Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

problem with tksurfer:no open gl window
by Battistella Giovanni 20 Mar '09

20 Mar '09

Dear freesurfer users, I've just installed freesurfer on my PC and I tried testing it using the sample subject. tkmedit works fine, but with tksurfer I see the window where the image should appear but no image. the error I have is: no open gl window. I'm using Ubuntu 8.10 version with a Intel Q45 graphic card. Somebody can help me solving the problem? thank you in advance, giovanni

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mri_surfcluster
by Yigal Agam 20 Mar '09

20 Mar '09

Hi, When I run mri_surfcluster on a surface with 12 timepoints, how do I know when each of the reported clusters occurred? Thanks, Yigal

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Outline files convert
by Flavio Seixas 20 Mar '09

20 Mar '09

Hi All, I've got from IBSR (Internet Brain Segmentation Repository) MR images and their subcortical structures segmented manually. The segmented images are saved in Outline (.OTL) format. How could I convert from .OTL to .IMG or .NII (Analyze) format using mri_convert? Are there any examples? I would appreciate any help. There are one image to each of image slice, as shown bellow: IBSR_01_seg_18.otl IBSR_01_seg_46.otl IBSR_01_seg_73.otl IBSR_01_seg_100.otl IBSR_01_seg_19.otl IBSR_01_seg_47.otl IBSR_01_seg_74.otl IBSR_01_seg_101.otl IBSR_01_seg_20.otl IBSR_01_seg_48.otl IBSR_01_seg_75.otl IBSR_01_seg_102.otl IBSR_01_seg_21.otl IBSR_01_seg_49.otl IBSR_01_seg_76.otl IBSR_01_seg_103.otl IBSR_01_seg_22.otl IBSR_01_seg_4.otl IBSR_01_seg_77.otl IBSR_01_seg_104.otl IBSR_01_seg_23.otl IBSR_01_seg_50.otl IBSR_01_seg_78.otl IBSR_01_seg_105.otl IBSR_01_seg_24.otl IBSR_01_seg_51.otl IBSR_01_seg_79.otl IBSR_01_seg_106.otl IBSR_01_seg_25.otl IBSR_01_seg_52.otl IBSR_01_seg_7.otl IBSR_01_seg_107.otl IBSR_01_seg_26.otl IBSR_01_seg_53.otl IBSR_01_seg_80.otl IBSR_01_seg_108.otl IBSR_01_seg_27.otl IBSR_01_seg_54.otl IBSR_01_seg_81.otl IBSR_01_seg_109.otl IBSR_01_seg_28.otl IBSR_01_seg_55.otl IBSR_01_seg_82.otl IBSR_01_seg_10.otl IBSR_01_seg_29.otl IBSR_01_seg_56.otl IBSR_01_seg_83.otl IBSR_01_seg_110.otl IBSR_01_seg_2.otl IBSR_01_seg_57.otl IBSR_01_seg_84.otl IBSR_01_seg_111.otl IBSR_01_seg_30.otl IBSR_01_seg_58.otl IBSR_01_seg_85.otl IBSR_01_seg_112.otl IBSR_01_seg_31.otl IBSR_01_seg_59.otl IBSR_01_seg_86.otl IBSR_01_seg_113.otl IBSR_01_seg_32.otl IBSR_01_seg_5.otl IBSR_01_seg_87.otl IBSR_01_seg_114.otl IBSR_01_seg_33.otl IBSR_01_seg_60.otl IBSR_01_seg_88.otl IBSR_01_seg_115.otl IBSR_01_seg_34.otl IBSR_01_seg_61.otl IBSR_01_seg_89.otl IBSR_01_seg_116.otl IBSR_01_seg_35.otl IBSR_01_seg_62.otl IBSR_01_seg_8.otl IBSR_01_seg_117.otl IBSR_01_seg_36.otl IBSR_01_seg_63.otl IBSR_01_seg_90.otl IBSR_01_seg_118.otl IBSR_01_seg_37.otl IBSR_01_seg_64.otl IBSR_01_seg_91.otl IBSR_01_seg_119.otl IBSR_01_seg_38.otl IBSR_01_seg_65.otl IBSR_01_seg_92.otl IBSR_01_seg_11.otl IBSR_01_seg_39.otl IBSR_01_seg_66.otl IBSR_01_seg_93.otl IBSR_01_seg_120.otl IBSR_01_seg_3.otl IBSR_01_seg_67.otl IBSR_01_seg_94.otl IBSR_01_seg_12.otl IBSR_01_seg_40.otl IBSR_01_seg_68.otl IBSR_01_seg_95.otl IBSR_01_seg_13.otl IBSR_01_seg_41.otl IBSR_01_seg_69.otl IBSR_01_seg_96.otl IBSR_01_seg_14.otl IBSR_01_seg_42.otl IBSR_01_seg_6.otl IBSR_01_seg_97.otl IBSR_01_seg_15.otl IBSR_01_seg_43.otl IBSR_01_seg_70.otl IBSR_01_seg_98.otl IBSR_01_seg_16.otl IBSR_01_seg_44.otl IBSR_01_seg_71.otl IBSR_01_seg_99.otl IBSR_01_seg_17.otl IBSR_01_seg_45.otl IBSR_01_seg_72.otl IBSR_01_seg_9.otl Thank you, Flavio

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clusterwise multiple comparison correction
by Elizabeth O'Hare 19 Mar '09

19 Mar '09

hello, i am working through the group analysis and multiple comparisons corrections tutorial using my own data. according to the tutorial, after running this command: mri_glmfit --y lh.thickness.10.mgz --glmdir LH_MRT_agecovar.glmdir -- fsgd matrixT_FSGD --surf fsaverage lh --fwhm 10 --C MRT_agecovar.mtz -- sim mc-z 100 1.3 mc-z.negative --sim-sign neg i should find CSD files in the LH_MRT_agecovar.glmdir/csd directory. my problem is that there is no /csd directory made as a result of the command that i run. there are also no CSD files in the contrast subdirectory. there is one CSD file (located at the same level as my glmdir) called: mc-z.negative-MRT_agecovar.mtz.csd but this file does not contain any CWP information. i'm running version 4.1.0 on fedora 10 any help would be much appreciated. thanks! libby

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merging rh and lh surfaces
by slew＠nmr.mgh.harvard.edu 19 Mar '09

19 Mar '09

Hi, I would like to have a single surf file that composed of both right and left pial surf. Is there a way to do it in freesurfer? Best. seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422

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Follow-up Question -- Multiple Comparison - Clusterwise Correction
by Devdutta W 18 Mar '09

18 Mar '09

Hi Doug, This is a follow up question regarding display issue from mri_glmfit-sim. The issue as you explained was that the original annotation was not being cleared. You suggested a short-term as well as a long-term fix. The temporary fix was deleting "-annot aparc" from mri_glmfit-sim. As a more permanent fix, you emailed me a modified copy of mri_surfcluster. 1. My question is when re-running mri_glmfit-sim with the new mri_surfcluster do I still need to delete "-annot aparc" from mri_glmfit-sim? In other words, are both of these needed or will using the modified mri_surfcluster alone solve the problem? 2. Another question: Is there any way to convert the previous "bad" .annot file to "good" .annot file so we can view it without having to run mri_glmfit-sim again? We ran it with 5000 iterations and it took over 10 days. If there is a way we can get the same results without having to re-run it, I would very much like to know about it. Thank you for your help so far. Devdutta On Tue, Mar 17, 2009 at 12:26 PM, Devdutta W <devdutta.w(a)gmail.com> wrote: > Hi Doug, > Thanks for your help. A followup question to your last email: the short > term fix that you mentioned earlier, do I need to make that fix in addition > to copying the new mri_surfcluster file in the binary dir? Or has that been > fixed already? > > Thanks, > Devdutta > > > On Mon, Mar 9, 2009 at 4:41 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > > wrote: > >> >> Try copying this: >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfclust… >> >> into your $FREESURFER_HOME/bin directory (make a backup first), and then >> re-run. >> >> doug >> >> >> Devdutta W wrote: >> >>> We are using Red Hat Enterprise Linux 5. >>> Thanks for your help. I'll try that out. >>> >>> On Mon, Mar 9, 2009 at 3:02 PM, Douglas N Greve < >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> I think I've found the problem in that the original annotation at >>> a vertex is not being cleared if a cluster is not there. >>> >>> The short term fix is to delete " --annot aparc" from >>> mri_glmfit-sim at line 353. I'll email when I have a longer term >>> fix. What platform are you using? >>> >>> doug >>> >>> Devdutta W wrote: >>> >>> When I load mc-z.abs.2.sig.cluster.mgh, if the "Draw filled >>> labels" button is toggled on, it looks no different from >>> before. Toggling the "show overlay" button doesn't do anything. >>> If the "Draw Outlined labels" button is toggled on, the >>> outlines of the colored regions can be seen (including the >>> outlines of the clusters). This time, toggling the overlay >>> button on-off shows the clusters. >>> >>> On Mon, Mar 9, 2009 at 2:12 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >>> >>> /what does it look like when you load >>> mc-z.abs.2.sig.cluster.mgh >>> as an overlay?/ >>> >>> >>> >>> Devdutta W wrote: >>> >>> Nick, Sita, >>> The average subject is created from our data, perhaps >>> that's >>> why it looks different. We were having problems getting >>> freesurfer to recognize our average subject. So we linked >>> fsaverage to our average subject. I didn't see a >>> button (or a >>> tool) to toggle on-off the annotation. The overlay >>> button is >>> there but toggling it doesn't do anything. >>> There indeed are clusters mixed in with the >>> annotations. But >>> from the documenation, it seems that the command we are >>> using >>> is /supposed/ to show clusters (but only the clusters, >>> not the >>> the annotations). And that is the question I am trying >>> to get >>> answered. >>> >>> Here is the command we are using: >>> /tksurfer fsaverage lh inflated -annot >>> mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray/ >>> I am running this command from the appropriate folder and >>> fsaverage is linked to our average subject. We are >>> using the >>> following documentation: >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh…<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh…> >>> < >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh… >>> > >>> < >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh… >>> > >>> < >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh… >>> >\_glmfit\-sim) >>> >>> Thanks, >>> Devdutta >>> >>> >>> >>> On Mon, Mar 9, 2009 at 12:09 PM, Nick Schmansky >>> <nicks(a)nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>>>> wrote: >>> >>> Devdutta, >>> >>> What version of freesurfer is being used? The fsaverage >>> subject you >>> show doesnt look right. Also, I see what appear to >>> be clusters >>> mixed in >>> with the annotations. The summary files output by >>> the multiple >>> correction step will tell you how many and the size >>> of the >>> clusters. >>> You should be able to toggle on-off both the >>> annotation and the >>> overlay >>> independently. >>> >>> I am cc'ing Sita, as she may be able to help you on >>> this (I >>> will have >>> limited email contact this week). >>> >>> Nick >>> >>> >>> On Mon, 2009-03-09 at 11:21 -0500, Devdutta W wrote: >>> > Forgot to attach the images, again. >>> > >>> > >>> > On Mon, Mar 9, 2009 at 11:20 AM, Devdutta W >>> <devdutta.w(a)gmail.com <mailto:devdutta.w@gmail.com> >>> <mailto:devdutta.w@gmail.com <mailto:devdutta.w@gmail.com>> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>>>> >>> >>> >>> > wrote: >>> > Hi Nick, >>> > Can you shed some light on why this might be >>> happening? I >>> > will attach the two picture again in case >>> you weren't >>> able to >>> > view them last time. I tried what I >>> thought you >>> meant by >>> > "turn off annotation display" and I have >>> stated what >>> happened >>> > in my previous email (please see below) >>> > >>> > * If I don't include the -annot >>> option in >>> tksurfer it >>> > only displays the fsaverage, >>> naturally. >>> > * If I toggle off the button that >>> says "show >>> labels", it >>> > looks like it is just the >>> fsaverage as well. >>> > * If I toggle on the "Draw outlined >>> labels" >>> button it >>> > shows the same regions as before >>> except >>> they are >>> > merely outlined, not filled. >>> > Any help you can give me will be appreciated. >>> > >>> > Thanks, >>> > Devdutta >>> > >>> > >>> > On Wed, Mar 4, 2009 at 10:36 AM, Devdutta W >>> > <devdutta.w(a)gmail.com >>> <mailto:devdutta.w@gmail.com> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com> >>> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>>>> wrote: >>> > Nick, >>> > I confess, I am not exactly sure >>> what you >>> mean by >>> > "turn off annotation display". I >>> tried a few >>> > things. >>> > >>> > * If I don't include the -annot >>> option in >>> > tksurfer it only displays the >>> fsaverage, >>> > naturally. >>> > * If I toggle off the button >>> that >>> says "show >>> > labels", it looks like it >>> is just the >>> > fsaverage as well. >>> > * If I toggle on the "Draw >>> outlined >>> labels" >>> > button it shows the same >>> regions >>> as before >>> > except they are merely >>> outlined, >>> not filled. >>> > These were the only ones that I could >>> think of. Is >>> > that what you meant or was it >>> something >>> else that I >>> > missed? >>> > >>> > Thanks, >>> > Devdutta >>> > >>> > >>> > On Tue, Mar 3, 2009 at 7:12 PM, Nick >>> Schmansky >>> > <nicks(a)nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>>>> wrote: >>> > What is displayed if you >>> turn off the >>> > annotation display? >>> > >>> > The threshold in the >>> simulation >>> is used to >>> > determine whether clusters >>> > are found or not. A >>> threshold of 2 >>> indicates >>> > a p-value of 0.01 >>> > (1/(10^2), 3 is 0.001, >>> etc. The >>> threshold >>> > referred to in the tksurfer >>> > display is just for color >>> thresholding. >>> > >>> > Nick >>> > >>> > >>> > On Tue, 2009-03-03 at >>> 17:17 -0600, >>> Devdutta W >>> > wrote: >>> > > Forgot the attachments >>> earlier. >>> Here they >>> > are now >>> > > >>> > > On Tue, Mar 3, 2009 at >>> 5:11 PM, >>> Devdutta W >>> > <devdutta.w(a)gmail.com >>> <mailto:devdutta.w@gmail.com> >>> <mailto:devdutta.w@gmail.com <mailto:devdutta.w@gmail.com >>> >> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>>>> >>> >>> >>> > > wrote: >>> > > Hi Freesurfers, >>> > > More questions >>> about this >>> analysis. >>> > > 1) Referring to the >>> documentation, >>> > we used the following >>> > > command: >>> > > tksurfer >>> fsaverage lh >>> inflated - >>> > annot mc- >>> > > >>> z.abs.2.sig.ocn.annot >>> -fthresh 2 - >>> > curv -gray >>> > > >>> > > The >>> documentation says we >>> should see >>> > an image as shown in >>> > > Figure 1 (attached). >>> But what we >>> > see is Figure 2 (also >>> > > attached). Can >>> somebody explain >>> > this? >>> > > >>> > > 2) When running the >>> simulation >>> does >>> > it matter what threshold >>> > > we use? For >>> example, >>> can we use a >>> > threshold of 2 or 3 >>> > > (instead of 4 as >>> shown in >>> > documentation) when running >>> > > mri_glmfit-sim? >>> And do >>> we have to >>> > use the same threshold >>> > > while displaying the >>> clusters >>> after? >>> > > >>> > > Thanks for any help. >>> > > >>> > > Devdutta >>> > > >>> > >>> > > >>> > >>> _______________________________________________ >>> > > Freesurfer mailing list >>> > > >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> >>> > > >>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > >>> > >>> > >>> > >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >

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avg ROI
by Gabriel Go.Es. 18 Mar '09

18 Mar '09

I have created a ROI in an average subject, how can i transpose that ROI to each subject? i mean, use it like a mask to make some statistics on each subject Regards Gabriel _________________________________________________________________ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx

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LABORATORY RESEARCH ASSISTANT - JOB POSTING
by Jean Augustinack 18 Mar '09

18 Mar '09

LABORATORY RESEARCH ASSISTANT POSITION AT MGH IN CHARLESTOWN MA Laboratory technician wanted for correlation studies in histological/pathological Alzheimer's disease and ex vivo structural magnetic resonance imaging. New Position Minimum requirement: Bachelor's Degree or higher Preferred degree: B.S. Degree in biological science Strong interest in basic research. Ability to work as a team. Responsibilities: The applicant will assist and support research using histological tissue processing in normal human and Alzheimer's disease brain samples, as well as standard lab techniques that include immunohistochemistry, and microscopy and quantitative analysis of brain areas involved in memory and several other areas. The applicant should be self-motivated, hard-working, conscientious, and independent, with the ability to learn new techniques. Some basic knowledge of Unix/Linux will be helpful. Experience with histology staining procedures and/or microscopy a plus. Interested parties should send a CV and contact information for three references to: jean(a)nmr.mgh.harvard.edu

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Changing from 1.4x1.4x1.4 mm slices to 1x1x1
by Jeff Sadino 18 Mar '09

18 Mar '09

Hello, I am analyzing some subjects from several years ago when we had a protocol that called for slices 1.4x1.4x1.4mm. I am also including in the study more recent scans with a protocol for 1x1x1mm slices. I am using freesurfer 3.0.5. I am wondering if the different slice dimensions will cause differences in the analysis. As I read on a previous post, freesurfer resamples all its input data into 1mm isovolumetric voxels anyways, so I should be ok? Regards, Jeff Sadino _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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making ROIs
by Gabriel Go.Es. 17 Mar '09

17 Mar '09

hello i'm trying to make a ROI wich not coincides with the FS parcellation, i've click the surrounding area, then click in custom fill buttom, i've tried all options, and each time all the brain gets white and then purple, wich i think that means it's not making the roi, i've tried clicking in make closed path and make path, then custom fill buttom and still can't make that single ROI i'm sending the images step by step Regards Gabriel _________________________________________________________________ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx

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