Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] automating tkmedit
by Krish Subramaniam 19 Sep '08

19 Sep '08

Hi Jared Few things: * I think primarily the error is because tcl doesn't have "sleep" command. tcl has an "after" command, however, which takes the arguments in milliseconds. So you'd use "after 5000" to make it wait for 5 seconds. * Also to force the screen to update immediately, use the "RedrawScreen" command * consolidating everything, the script that seems to work is after 5000 SetDisplayFlag 16 0 RedrawScreen after 5000 SetDisplayFlag 16 1 RedrawScreen after 5000 I saved this is test.tcl and gave tkmedit <subj_name> brain.mgz -segmentation aseg.mgz -tcl test.tcl * Also note that you can give "source" command in the tcl command window i.e. if you had loaded tkmedit with just "tkmedit <subj_name> brain.mgz -segmentation aseg.mgz " then in the prompt if you give %source test.tcl it's equivalent to the -tcl switch. * Finally, the tkmedit scripting does have a guide/reference http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMe… Best Krish On Sep 19, 2008, at 1:09 PM, Jared Price wrote: > Sure, thanks for the interest. It is my first time trying to > automate something so it is an admittedly novice attempt. Tkmedit > is invoked with the usual syntax using "tkmedit (Patient id) > brainmask.mgz -segmentation aseg.mgz" The script was created in > nano and I have attached it. I think the issue is just getting the > file to read properly when in the tkmedit environment. Also, it > might be helpful to know that the file is located in usr/bin. It > might also be helpful to know that we use Mac OS X and we are using > X11 as the graphical interface program for tkmedit and Terminal > (running a tcsh shell) as our command-line interpreter. Also, I > have not added looping to it yet, I want to make sure I can get it > to run properly before trying to loop it. Thanks again. > Jared > > Jared Price > Center for Neurological Imaging > Brigham and Women's Hospital > Harvard Medical School > 1249 Boylston Street > Boston, MA 02115 > > 617-525-6076 > jcp44(a)bwh.harvard.edu > > The information transmitted in this electronic communication is > intended only for the person or entity to whom it is addressed and > may contain confidential and/or privileged material. Any review, > retransmission, dissemination or other use of or taking of any > action in reliance upon this information by persons or entities > other than the intended recipient is prohibited. If you received > this information in error, please contact the Compliance Help Line > at 800-856-1983 and properly dispose of this information. > > Krish Subramaniam wrote: >> >> Hi Jared >> >> Could you give the script as well as the command you used to invoke >> tkmedit? >> >> Krish >> >> >> On Sep 19, 2008, at 8:32 AM, Jared Price wrote: >> >>> Hi everyone, >>> I have written a simple script to automate the switching between >>> the grayscale MRI image and the segmentation volume. All it is is >>> a script that types "SetDisplayFlay 16 1" followed by a waiting >>> period and then "SetDisplayFlag 16 0" followed by another waiting >>> period and then loops. However, even though these commands work >>> just fine when entered directly into Terminal, when I try to run >>> the script I get an error saying essentially that the command or >>> script itself can't be found. Of course, this is done while >>> running tkmedit and so the title bar of my terminal reads >>> "terminal - tkmedit.bin". When I type "echo $PATH" I get the >>> respone that the PATH variable does not exist. Does anyone know >>> how to make the command function in tkmedit? >>> Thanks, >>> >>> Jared Price >>> Center for Neurological Imaging >>> Brigham and Women's Hospital >>> Harvard Medical School >>> 1249 Boylston Street >>> Boston, MA 02115 >>> >>> 617-525-6076 >>> jcp44(a)bwh.harvard.edu >>> >>> The information transmitted in this electronic communication is >>> intended only for the person or entity to whom it is addressed and >>> may contain confidential and/or privileged material. Any review, >>> retransmission, dissemination or other use of or taking of any >>> action in reliance upon this information by persons or entities >>> other than the intended recipient is prohibited. If you received >>> this information in error, please contact the Compliance Help Line >>> at 800-856-1983 and properly dispose of this information. >>> _______________________________________________ >>> 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 > > SetDisplayFlag 16 0 > sleep 5 > SetDisplayFlag 16 1 > sleep 5 >

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automating tkmedit
by Jared Price 19 Sep '08

19 Sep '08

Hi everyone, I have written a simple script to automate the switching between the grayscale MRI image and the segmentation volume. All it is is a script that types "SetDisplayFlay 16 1" followed by a waiting period and then "SetDisplayFlag 16 0" followed by another waiting period and then loops. However, even though these commands work just fine when entered directly into Terminal, when I try to run the script I get an error saying essentially that the command or script itself can't be found. Of course, this is done while running tkmedit and so the title bar of my terminal reads "terminal - tkmedit.bin". When I type "echo $PATH" I get the respone that the PATH variable does not exist. Does anyone know how to make the command function in tkmedit? Thanks, Jared Price Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 1249 Boylston Street Boston, MA 02115 617-525-6076 jcp44(a)bwh.harvard.edu The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance Help Line at 800-856-1983 and properly dispose of this information.

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frontal lobe volume
by dfwang 19 Sep '08

19 Sep '08

Dear all, I would like to calculate the frontal lobe volume from the outputs of freesrufer. Could any body here please tell me the way to do this? Any comments are welcome! Best wishes, Vincent

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Re: [Freesurfer] Command mris_calc error
by Yuan Xu 18 Sep '08

18 Sep '08

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Command mris_calc error
by Yuan Xu 18 Sep '08

18 Sep '08

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labels->annot->wmparc
by Lars Tjelta Westlye 18 Sep '08

18 Sep '08

Hi, I have several labels drawn on the white surface of average7 (ancient project). I want to generate one annotation file per hemisphere comprising these labels only in order to use mri_aparc2aseg --labelwm and then compute the volume of the underlying WM of each label. Please see the employed strategy below. The annotation file overlaid the subject's surface is indeed reasonable, both in terms of locations and labels. After running mri_aparc2aseg, though, the resulting segmentation does not label the areas correctly. That is, the localizations of all areas are ok, but the labels (namings) are wrong. Left hemi is ok, but all five labels in the right hemi are called rh_unknown. Thus also the output from the subsequent mri_segstats is incorrect for right hemi. What am I doing wrong? Thank you very much! What I have done is the following: #A. map average7 label to individual subject surface per hemi mri_label2label --srclabel average7/label/${leftlabel} \ --srcsubject average7 \ --trgsubject ${s} \ --trglabel ${s}/label/${leftlabel} \ --regmethod surface --hemi lh mri_label2label --srclabel average7/label/${rightlabel} \ --srcsubject average7 \ --trgsubject ${s} \ --trglabel ${s}/label/${rightlabel} \ --regmethod surface --hemi rh #B. generate annotation from several labels for each hemi (FreeSurferColor files attached) mris_label2annot --s ${s} \ --h lh --ctab FreeSurferColorLUT_Left.txt \ --l ${s}/label/APOE_ERP_grupper_left_lat_front_pole.label \ --l ${s}/label/APOE_ERP_grupper_left_OccTemp.label --a APOE mris_label2annot --s ${s} \ --h rh --ctab FreeSurferColorLUT_Right.txt \ --l ${s}/label/APOE_ERP_grupper_right_lat_front_pole.label \ --l ${s}/label/APOE_ERP_grupper_right_OccTemp.label \ --l ${s}/label/APOE_ERP_grupper_right_med_front_pole.label \ --l ${s}/label/APOE_ERP_grupper_right_TPJ.label \ --a APOE #C. segmenting WM based on the generated annot files mri_aparc2aseg --s ${s} --ribbon --o APOE.mgz --annot APOE --labelwm --rip-unknown Cheers, Lars FREESURFER_HOME: /psyklab/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 RedHat release: Red Hat Enterprise Linux Client release 5.2 (Tikanga) Kernel info: Linux 2.6.18-92.el5 x86_64

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mri_preproc
by Cibu Thomas 18 Sep '08

18 Sep '08

Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh Any help would be greatly appreciated Thankyou Cibu Thomas

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mri_convert and image orientation; Analyze format
by Watson, Christopher 18 Sep '08

18 Sep '08

Hello Freesurfers, Lately I've been scratching my head about image orientation problems. What I do here is take the DICOM images and use mri_convert to convert them into SPM Analyze format. The command I use is: mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \ "path/to/subj/dir/image" --out_type spm So the output files we get are imageXXX.{hdr,img,mat}. So, I assume these truly are Analyze format and not NIfTI (if i'm incorrect please tell me, this would be very important). There are weird things SPM does concerning image orientation, so it's *very* important that I get this right (we do functional imaging on surgery candidates): *Does mri_convert flip the images in any way?* That is, if my DICOM images are in radiological convention, will the imageXXX images still be in radiological convention? I've been searching far and wide and have hit a wall. With patients, we can see the water pill on the right side of the forehead easily, but with the EPI functional images for our research subjects it's pretty much impossible to tell. Thanks very much, Chris Watson

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neuroimaging job announcement
by Paymon Hosseini 18 Sep '08

18 Sep '08

Greetings, The MIT Center for Neuroeconomics is seeking a technical assistant who will take a lead role in the design, implementation, and analysis of functional MRI studies. A candidate with FreeSurfer/FSL experience will have a distinct advantage. Here is a link to the full job description and online application page: https://sh.webhire.com/servlet/av/jd?ai=631&ji=2275928&sn=I

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RE: [Freesurfer] freesurfer
by Bruce Fischl 17 Sep '08

17 Sep '08

they are listed in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers, Bruce On Wed, 17 Sep 2008, Hwee Ling Lee wrote: > Hi Bruce, > > Thanks for the advice. > It works well. > I was wondering if there's any way I could check what values of the label > correspond to a particular brain region. > Thanks. > > Cheers, > HL > > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: 16 September 2008 22:51 > To: Hwee Ling Lee > Cc: freesurfer(a)nmr.mgh.harvard.edu; 'Doug Greve' > Subject: Re: [Freesurfer] freesurfer > > Hi HweeLing, > > you can use mri_extract_label aparc+aseg.mgz <label> <output volume> > > then the command line Jenni posted before to transform it to MNI space (or > you can try giving the talairach.xfm to mri_extract_label with -t, but I'm > not positive that works) > > cheers, > Bruce > > > > On Tue, 16 Sep 2008, Hwee Ling Lee wrote: > >> >> Hi, >> >> I wanted to write out a mask image for left and right STS as Analyze > format file. >> Using this, I plan to plot the parameter estimates along the STS, > posteriorly to anteriorly. >> I know this is an unusual way of doing things, however, I thought this > might be best suited to customize each STS mask for individual subjects as > many studies have shown differences in STS morphology. >> >> Thanks, >> HweeLing >> >> >> On Tue, 16 Sep 2008 15:44:11 -0400 (EDT) >> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> can you tell us exactly what you would like to do with it? >>> On Tue, 16 Sep 2008, Hwee Ling Lee wrote: >>> >>>> Hi, >>>> >>>> I'm re-posting a question. >>>> >>>> Pardon my ignorance. >>>> >>>> How do I use this mri_vol2vol command? I tried to follow the notes, > however, >>>> I'm not quite sure, hence I was not able to write a ROI mask. >>>> >>>> Cheers, >>>> HL >>>> >>>> >>>> -----Original Message----- >>>> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve >>>> Sent: 12 September 2008 18:10 >>>> To: Bruce Fischl >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu; Hwee Ling Lee >>>> Subject: Re: [Freesurfer] freesurfer >>>> >>>> You can also skip the 1st two steps and just convert aparc+aseg.mgz to >>>> MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then >>>> look for voxels with values 1030 (left STG) or 2030 (right STG). >>>> >>>> doug >>>> >>>> Bruce Fischl wrote: >>>> >>>>> Hi HweeLing, >>>>> >>>>> I think the aparc.a2005s has the STS labeled in it, so you should >>>>> already have what you need in individual space. You could use >>>>> mri_annot2label, mri_label2vol and mri_vol2vol to transform this into >>>>> MNI if you need to. >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> >>>>> >>>>> On Fri, 12 Sep 2008, Hwee Ling Lee wrote: >>>>> >>>>>> >>>>>> Hi All, >>>>>> >>>>>> I was looking for methods to create a superior temporal sulcus >>>>>> mask (upper and lower boundary). >>>>>> >>>>>>> From my understanding, Freesurfer does a pretty good job in labeling >>>>>>> the >>>>>> >>>>>> sulcus, hence I was wondering if there are possible ways to write the >>>>>> particular ROI as a mask image for each individual subject, and >>>>>> preferably >>>>>> to be in the MNI space or if not, at least in the native space. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> Best wishes, >>>>>> HweeLing >>>>>> >>>>>> >>>>>> >>>>>> > ----------------------------------------------------------------------- >>>>>> Hwee Ling, Lee >>>>>> Max-Planck Institute for Biological Cybernetics >>>>>> Cognitive Neuroimaging >>>>>> Spemannstrasse 41 >>>>>> 72076 Tuebingen >>>>>> Germany >>>>>> Tel: +49-70701-601-1785 >>>>>> Fax: +49-7071-601-616 >>>>>> hwee-ling.lee(a)tuebingen.mpg.de >>>>>> hweeling.lee(a)gmail.com >>>>>> http://www.kyb.mpg.de/~hweeling >>>>>> > ----------------------------------------------------------------------- >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> Hwee Ling, Lee >> >> PhD student >> http://www.kyb.mpg.de/~hweeling >> Max-Planck Institute for Biological Cybernetics >> NWG Noppeney >> Spemannstr 41 >> 72076 Tuebingen >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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