Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

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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Problem with aseg - Other segmentations fine
by preciado＠nmr.mgh.harvard.edu 03 Apr '13

03 Apr '13

I am having a bit of a problem the aseg on this subject. (See 2013.03.22.cor108.aseg.jpg attached) It is way overestimating the white matter bilaterally. The problems are about this bad for about 20 or more slices so editing manually seems like... a less than efficient proposition. Any thoughts on how to fix this programmatically? For reference, I have a attached some other images with no segmentation and using the Desikan-Killiany atlas (aparc+aseg) and the Destrieux atlas (aparc.a2009s+aseg) which look fine. Thanks, -Ronny

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Research Coordinator Position at the University of Washington
by McLaughlin, Katie 03 Apr '13

03 Apr '13

An experienced, independent, and organized individual is sought for a full-time Research Study Coordinator position in the Stress and Development Laboratory at the University of Washington Psychology Department, run by Katie McLaughlin, PhD. The individual in this position would coordinate the operations of a child clinical psychology laboratory focused on studying the impact of trauma exposure on children’s brain and behavioral development. Principle responsibilities include developing, coordinating, and monitoring research activities for several psychophysiology and neuroimaging studies of children and adolescents; recruiting children, adolescents, and parents from community sources; conducting clinical interviews and neuropsychological tests; supervising and monitoring undergraduate research assistants; and coordinating the management of study data. This position would be an excellent fit for applicants interested in obtaining doctoral training in clinical or developmental psychology or developmental cognitive neuroscience. Specific duties include: · Assistance in the development of recruitment methods; recruitment and screening of potential participants to determine eligibility. · Assistance in the preparation of IRB applications, consent forms and progress reports for institutional review board. · Development and implementation of standardized protocols for collecting and scoring behavioral, psychophysiology, and fMRI data. · Data collection and data quality control to ensure fidelity to study protocol · Development and programming of behavioral and fMRI tasks . Recruitment, training and supervision of volunteer undergraduate and post- baccalaureate research assistants. . Administration of neuropsychological tests and clinical interviews Previous research or clinical experience with children and the ability to work in command line environments such as Unix or Linux operating systems is preferred. The position begins in August or September 2013. Please email a CV and cover letter to Katie McLaughlin at: mclaughk(a)uw.edu<mailto:mclaughk@uw.edu>. -- Katie McLaughlin, Ph.D. Director, Stress & Development Laboratory, Boston Children's Hospital Assistant Professor of Pediatrics and Psychiatry Harvard Medical School 21 Autumn Street, Boston, MA 02115 Phone: (857) 218-5598; Fax: (617) 730-0957

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Re: [Freesurfer] Error from mri_concat while using QDEC
by Tudor Popescu 03 Apr '13

03 Apr '13

Hi Doug, I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file? Anyway, after trying out the command with only one of the files from the tutorial, *mri_concat --debug /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/y.mgh* ..the same thing happens, namely it returns to the command prompt, with no message whatsoever. What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help! Tudor On 20 December 2012 05:24, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > That does not make sense. Try using only one input file. Also, put --debug > as the first option. > doug > > > > > > > On 12/19/12 8:32 AM, Tudor Popescu wrote: > > Hi Doug, > So the full command is > > mri_concat > /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/141/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/084/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/021/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/093/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/080/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/091/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/040/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/017/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/138/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/106/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/108/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/092/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/124/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/129/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/103/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/130/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/039/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/123/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/095/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/067/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/004/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/133/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/097/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/073/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/149/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/045/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/136/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/144/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/032/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/131/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/145/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/111/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/102/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/074/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/114/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/008/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/128/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/099/surf/lh.thickness.fwhm10.fsaverage.mgh > --o > /media/Dell/_FS/buckner_data/subjects/qdec/lh-thickness-age-fwhm10/y.mgh > --debug > > ..however, as soon as I press Enter, I'm just taken to the command prompt > again, with no output whatsoever! Am I calling mri_concat wrongly?! > > Tudor > > On 18 December 2012 17:15, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> Hi Tudor, >> Can you run mri_concat from the command line with the --debug option >> first. Send us the FULL command line and the full terminal output. >> doug >> >> >> >> On 12/18/2012 09:35 AM, Tudor Popescu wrote: >> > Hello everyone, >> > >> > I tried doing the QDEC group analysis tutorial, however after doing >> > everything as instructed in the tutorial, when pressing Analyze I get >> > the error message: >> > >> > /Error in Analyze: command failed: mri_concat >> > >> /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh >> > >> /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh >> > (..)/ >> > >> > ..even though those files are all accessible there! I pasted that same >> > mri_concat manually into the terminal, however no output is produced >> > at the command prompt, nor any files are created. >> > >> > In previous attempts, I used to also get this error >> > >> > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in >> > SUBJECTS_DIR "/ >> > /Syntax error: Bad fd number"/ >> > >> > after following the sh/bash workaround from this >> > < >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.h… >> >previous >> > thread, I no longer get that error, however get stuck with the error >> > mentioned above. >> > >> > My SUBJECTS_DIR already contains a copy of the default subjects folder. >> > >> > Debug info below. Any help greatly appreciated! >> > Tudor >> > >> > -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > FREESURFER_HOME /home/virtualuser/freesurfer >> > FSFAST_HOME /home/virtualuser/freesurfer/fsfast >> > FSF_OUTPUT_FORMAT nii.gz >> > SUBJECTS_DIR /media/Dell/_FS/buckner_data/subjects >> > MNI_DIR /home/virtualuser/freesurfer/mni >> > >> > >> > >> > _______________________________________________ >> > 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 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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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Re: [Freesurfer] mris_preproc with --xhemi
by Gabriel Gonzalez Escamilla 03 Apr '13

03 Apr '13

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