Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

Doubt in the no. of dicom images
by Anupa AV 04 Apr '13

04 Apr '13

Dear All, I use Philips Achieva 3T scanner for the MRI study. When I open the Dicom folder, (say for MPR ) the no. of items I can see is 222 images (IM_xx) for one subject and for other subject, I find it as 166 images. Is it an error in saving the data or the no.of images vary among individuals. Thanks in advance for clarifying my doubt.

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Fw: Making cuts using tksurfer
by Anupa AV 04 Apr '13

04 Apr '13

----- Forwarded Message ----- From: Anupa AV <av.anupa(a)yahoo.com> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Wednesday, April 3, 2013 11:57 AM Subject: Re: [Freesurfer] Making cuts using tksurfer Dear Sir, As you recommended, I have made a cut using plane option. Kindly see the attachment. My research interst is to make a coronal cut. I've done it by merging the standard FreeSurfer parcellation labels of the superior frontal gyrus, the rostral middle frontal gyrus and caudal middle frontal gyrus (after loading DKatlas). Then I cut the merged merged region using cut plane option. Now I want to make a coronal cut at Talairach coordinate y=26(say), so as to seperate dorsolateral prefrontal cortex from premotor cortex. Can you please tell me how to make a coronal cut at y=26? Thanks in advance for your response. ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Anupa AV <av.anupa(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Monday, April 1, 2013 6:15 PM Subject: Re: [Freesurfer] MAking cuts using tksurfer you might try using a cutting plane instead of having to draw the entire cut. cheers Bruce On Mon, 1 Apr 2013, Anupa AV wrote: > Dear All, > > How to explore the "cut" tools in freesurfer using tksurfer? > I'd like to make a cut along the vertex on the cortical surface (say, inflated) to divide medial and lateral components. > How to do it after loading DKatlas labels and I want to cut along the vertex to divde medial and lateral components.? > > Thanks in advance for your response. > > 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.

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Re: [Freesurfer] Bad Talairach Registration
by Bruce Fischl 03 Apr '13

03 Apr '13

Do you know why it has multiple frames? What kind of image is it? On Apr 3, 2013, at 10:51 PM, "Cherise R. Chin Fatt" <cherise.chinfatt(a)utdallas.edu> wrote: > Hello Bruce: > > I am using a T1-weighted image. > > > > > On Wed, Apr 3, 2013 at 9:44 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Ae you trying to put a diffusion scan through recon-all? That won't work, it needs to be T1 weighted > Bruce > > > > On Apr 3, 2013, at 10:23 PM, "Cherise R. Chin Fatt" <cherise.chinfatt(a)utdallas.edu<mailto:cherise.chinfatt@utdallas.edu>> wrote: > > Hello: > > I have been trying to use FreeSurfer on an aging population and running into difficulties with Talairach Registration. I am able to run the demonstrate date, but when I run my own data I am getting some very weird results. I have attached screenshots of the different planes for one subject. I have tried this with 5 subjects and getting the same kind of results. > > In terms of scripting: I tried to run autorecon1 first and it failed with this error: ERROR: input(s) cannot have multiple frames! > > I changed the script and did the following (running one line at a time): > > setenv SUBJECTS_DIR test/DTI > recon-all -i DTI/00001.dcm -subjid again > > cd $SUBJECTS_DIR/again/mri/orig > mv 001.mgz multiframe.mgz > mri_convert -nth 0 multiframe.mgz 001.mgz > > recon-all -motioncor -subjid again > recon-all -talairach -subjid again > recon-all -nuintensitycor -subjid again > recon-all -normalization -subjid again > recon-all -skullstrip -subjid again > % checking registration > tkregister2 --mgz --s again --fstal > > If anyone can provide some insight in terms of what I am doing wrong or how to fix the registration would be greatly appreciated. > > Thank you, > Cherise. > -- > Cherise R. Chin Fatt; MSc > Doctoral Student in Cognition and Neuroscience > School of Behavioral and Brain Sciences > The University of Texas at Dallas > <Screen Shot 2013-04-03 at 8.39.26 PM.png> > <Screen Shot 2013-04-03 at 8.39.40 PM.png> > <Screen Shot 2013-04-03 at 8.39.54 PM.png> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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. > > > > -- > Cherise R. Chin Fatt; MSc > Doctoral Student in Cognition and Neuroscience > School of Behavioral and Brain Sciences > The University of Texas at Dallas

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Bad Talairach Registration
by Cherise R. Chin Fatt 03 Apr '13

03 Apr '13

Hello: I have been trying to use FreeSurfer on an aging population and running into difficulties with Talairach Registration. I am able to run the demonstrate date, but when I run my own data I am getting some very weird results. I have attached screenshots of the different planes for one subject. I have tried this with 5 subjects and getting the same kind of results. In terms of scripting: I tried to run autorecon1 first and it failed with this error: *ERROR: input(s) cannot have multiple frames! * I changed the script and did the following (running one line at a time): setenv SUBJECTS_DIR test/DTI recon-all -i DTI/00001.dcm -subjid again cd $SUBJECTS_DIR/again/mri/orig mv 001.mgz multiframe.mgz mri_convert -nth 0 multiframe.mgz 001.mgz recon-all -motioncor -subjid again recon-all -talairach -subjid again recon-all -nuintensitycor -subjid again recon-all -normalization -subjid again recon-all -skullstrip -subjid again % checking registration tkregister2 --mgz --s again --fstal If anyone can provide some insight in terms of what I am doing wrong or how to fix the registration would be greatly appreciated. Thank you, Cherise. -- Cherise R. Chin Fatt; MSc Doctoral Student in Cognition and Neuroscience School of Behavioral and Brain Sciences The University of Texas at Dallas

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template label map
by Johnson 03 Apr '13

03 Apr '13

Dear FS Can you please tell me what is the default template file used in the recon-all script ? thanks -- Johnson J. GadElkarim Research Assistant, Department of Psychiatry, PhD Candidate, Dept. of Electrical & Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

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lta files and mri_robust_register
by Deniz Ozgen 03 Apr '13

03 Apr '13

I registered two images using mri_robust_register. Is possible to apply the same transformation to another image (a mask) in the same space as the initial "mov" image? (using the lta files?) I could not find the information in Freesurfer site. Thanks Deniz

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Re: [Freesurfer] How to get surface-based AAL template
by Martijn Steenwijk 03 Apr '13

03 Apr '13

I think you should use mriS_ca_label. Apart from that, mris_ca_train/mris_ca_label require multiple examples to work correctly. So what I did is non-linearly register the AAL atlas to multiple healthy subjects and used them all to train with mris_ca_train. Best, Martijn Van: ZhiLiangLong [mailto:lagosslong1987@163.com] Verzonden: woensdag 3 april 2013 15:32 Aan: martijnsteenwijk(a)gmail.com Onderwerp: Re:RE: [Freesurfer] How to get surface-based AAL template Dear Martijin: Indeed, there are holes in generated labels on surface after registration. I have tried commands : mris_ca_train and mris_ca_label . But i got errors. The process is as follow: 1\ use bbregister to obtain registration file (register.dat) between Colin27 and single_subj_T1.nii. 2\ with mri_vol2vol obtain anatomical atlas from AAL: mri_vol2vol --reg register.dat -mov AAL.nii --fstarg --0 f-in-anat.mgh where the register.dat is obtained from step 1\, and AAL.nii is the original AAL template. 3\ mris_sample_parc Colin27 lh f-in-anat.mgh ./lh.aal.annot this command results in lh.aal.annot file resampled from f-in-anat.mgh. 4\ mris_ca_train lh lh.white lh.aal.annot Colin27 ./lh.aal.gcs 5\ mri_ca_label Colin27 lh lh.white ./lh.aal.gcs ./lh.aal2surface.annot When run sep 5, there was an error: Segmentation fault. I don't know what is wrong with the process. Can you give some suggestions? Best. zhiliang 在 2013-03-31 20:28:01，"Martijn Steenwijk" <martijnsteenwijk(a)gmail.com> 写道： I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn’t work sufficiently for sampling the labels, all had problems with the registration causing holes in the sulci and gyri ending up in the wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but might also be bad, since you often don’t want to look at an in complete label). I ended up making my own gcs fom a training set with mris_ca_train. Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects. Best, Martijn Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens ZhiLiangLong Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template Dear Gari: Thank you for give me suggestions patiently. i figured it out as you suggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something like this) to do research (e.g. cortical network analysis based on this template)? Best wishes. zhiliang At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" <garikoitz(a)gmail.com> wrote: Hi Zhiliang, 1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all 2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well. The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all. 3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI. Hope this helps! Gari On 27/03/2013, at 14:06, ZhiLiangLong <lagosslong1987(a)163.com> wrote: Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information. 2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing. Looking forward to your reply. Best wishes. zhiliang At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" <garikoitz(a)gmail.com> wrote: Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats. Br! On 27/03/2013, at 05:35, ZhiLiangLong <lagosslong1987(a)163.com> wrote: Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.

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recon-all head motion
by Allison Gruber 03 Apr '13

03 Apr '13

Dear experts, I was wondering if there is an output from the recon-all procedure that quantifies the motion/ motion correction. I am thinking it may be the talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt file, but am not sure how to interpret this. I tried to review the list serv, but couldn't find anything that exactly answered the question. Thanks for your help, Allison

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[FSL] UCLA Advanced NeuroImaging Summer Program (fwd)
by Bruce Fischl 03 Apr '13

03 Apr '13

FYI ---------- Forwarded message ---------- Date: Wed, 3 Apr 2013 16:22:57 +0100 From: Mark Cohen <mscohen(a)UCLA.EDU> Reply-To: FSL - FMRIB's Software Library <FSL(a)jiscmail.ac.uk> To: FSL(a)jiscmail.ac.uk Subject: [FSL] UCLA Advanced NeuroImaging Summer Program The UCLA Semel Advanced Neuroimaging Summer Program 2013 We are pleased to announce that we are now accepting applications for the 2013 session of the UCLA Advanced Neuroimaging Summer Program. This unique two-week course is designed for scientists who wish to extend their knowledge of cutting edge tools and image research. A distinguished international faculty will share their expertise in the latest approaches to imaging, principally in MRI methods and analytic techniques. This year, the course will run from July 8-20, 2013 in Los Angeles on the UCLA campus. Thanks to the generosity of our federal sponsors, tuition for the entire program is covered for all students. Travel costs are the responsibility of the attendees. The course consists of a combination of didactic lectures, hands-on sessions and group experiment projects. Admission to the summer program is highly selective. Applicants are chosen based on a variety of factors, including their demonstrated background in neuroimaging, their ability to work well in collaborative environments and their likelihood of having long-term impacts in the field. Although seating is limited sharply, the lectures and course materials are presented online in real-time for those who are unable to attend. Applications to the summer program must be submitted using our online form (http://www.brainmapping.org/NITP/NITPSummer2013Apply.php) Applications must be complete, including letters of reference, by May 15. No exceptions will be made for late applications.

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Tracula the inverse of TBSS results
by Sean Hatton 03 Apr '13

03 Apr '13

Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney

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Freesurfer April 2013