Freesurfer

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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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trac-all -bedp terminated job
by stobyne＠nmr.mgh.harvard.edu 04 Jun '12

04 Jun '12

Hello, I'm running bedpostx_seychelles from the seychelles prompt (via trac-all -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The processes are generated and run correctly, as far as I can see, until the post-processing job. I receive and email stating: PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00 Why might the process be terminated? -Sean

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Re: [Freesurfer] Concatenating Transforms
by Clark Fisher 04 Jun '12

04 Jun '12

Hi Doug, I do plan to manually align the functionals to the structural as a final step, but our epi scans look different enough from our T1s that I want to use this as a starting point. Also, combining transforms is something I've wanted to be able to do a few times now as I explore different ways of looking at my data, so I think it could be useful for the future. One thing that seems to have worked for my current case is to convert my registrations to the xfm format, add a final row to make a 4x4 matrix, multiply them in matlab, and make a new xfm file with the resulting matrix. Is there a better way to do this? -Clark

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Assertion failed at line 827
by Kiley Seymour 04 Jun '12

04 Jun '12

Dear Freesurfers, I have previously had no trouble using recon-all to process my structural scans. However, today I encountered the problem below. I have looked at postings on this mailing list and it seems this issue is not a freesurfer one. During my last functional analysis of retinotopy data in freesurfer, I came across a problem that required me to install a full version of FSL on my ubuntu machine. Do you think this could be the source of the problem somehow? Otherwise, I am not sure what could have changed since the last time I processed my data with recon-all. Your input would be very much appreciated. Thanks Kiley Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Dr Kiley Seymour Alexander von Humboldt Postdoctoral Fellow Klinik für Psychiatrie und Psychotherapie Charité Campus Mitte Charitéplatz 1 D-10117 Berlin tel: 0049-(0)30-450 517131

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Anatomic Inferences
by Govindarajan, Koushik Athreya 04 Jun '12

04 Jun '12

Dear Freesurfers, I had a question about interpreting the results of the Monte-Carlo simulation. It is my understanding that the clusters are labeled based on the value of the maximum significant vertex in a cluster. So, assuming that a cluster kind of borders or extends over 2 adjacent regions, it could well be labeled as a single region whereas anatomically, it would actually be 2 separate regions. Are there any suggestions for an atlas that could help me make my inferences more meaningful? Sorry if this is a naive question, my knowledge of anatomic labelling is less than impressive :-) Thanks Koushik

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when are uncorrected 0, 001 results permitted instead of FWE?
by Daniel Ferreira 04 Jun '12

04 Jun '12

Dear all, I have heard that the FWE correction sometimes could be demanding and kill very subtle differences, overall for example in aging studies with normal people and narrow-age intervals, or young people, where changes are supposed to be not very big. So, do you know when uncorrected results are justified or at least permitted instead of FWE? Any paper or information about this specific FWE disadvantages in aid of p<0,001 uncorrected results? Thank you very much in advance Daniel Ferreira

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Couldn't download rtview
by Michael Bannert 04 Jun '12

04 Jun '12

Dear freesurfer community, I tried to download rtview but it didn't work. I used the following URL: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview ... as described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21560.html I need this function to interpret retinotopic mapping data. I followed the instructions for running retinotopic mapping using Freesurfer 5 I found here ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis ) and everything seems to work fine but I find it hard to interpret the results and to determine the boundaries between visual areas. Could you please tell me where the file can be found? (Or is there a more elegant way to get a nice color wheel in Freesurfer 5?) Thank you very much! Michael PS: The URL for the FsFast tutorial data still seems to be incorrect as well. See also http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23019.html -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031

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qdec table file
by Laura M. Tully 04 Jun '12

04 Jun '12

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 -- 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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