin

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Re: [Freesurfer] how to generate aparc.annotion files?
by Douglas N Greve 08 Nov '10

08 Nov '10

You'll probably have to do it by hand with tkregister2. Someone on the list may have solved this problem before. doug Shahin wrote: > Ok now I faced another problem saying that I dont have talairach.xfm > for monkeys. Would you tell me how can I generate it for monkeys? > > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Shahin <shahin(a)nmr.mgh.harvard.edu> > *Cc:* Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Mon, November 8, 2010 12:55:37 PM > *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? > > It is needed in make_average_surface. I've created a new version that > does not use the aparc (thought I have not tested it). You can get it > from here: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > > Make a backup of your current version of make_average_surface and then > copy this one over it > > douig > > > > Shahin wrote: > > Yes, I have made a template on the basis of many monkeys > > (mris_make_template) and then I have done spherical registeration for > > each individual monkey (to this template) by using mris_register. Now > > it is the final step and I have to run the make_average_subject but it > > generates an error saying that I don't have a lh and rh.aparc.annot > files. > > > > Apparently very old versions of freesurfer (version 3) didnt need > > these files. Am I right? Do you suggest to use old versions? > > > > Shahin Nasr > > > > PhD in Cognitive Neuroscience > > Martinos Imaging Center, MGH > > Harvard Medical School > > > > > > ------------------------------------------------------------------------ > > *From:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > *To:* Shahin <shahin(a)nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu>> > > *Cc:* Freesurfer <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Mon, November 8, 2010 12:33:03 PM > > *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? > > > > Hi Shahin > > > > have you run spherical registration? If so, to what target? I don't > think > > the monkey-to-human atlas aligment is that robust, so you would need a > > monkey geometry atlas (which is a lot easier to build as you don't > > need to > > do manual labeling for it). Probably someone on list has one? > > > > Bruce > > > > On Mon, 8 Nov 2010, Shahin wrote: > > > > > Thanks Bruce, > > > > > > To avoid this problem, is there anyway to run > > make_average_subject without > > > having lh and rh.aparc.annot files? > > > Shahin Nasr > > > > > > > > > PhD in Cognitive Neuroscience > > > Martinos Imaging Center, MGH > > > Harvard Medical School > > > > > > > > > > > > > > > ________________________________ > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > > To: Shahin <shahin(a)nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu> > > <mailto:shahin@nmr.mgh.harvard.edu <mailto:shahin@nmr.mgh.harvard.edu>>> > > > Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Sent: Mon, November 8, 2010 12:10:38 PM > > > Subject: Re: [Freesurfer] how to generate aparc.annotion files? > > > > > > Hi Shahin > > > > > > you'll need a monkey atlas based on manually labeled monkey folding > > > patterns. we don't have one, but it's possible that someone else > on the > > > list does (it would be a lot easier to do for monkey than it was for > > human > > > as the folds are so much simpler) > > > > > > cheers > > > Bruce > > > > > > On Mon, 8 Nov 2010, Shahin wrote: > > > > > >> Hi Freesurfers, > > >> > > >> Anybody knows how can I make lh and rh.annotation.aparc files > > for a monkey? > > >> I > > >> need them initiate an brain averaging process. > > >> Shahin Nasr > > >> > > >> > > >> PhD in Cognitive Neuroscience > > >> Martinos Imaging Center, MGH > > >> Harvard Medical School > > >> > > >> > > >> > > > > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > > contains patient information, please contact the Partners Compliance > > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > > but does not contain patient information, please contact the sender > > and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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how to generate aparc.annotion files?
by Shahin 08 Nov '10

08 Nov '10

Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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DTI question
by Gabriel Go.Es. 08 Nov '10

08 Nov '10

Hello Freesurfers I'm starting to work with DTI data and I have a couple of questions; I have 2 identical DTI sequences for some subjects and I would like to work with them, does anyone knows if it's better to concatenate them or to make an average of them? And I'm wondering when I make an eddy-current or motion correction (alignment to the B0 or T2) if there is any algorithm to change the vectors to the corresponidng alignment? Best Regards Gabriel

1 1

FS 5.1
by Alan Francis 08 Nov '10

08 Nov '10

Hi Bruce, Doug: I am planning to process scans in a longitudinal study on First break SZ. I heard that FS 5.1 will have features that will be better than 5.0. Any idea on when 5.1 will be released? thanks much, Alan BIDMC

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QDEC or SPSS?
by liyari5018 08 Nov '10

08 Nov '10

Hi all, I do group analysis using QDEC to detect the difference between the normal group and the patient group, the result shows some significant difference brain area (normal > patient, red, uncorrected p=0.001). I extract the average cortical thickness in this area(ROI), then export those thickness data into SPSS to do statistic analysis, but I do not find the difference between two groups in this areas, even find some opposite results. （I checked my data carefully!） So I want to know how does this happen? Thanks for your reply! Best, LJ

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Old FS version
by pikase＠tin.it 07 Nov '10

07 Nov '10

Hello Freesurfers! Is it possible to obtain a copy of an old version of FS? More specifically, I need this version to complete some analyses: freesurfer-Darwin-leopard-i686-stable-pub-v4.3.1-full.dmg Thank you in advance (and great job with the 5.0!) Laura

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Freesurfer November 2010