Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

63 participants
95 discussions

mgz to dicom or NiFTI
by Stoffers, D. 13 May '08

13 May '08

Dear all, Our imaging techs use a specific artifact correction which requires converting the DICOM images to mgz files. Does anybody know a good tool to convert the mgz files back to DICOM or, even better, to NiFTI? Any suggestions would be really appreciated! Cheers Diederick

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Fwd: [Freesurfer] Re: mri_mask
by Daniel H Choi 12 May '08

12 May '08

Hi Bruce, The following is the output that my colleague was able to render after running the mri_mask again. Also attached are the brainmask.mgz and lh.stg.mask.mgz files too. Would you be able to point out what went wrong? Thanks. Dan [root@slr08 masks]# mri_info lh.stg.mask.mgz Volume information for lh.stg.mask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2300.00 msec, TE: 3.36 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -0.4948 : x_a = -0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 47.1750 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 19.0414 talairach xfm : /mnt/win/MRI_data/Trial_Runs/Freesurfer/E-08/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 -0.0000 127.5052 -0.0000 -0.0000 1.0000 -80.8250 -0.0000 -1.0000 -0.0000 147.0414 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 0.0000 127.5052 0.0000 0.0000 -1.0000 147.0414 -0.0000 1.0000 0.0000 80.8250 0.0000 0.0000 0.0000 1.0000 Anil. On Sat, May 10, 2008 at 1:50 PM, Daniel H Choi <dhchoi(a)u.northwestern.edu> wrote: > Hey Anil, > > This is what Bruce sent me just in case you needed verbatim what he said. > Thanks. And i'll forward him your results as soon as I get them from you. > Laters > > Dan > > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: Fri, May 9, 2008 at 8:21 PM > Subject: Re: [Freesurfer] Re: mri_mask > To: Daniel H Choi <dhchoi(a)u.northwestern.edu> > Cc: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > > > Hi Daniel, > > I just tested this on some data and it seemed to work for me. Can you run > mri_info on the lh.STG.mgz volume and send us the results? And maybe you can > email me and Krish (ccd) the 2 volumes (brainmask.mgz and lh.STG.mgz) so we > can see if we can replicate it. > > cheers, > Bruce > > On Fri, 9 May 2008, Daniel H Choi wrote: > > Please note the command we used: >> >> mri_mask brainmask.mgz lh.stg.mask.mgz brainout.mgz >> >> and the result we got was: >> >> Writing masked volume to brainout.mgz...done. >> >> On Fri, May 9, 2008 at 2:39 PM, Daniel H Choi <dhchoi(a)u.northwestern.edu> >> wrote: >> >> Hi, >>> >>> I have tried applying a binary mask, specifically for STG, in conjunction >>> with the mri_mask command. We applied it to a brainmask volume, but we >>> did >>> not get the result we wanted. The output we recieved was simply the mask >>> that we used. We wish to produce an output that gives the STG volume >>> alone >>> from the brain, and not from the binary mask. Are we using the command >>> incorrectly? Thanks >>> >>> -- >>> Daniel Horim Choi >>> Northwestern University >>> Class of 2009 >>> dhchoi(a)u.northwestern.edu or >>> dchoi1024(a)gmail.com >>> >> >> >> >> >> >> > > > -- > Daniel Horim Choi > Northwestern University > Class of 2009 > dhchoi(a)u.northwestern.edu or > dchoi1024(a)gmail.com > -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

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mri_mask
by Daniel H Choi 09 May '08

09 May '08

Hi, I have tried applying a binary mask, specifically for STG, in conjunction with the mri_mask command. We applied it to a brainmask volume, but we did not get the result we wanted. The output we recieved was simply the mask that we used. We wish to produce an output that gives the STG volume alone from the brain, and not from the binary mask. Are we using the command incorrectly? Thanks -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

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Optseq2 and 2-way design?
by Elizabeth Reynolds Losin 09 May '08

09 May '08

Hello all, I am new to Optseq2 and I have a question about generating 2-way design orders using the program and about a question about temporal jitter. I am working on a design with 7 conditions. I have run the following design through optseq2 and gotten out reasonable looking orders. --ntp 160 --tr 3 --psdwin 0 21 --ev imi_touch 3 20 --ev imi_separate 3 20 --ev obs_touch 3 20 --ev obs_separate 3 20 --ev exe_touch 3 20 --ev exe_separate 3 20 --ev ident 3 20 - -o pilot_order_evrltd --nsearch 10000 --nkeep 3 1) The stimuli are hand signs presented for 3 seconds each and there are 20 repetitions for each of the conditions. The conditions that have seperate or touch in their labels involve presentation of the same set of hand signs in each condition; the different conditions just involve doing different things in response to seeing these hand signs, e.g. imitating or observing them, etc. For example, ev imi_touch, obs_touch and ev exe_touch involve seeing the same set of 20 signs and either observing, imitating or executing them. So, while I'm not interested in analyzing responses to the 20 different hands signs separately, I also don't want the same sign to appear in different conditions successively or even close in time, i.e. imitate and then observe the same sign close in time. I'm wondering if there is a way to tell optseq2 all of this information so that it will generate an order specifying not only my conditions but also randomize the specific repetition of the condition. Basically I want all of the considerations such as psdwin taken into account for condition order and only randomization taken into account for the order of trial repetitions. Somehow I need to let optseq know that the same repetition numbers in different conditions are linked. Is there any way to do this with Optseq2? If not, can you suggest some way I can achieve this, perhaps using optseq2 for condition order and then another program for trial order? Thanks! 2) The second question I have is regarding ISI jitter. I have heard that it is optimal in fast event-related designs that the stimulus duration NOT be a multiple of the TR, yet it seems that this is what optseq is looking for. It doesn't seem that optseq is generating jitter between successive stimuli but only between successive presentations of the same condition. Is this all that is necessary for deconvolution of the signal during post processing, or is a jittered ISI between successive stimuli also necessary (or desirable), and if so, how can this be achieved? One strategy I have heard of is moving the stimulus onset time around within a larger TR. For example shifting a 1.5 sec stimulus around within a 3 sec TR to create temporal jitter. Is this type of timing something optseq could generate? Thanks. Liz

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unpacksdcmdir issue
by jake＠nmr.mgh.harvard.edu 09 May '08

09 May '08

Hello, I am getting an error saying that the path from the findsession command is not found. Here is the bugr information and following is the log from my terminal window; could anyone explain why the directory from findsession is missing? THANKS! FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.0.4-20080508 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/amaebi/35/users/ablood/R01_Botox PWD: /space/amaebi/35/users/ablood/R01_Botox striatum:jake[81] cd /space/amaebi/35/users/ablood/R01_Botox striatum:jake[82] source /usr/local/freesurfer/nmr-std-env -------- freesurfer-Linux-centos4-stable-v4.0.4-20080508 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current [striatum:R01_Botox] (nmr-std-env) setenv SUBJECTS_DIR /space/amaebi/35/users/ablood/R01_Botox [striatum:R01_Botox] (nmr-std-env) findsession CD_RO1BTX_pat1_sess1 ======= SUBJECT: CD_RO1BTX_pat1_sess1 SUBJ ID: CD_RO1BTX_pat1_sess1 DATE : May 03, 2008 TIME : 19:27:12 XPRMNTR: PATH : /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 [striatum:R01_Botox] (nmr-std-env) unpacksdcmdir -src /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 -targ /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_pat1_sess1 -scanonly CD_RO1BTX_pat1_sess1_info $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /autofs/space/amaebi_035/users/ablood/R01_Botox -src /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 -targ /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_pat1_sess1 -scanonly CD_RO1BTX_pat1_sess1_info Fri May 9 10:51:51 EDT 2008 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2008/05/09-14:51:51-GMT BuildTimeStamp: May 8 2008 03:44:12 CVS: $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ User: jake Machine: striatum Platform: Linux PlatformVersion: 2.6.18-8.1.15.el5 CompilerName: GCC CompilerVersion: 30400 striatum Linux striatum 2.6.18-8.1.15.el5 #1 SMP Mon Oct 22 08:32:04 EDT 2007 i686 i686 i386 GNU/Linux ERROR: directory /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 does not exist [striatum:R01_Botox] (nmr-std-env) cd /space/archive/160/siemens/ /space/archive/160/siemens/: No such file or directory. [striatum:R01_Botox] (nmr-std-env)

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Fixing Inaccuracies in White Matter Surfaces
by Pradeep Reddy Ramana 09 May '08

09 May '08

Hello Everybody, This is Pradeep Reddy, just started my PhD in Medical Image Analysis and hence a newbie to FreeSurfer. I've passed the auto-recon2 stage in the reconstruction procedure. Now I am trying to verify WM segmentation produced by the recon-all/auto-recon2, before I move on to further processing. The excercise given in the freesurfer tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits ) gives me one example on how to detect if there were a lesion and outlines how to fix it. But now when I observe the outputs I have, I am quite confused as to how to detect inaccuracies in the segmentation of white matter. To make it more specific, I show you a slice of wm.mgh I have ( wmConfusion1 attached). Please look at the small yellow circle on the right. If I just follow the exercise, this looks like a lesion, as the yellow line cuts into it. but when I move up to next few slices, this hole opens up ( close to the green line ) giving me indications that it may NOT be a hole ( keeping in mind the inherent 3D nature of the MR image ). Also I am not sure whether there is an error in the image ( wmConfusion5 ) attched is an error is WM segmentation. So my questions: 1. What are the things I have to look for, while trying to verify the WM segmentation ( after autorecon2 )? 2. Any thumb-rules laid out for this already? My googling was in fact in vain. 3. Any other tutorials/resources/books stating clearly what to verify, in different stages of reconstruction? I am sorry to write a long email. Please be kind to help me in this regard. Regards, Pradeep Reddy PhD Student, Simon Fraser Unviersity, Canada. -- There's more to life. Finding it is my job. -- raamana(a)gmail.com NOTICE my new contact Number in Canada: +1 604 720 2233

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LGI of annotated cortex
by Martin Kavec 09 May '08

09 May '08

Hi, is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files? Thanks in advance, Martin -- ********************************** Senior Clinical Research Associate MRI Unit of the Department of Radiology Erasme Hospital Lennik Street 808 B-1070 Brussels BELGIUM tel: +32-2-555-4325 fax: +32-2-555-3994 email: martin.kavec(a)gmail.com ********************************** ----------------------------------------------- Find a way, or make one!

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[Fwd: Re: [Freesurfer] Thickness repeatability]
by Doug Greve 08 May '08

08 May '08

FYI -------- Original Message -------- Subject: Re: [Freesurfer] Thickness repeatability Date: Thu, 8 May 2008 12:27:35 -0500 From: Xiao Han <elehanx(a)gmail.com> To: Doug Greve <greve(a)nmr.mgh.harvard.edu> CC: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> References: <200805081511.40394.martin.kavec(a)gmail.com> <48232A69.1030408(a)nmr.mgh.harvard.edu> <48232AEA.9020801(a)nmr.mgh.harvard.edu> Hi Doug, How are you? I couldn't send email to the list. But regarding that two questions, here are my thoughts: 1. I remember we used about 50 iterations. We also have a formula in the paper (Pg 183, right column) that relates the kernel size to the number of iterations. 50 iterations equals 5.6 mm kernel size by that formula. 2. That 6mm (or 50 iterations) is not totally arbitrary. We studied the effect of thickness variability w.r.t. smoothing kernel size. The result is summarized in Fig. 3 of the paper. Fig. 3 showed that a kernel of 6mm is effective and sufficient to remove noise. Larger kernel will give better repeatability, but may reduce sensitivity in a thickness study. The point we want to make is that FreeSurfer gives very good repeatability even with a very small smoothing kernel (6mm). That 6mm kernel is indeed much smaller than what other group used when reporting their thickness results (30mm!). We made the statement in the 2nd paragraph in the right column of Pg 185. Best wishes, Xiao On Thu, May 8, 2008 at 11:31 AM, Doug Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Sorry, that was supposed to be a reply to this email Damian Jenkins wrote: We have been following the protocol in Han's paper to test repeatability and the following questions cropped up: 1) how many smoothing iterations were run to achieve a smoothing kernel size of 6mm?; 2) what was the reason for choosing this size? Thanks, D Doug Greve wrote: Probably about 26. You can figure it out from this command: mris_fwhm --fwhm 6 --niters-only --s fsaverage --hemi lh dont know how they chose 6 doug Martin Kavec wrote: Hi, is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files? Thanks in advance, Martin -- 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> _______________________________________________ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Thickness repeatability
by Damian Jenkins 08 May '08

08 May '08

We have been following the protocol in Han's paper to test repeatability and the following questions cropped up: 1) how many smoothing iterations were run to achieve a smoothing kernel size of 6mm?; 2) what was the reason for choosing this size? Thanks, D Dr Damian Jenkins Department of Clinical Neurology Oxford University

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--label2path option in mri_path2label
by Michael Harms 06 May '08

06 May '08

Hello, I'm trying to get the vertices of the border/edge/boundary (whatever you want to call it) of a contiguous, closed ROI/label on the surface. I've noticed an option "--label2path" in 'mri_path2label' (FS v4.0.2) that "will treat input as a label and output a path". When I tried this, I got the following output: ----------------- $ mri_path2label --label2path rh.middletemporal.label test.path INFO: Converting rh.middletemporal.label INFO: to test.path INFO: Label to path No encoded paths found in label file ------------------ So, my question is whether the "--label2path" option is supported, and if so, how is it intended to be used? (The output message implies that the path already has to be "encoded" somehow in the label file itself?) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Freesurfer May 2008