Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

fsaverage across versions
by Steinmann, Iris 22 Sep '08

22 Sep '08

Hi, we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5. Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother. We would like to know what constitutes the exact difference between these two fsaverage datasets and whether it is possible to use the new version for analysis with the "old" fsaverage data without getting inconsistent results. Thanks a lot, Iris

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Methodology Papers.
by Matt Clarkson 22 Sep '08

22 Sep '08

Dear everyone, Hopefully someone can help me. If I do "recon-all --help" i can see a list of 31 steps for the main cortical thickness pipeline. Does anyone have a list that links each of the 31 steps to the most current methodology paper? I've been reading most of the methodology papers referenced in the wiki, but the software has clearly evolved over the years, and even though you can read the wiki, and trawl through log files, I want to be absolutely sure that for each step, I know exactly what algorithm is applied. Has anyone gone through this before? Thanks in advance, Matt Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

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Re: [Freesurfer] automating tkmedit
by Graham Wideman 20 Sep '08

20 Sep '08

... also if anyone might find these helpful, there's an article that may be of interested here: http://surfer.nmr.mgh.harvard.edu/fswiki/QaImageScripts This shows tcl scripts to do something substantial in tkmedit and tksurfer, and bash scripts to activate FreeSurfer and the tcl scripts. Hope that helps, Graham

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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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