Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

Fw:Re: Re: questions about ROI analysis
by Rujing Zha 08 Apr '14

08 Apr '14

Hi FS experts and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: ==================================================================================== mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat ==================================================================================== Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha -------- 转发邮件信息 -------- 发件人：charujing123 <charujing123(a)163.com> 发送日期：2014-02-27 09:46:23 收件人："freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> 主题：Re: Re: [Freesurfer] questions about ROI analysis Thanks doug, All the best. Rujing Zha 2014-02-27 charujing123 发件人：Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-02-27 01:49 主题：Re: [Freesurfer] questions about ROI analysis 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： On 02/25/2014 08:34 PM, charujing123 wrote: > Hidoug, > Thanks doug. > For 1st question,I want to reduce the search space of vertex-wise > analysis to a cluster. Extract the cluster that you want from the ocn to create a mask, eg, to get cluster2 mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh The run mri_glmfit with --mask cluster2.mgh Then run mri_glmfit-sim with simulation > For 2nd question, i try freeview as tksurfer cannot work. However this > website cannot be logged > in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/Roi…. try http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide > Thanks. > All the best. > Rujing Zha > 2014-02-26 > ------------------------------------------------------------------------ > charujing123 > ------------------------------------------------------------------------ > *发件人：*Douglas Greve <greve(a)nmr.mgh.harvard.edu> > *发送时间：*2014-02-25 23:46 > *主题：*Re: [Freesurfer] questions about ROI analysis > *收件人：*"freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > *抄送：* > > On 2/25/14 10:09 AM, Rujing Zha wrote: >> Hi FS experts and others, >> I have done two group thickness difference analysis based on whole >> brain. Now I want to do correlation analysis between specific ROI >> thickness and behavior score. I searched roi in the FS website, but I >> cannot distinguish the volume ROI and surface ROI very clearly. So I >> have some questions as below: >> 1,As I get some clusters in the two group t-test,I want to use one of >> these clusters to correlate thickness with behavior score. How to >> generate this mask and how to use this mask in the mri_glmfit and >> mri_glmfit-sim? > Do you mean you want to reduce the search space of a vertex-wise > analysis to a cluster or that you want to compute the mean thickness > within the cluster and correlate with your behavioral score? >> 2,If I want to draw ROI manually or set ROI according previous >> studies, how to create this ROI mask. > tksurfer can draw a label (as can freeview I think) > >> Any detailed information will be highly appreaciated. >> Thanks. >> All the best. >> Rujing Zha >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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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NHP surface reconstruction in FS5.3
by S.V.Shepherd [work] 07 Apr '14

07 Apr '14

Greetings, I've been reconstructing a surface in an NHP using a Kolster T1 scan and FS5.3. It went very well, at first, but I've hit a wall. I have trouble in occipital (due to poor signal strength/constrast) and some typical-with-NHP problems in ACC and OFC. I think there are three related questions. 1) I lose parts of the ACC near the genu of the corpus callosum. I have attached a screen shot -- the white matter and gray matter both look decent. I wondered if the corpus callosum might be handled specially, and if differences between human and nhp callosi might prevent the ACC from growing normally? 2) In trying to deal with this, I greyed out the ACA, which was bright and potentially confounding. I wasn't sure how to do this in brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) and 255s (wm) were preserved. I tried brain, which got overwritten, but ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, if I continue editing brainmask (or equivalent) directly, should I be darkening or lightening the gray matter in the excluded section of the ACC? I would assume lighten -- but in the OFC, some gray matter (not shown) appears to be excluded for being too bright. 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't stuck. I assume this is because autorecon isn't convinced by the wm specification after looking at brain.finalsurfs -- how might I (gently!) override this? Thanks very much for your time and patience. stephen [image: Inline image 2][image: Inline image 1] *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

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QDEC tutorial data- problem in downloading
by Saurabh Thakur 07 Apr '14

07 Apr '14

Hello Freesurfer , I am looking forward for alternative mirror link to download the QDEC data. i.e Buckner_data_tutorial_subj Since link provided is not working. I have tried many times. Thanks in advance, cheers Saurabh Thakur,

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Re: [Freesurfer] SNR on DTI data
by Anastasia Yendiki 07 Apr '14

07 Apr '14

Signal-to-noise ratio = mean / standard deviation On Tue, 18 Mar 2014, Yuko Yotsumoto wrote: > Anastasia, > > Thank you so much for your reply. > > So I should calculate the mean and s.d. of the values of the low-b within the white matter region for each subject, and compare those numbers between groups. > Is it correct to say that the higher mean values indicate larger SNR? > > Yuko > > On Mar 18, 2014, at 12:53 AM, Anastasia Yendiki wrote: > >> >> Hi Yuko - You can use the low-b images and compute the SNR of those images inside a mask of the white matter. Because dt_recon computes a registration from the diffusion to the structural data, you can use that registration to map the white matter label from the freesurfer segmentation (aseg) to the diffusion data. Then calculate the mean and standard deviation of the values of the low-b images inside that white matter mask. >> >> Hope this helps, >> a.y >> >> On Mon, 17 Mar 2014, Yuko Yotsumoto wrote: >> >>> Hello Freesurfers, >>> I have DTI data for two groups of subjects, and were asked SNR for each >>> group. >>> I did ROI analysis on FA values, therefore, I do not have the averaged DTI >>> data. >>> I am wondering if there is any way to compute SNR from dt_recon output. It >>> doesn't have to be the ROI specific SNR values, I just need SNR for the >>> whole DTI data for each group. >>> Any suggestions will be appreciated! >>> Yuko Yotsumoto >>> --- >>> ------------------------------------------------------------- >>> Yuko Yotsumoto, Ph. D. >>> Associate Professor >>> The University of Tokyo, Department of Life Sciences >>> Bldg #2, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan >>> phone : (+81)-3-5454-4332 >>> E-mail: cyuko(a)mail.ecc.u-tokyo.ac.jp >> _______________________________________________ >> 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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mri_ca_label killed process
by Francesco Baldacchini 07 Apr '14

07 Apr '14

Hi everybody, I'm studying every command contained inside recon all to track a probable problem we have with our patients. I've reached mri_ca_label command but the process stop while running and it's not giving me any error, the terminal just show the word "killed", I pasted it here: Left_Pallidum (13): linear fit = 1.01 x + 0.0 (207 voxels, overlap=1.017) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (207 voxels, peak = 97), gca=97.4 gca peak = 0.27536 (62) mri peak = 0.08851 (78) Right_Hippocampus (53): linear fit = 1.24 x + 0.0 (667 voxels, overlap=0.021) Right_Hippocampus (53): linear fit = 1.24 x + 0.0 (667 voxels, peak = 77), gca=76.6 gca peak = 0.32745 (63) mri peak = 0.09108 (77) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (655 voxels, overlap=0.253) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (655 voxels, peak = 77), gca=76.5 gca peak = 0.08597 (105) mri peak = 0.06731 (110) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (15659 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (15659 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.05510 (99) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (13532 voxels, overlap=0.871) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (13532 voxels, peak = 104), gca=104.4 Killed francesco@francesco-F3JP:~$ I wasn't able to find any log file to find the cause. Anybody can help me with this? Thanks in advice, Francesco Baldacchini

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ROI analyses
by Emily Boeke 07 Apr '14

07 Apr '14

Hi Freesurfers, I have some questions about ROI analyses. 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be done using the left amygdala from that individual's aseg, but instead will be done in mni305 space with the fsaverage left amygdala ROI? 2. I sometimes want to use labels I've created on fsaverage from averaged group activation to do ROI analyses. If the ROI is in the volume, I convert the label to a mask and run: mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat In the appropriate contrast folder. What should I do if I want to do the same thing, but with a surface label (in a lh or rh surface analysis, not an mni305 analysis)? Thanks! Emily

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ESMRMB Lectures on MR:Resting State fMRI - basic concepts, methods & applications {Disarmed}
by Leemon Albert 07 Apr '14

07 Apr '14

*ESMRMB Lectures on MR:* *Resting State fMRI - basic concepts, methods & applications* *Cambridge - May 19-21, 2014* *Only few places left!* Dear all, After the big success of our previous workshops in Magdeburg and Vienna, we are glad to announce the *2014* *Resting State Educational Workshop* taking place in *Cambridge (UK), May 19-21*. The 3-day educational workshop, organized together with the ESMRMB - Lectures on MR Series, is specifically aimed at researchers novel to the field of resting state fMRI, who are currently planning or carrying out resting state experiments. The lectures will provide an in-depth overview of all relevant features of resting state fMRI, including physiology, data acquisition and analysis, as well as applications in both healthy and patient populations. In addition, we offer *a full day hands-on training session*, in which participants will learn to carry out the basic steps of three commonly used analysis methods: seed based correlations, ICA, and graph analysis. The workshop has an intimate and highly interactive character and provides a unique chance for participants to discuss methodological issues with experienced researchers in the field of resting state. Confirmed faculty: Catie Chang (NIH, USA) Peter Fransson (Stockholm, Sweden) Mika Rubinov (Cambridge, UK) Vesa Kiviniemi (Oulu, Finland) Ilya Veer (Berlin, Germany) Martin Walter (Magdeburg, Germany) For more information on the course program and speakers, or to simply register, please visit *www.esmrmb.org <http://hwww.esmrmb.org>*. The registration fee for PhD students and physicians in training is EURO 240 for ESMRMB members and EURO 335 for non-members, which includes access to the workshop, a digital course syllabus, full catering of lunches and coffee breaks, and a welcome reception. We are looking forward to see you in Cambridge! Martin Walter Mika Rubinov Ilya Veer

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reading colorized labels in tcl file to tksurfer...
by Rudolph Pienaar 07 Apr '14

07 Apr '14

Hi all -- I have a process that generates a list of ROIs (from aparc.annot) based on some cost condition. I wanted to view these labeled ROIs in 'tksurfer'. I created the following rough tcl script: 'label_load.tcl' set label lh.bankssts.label ; read_and_color_labeled_vertices 255 255 0 set label lh.caudalanteriorcingulate.label ; read_and_color_labeled_vertices 255 255 10 set label lh.caudalmiddlefrontal.label ; read_and_color_labeled_vertices 255 255 20 set label lh.cuneus.label ; read_and_color_labeled_vertices 255 255 30 set label lh.inferiorparietal.label ; read_and_color_labeled_vertices 255 255 40 set label lh.lateraloccipital.label ; read_and_color_labeled_vertices 255 255 50 and then ran with tksurfer <subj> <hemi> <surface> -tcl label_load.tcl The labels all load, but they are all the same teal-like color. I'm guessing that I am using the wrong tksurfer internal command... I have looked through the wiki, but didn't immediately see a solution. Help? Best -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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wm and pial edits - what to correct and what not?
by Markus Gschwind 07 Apr '14

07 Apr '14

Dear all, I would like to show some very frequent and typical cases of segmentation problems in my bunch of data of normal subjects (after recon-all), of which I couldn't find a description in the wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithD… ). I am therefore not sure if these types of error are serious and will affect later results like thickness, curvature, GWR, etc. Here are the examples (c.f. attached screenshots from Freeview) 1) In the primary sensory-motor cortex it frequently happens that the "?h.white" line lies several mm within the wm border (c.f. yellow arrow), I did not observe this behavior in other places. >>Would I need to edit that? 2) Sometimes the "?h.pial" line includes also dura or parts of the skull (green arrow). >>Is it necessary to edit that as well? 3) Another question concerns the yellow parts of the wm which sometimes are much larger than the ventricles and also include both caudate nuclei (not shown). >>Is this a problem? Thanks in advance!! Markus

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Applications open for the Neurobiology of Cognition GRC/GRS!
by Caspar M. Schwiedrzik 06 Apr '14

06 Apr '14

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Freesurfer April 2014