Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

SNR and voxWM
by Kushal Kapse 06 Jun '12

06 Jun '12

hi doug and fellow FS users, i am going thru the recon_checker.log file to look into anat SNR, mWM, stdWM and voxWM.....the ones with lowest SNR are seemed to be marked with arrow....may i know the reason why some of them have lowest SNR and they are marked with arrow in front of em?..the data is acquired on 3t scanner kk

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acquiring substancia nigra volume
by Zohra Ahmadzai 05 Jun '12

05 Jun '12

The final recon process, autorecon3 - uses "ASegStatsLUT.txt" by default to segment certain subcortical structures listed within this textfile. On the otherhand, FreeSurferColorLUT.txt has labels for more subregions, including the substancia nigra which is a region of interest for a particular project we are doing here. The Aseg. output does not label or calculate the volume of the substancia nigra and I was wondering if there is a way to do this? cheers ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Re: [Freesurfer] freesurfer question
by Douglas Greve 05 Jun '12

05 Jun '12

Hi Tony, you can use bbregister to create the registration file. You might also look at the multi-modal tutorial on our wiki as this goes over the steps that you will need to get and apply the registration. For the 2nd question, you can use mris_anatomical_stats. doug ps. Please send questions to the list instead of me directly. Thanks! On 6/5/12 2:37 PM, Jiang, Zhiguo wrote: > > Hi, Douglas > > Thanks for your comments. I was trying to run mri_vol2surf. But it > asks for a registration file. Would youp lease tell me how to get that > registration file? I figured that must be registering volume file to > subject's T1. (of course in my case, the volume file is already in T1 > space since I drawed them on top of the subject T1 image). > > Another quick question is, once the label is created, is there a quick > command to pull out the thickness values (mean etc ) > > Thanks a lot, > > Best, > > Tony > > Zhiguo Jiang, Ph.D. > > http://pain.loni.ucla.edu > > > IMPORTANT WARNING: This email (and any attachments) is only intended > for the use of the person or entity to which it is addressed, and may > contain information that is privileged and confidential. You, the > recipient, are obligated to maintain it in a safe, secure and > confidential manner. Unauthorized redisclosure or failure to maintain > confidentiality may subject you to federal and state penalties. If you > are not the intended recipient, please immediately notify us by return > email, and delete this message from your computer.

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Re: [Freesurfer] using own average subject
by Schuster, Christina /DZNE 05 Jun '12

05 Jun '12

Hi, many thanks for your help! Unfortunately, I still have some questions: 1) Why would someone only want to display the results on a cohort-specific average, but not use that average for calculation? 2) So if I want to use my cohort-specific average for calcuation of the cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that? If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg? Best wishes, Christina _______________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug On 06/01/2012 11:37 AM, Douglas N Greve wrote: > Hi Christina, if you want to use the registration to your new > template, then you need to run mris_register on each subject to > register to the new template. You can actually do this with surfreg, > something like: > > foreach subject (subj1 subj2) > surfreg --s $subject --t newtemplate --lh > end > > This will create $subject/surf/lh.newtemplate.sphere.reg > > You can then run > > mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ... > > Note that the surfreg cmd above will take about an hour for each subject > > doug > > > > > On 06/01/2012 11:05 AM, Bruce Fischl wrote: >> Hi Christina >> >> you should cc the list so others (Doug!) can answer. The purpose of >> mris_register is to bring your subjects into a common surface-based >> coordinate system. fsaverage lives in that space, but so will the >> average that you make >> >> cheers >> Bruce >> >> >> On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote: >> >>> Hi Bruce, >>> >>> just to be sure that I understood it correctly: >>> >>> I just use make_average_subject to create my template and then I use >>> mris_preproc --target newtemplate and not further --surf-reg >>> specification. >>> Then after mri_glmfit --surf newtemplate ... I have my final results?! >>> >>> So what is the purpose of the mris_register command? >>> >>> Many thanks for your help. >>> Best wishes >>> Christina >>> >>> ________________________________________ >>> Von: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 31. Mai 2012 20:39 >>> An: Schuster, Christina /DZNE >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] using own average subject >>> >>> Hi Christina, >>> >>> the new template will already be in the same target space as fsaverage >>> since you used the sphere.reg to create it. Just use it as a >>> background for >>> your group results. >>> >>> cheers >>> Bruce >>> >>> On Thu, 31 May 2012, Schuster, >>> Christina /DZNE wrote: >>> >>>> Dear FreeSurfer experts, >>>> >>>> I am trying to create an average subject based on a matched >>>> subsample (2 different scanners, patients and healthy controls). >>>> >>>> I successfully ran make_average_subject receiving a "newtemplate". >>>> Now I am unsure how to proceed: >>>> >>>> As far as I understand it, according to the SurfaceRegAndTemplates >>>> page >>>> (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) >>>> I should use mris_register for each subject from my subsample >>>> receiving ?h.sphere.reg.newtemple files with which I should make >>>> again an average subject, let's call it "newnewtemplate". >>>> >>>> Is that correct? >>>> >>>> Now, if I want to assemble the data into common space using >>>> mris_preproc: what do I need to specify? >>>> Would --target be the newtemplate or newnewtemplate? Do I need to >>>> specifiy the --surf-reg as well? >>>> >>>> >>>> On the other hand, I read in one of your tutorials that I only need >>>> to run make_average_subject receiving a "newtemplate" which I then >>>> specify using mris_preproc as --target and that --surf-reg is not >>>> needed. >>>> >>>> >>>> So what would be the correct way to use my own template for the >>>> group analysis? >>>> >>>> Many thanks for you help! >>>> >>>> Best wishes >>>> Christina >>>> >>>> >>> >>> 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. >>> >>> >>> >> >> > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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aparc+aseg labels
by Sarosh, Cyrus 05 Jun '12

05 Jun '12

Hello, I was hoping somebody could help me out. I am trying to create a label file for the aparc+aseg file. All I'm wanting is the pixel value and the label. I know there is the FreeSurferColorLUT.txt file which contains this information, but looking at this file I can tell that all of these labels aren't included in every file, so I'm trying to create a file like this for each individual MR I use only containing the labels needed for each individual scan. I don't know if this is possible, but hopefully it is and somebody could give me the commands to use to generate this file? Thanks for your help. Cyrus ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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mris_preproc
by Richter, Julia 05 Jun '12

05 Jun '12

Dear FreeSurfer experts, I am trying to run mris_preproc after caching my data. As command lines, I am typing: mris_preproc --fsgd file.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.allpatients.thickness10.mgh Everytime I am trying to run these commands, it tells me that it does not know the command mris_preproc. I have no clue what is going on here. Any suggestions? Thanks for your help, best Julia

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Re: [Freesurfer] qdec table
by Laura M. Tully 04 Jun '12

04 Jun '12

Thanks Doug - Nick, do you have any idea what might be happening here? Why might qdec stop allowing me to select more than one continuous variable? Thanks! Laura. Message: 24 Date: Mon, 04 Jun 2012 11:19:57 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec table file To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4FCCD21D.4040105(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed OK, I've replicated that this is happening, but Nick will have to take a look. doug On 06/04/2012 11:05 AM, Laura M. Tully wrote: > > > > Hi Doug, > > Attached is the qdec table file and associated levels files. It's > strange that qdec won't let me select more than one continuous > variable. What's even more strange is that I have been able to do that > last month when I originally looked at these data before doing manual > edits and quality control. I don't think that I have changed anything > since then, but I'm not sure what to look for. Any help you have would > be most appreciated! > > Best, > > Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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Re: [Freesurfer] no aseg
by Gregory Kirk 04 Jun '12

04 Jun '12

so it seems that i ran make_average_volume which does have a --no-aseg flag make_average_subject really just runs 2 other commands make_average_surface and make_average_volume. bruce the reason i did this is that mike was running a `super` average, i.e. the average subject of 2 different syudies, i.e. ave_study1, ave_study2 and he was running make_average_subject --subjects ave_study1 ave_study2 --out superave. we were doing this so we could map labels from one study to another and we were getting an error in the log file from make_average_volume that indicated it was having a problem with the aseg after the make_average_surface had already finished without error. really we could just skip it i think as we are not actually doing anything with the average volume. greg On 06/04/12, Bruce Fischl wrote: > Hi Michael > > a couple of typos. It should be "make_average_subject" (note no "s"), and it should be --subjects (note the ending "s"). I also don't see a flag named --no-aseg, which I think is why it's being included as a subject. What are you trying to do? > > cheers > Bruce > > On Mon, 4 Jun 2012, michael kruepke wrote: > > >Hi all - > >Having a bit of an issue with trying to run a make_average with the flag > >--no-aseg. When written > > > >make_average_subjects --subject subject1 subject2 --no-aseg --out > >superaverage > > > >the propt runs as if --no-aseg and --out superaverage are subjects i wish to > >average in with subjects1 and subject2. This is obviously and issue, hoping > >someone might have an idea of a solution. I have tried moving these flags to > >somewhere else in the prompt seeing if that would solve it, no luck there. > > > >Best- > >Michael > > > >-- > >Michael D. Kruepke > >PhD - University of Illinois at Urbana-Champaign > >BA - Psych - University of Wisconsin-Madison > >mdkruepke(a)gmail.com > >(262)-483-7449 > > > > > > > > > _______________________________________________ > 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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exclude ROIs in an annotation file under a label
by Leon 04 Jun '12

04 Jun '12

Hi, FreeSurfer experts I have one annotation file with many ROIs and one label file that denotes medial wall. Now I want to remove the ROIs in the annotation file that is covered by the medial wall. Is there any way that I can realize that in the surface space? Thank you! Leon

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A few beginner questions about thickness analysis using freesurfer
by Jiang, Zhiguo 04 Jun '12

04 Jun '12

1. How do I register subjects' thickness maps to a common space to be able to do vertex wise comparison? And can any brain map be used as the common space? 2. If I have a hand-drawn ROI on subject's original T1, is it possible to resample the volume ROI to the surface (so I can extract the thickness values from that ROI) Any command lines would be appreciated. Best, Tony Zhiguo Jiang, Ph.D. [cid:image002.png@01CD4250.DA877620] ________________________________ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Freesurfer June 2012