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30132 discussions

Repost: empty CSD folder?
by lordowen 03 Sep '12

03 Sep '12

Dear Freesurfer experts: I post this question 2 weeks ago, but no answer since then. Thus I repost it to avoid possible missing mail. Please help us to fix this situation, thanks you. ----------轉寄的簡訊 ---------- 寄件者："lordowen" <lordowentu(a)gmail.com> 日期：2012-82012/8/20 lordowen <lordowentu(a)gmail.com>: > The enclosed file please find the edited log file and screen-shot > picture. We edit the log file because it is too big (about 20 MB). We > kept the command-line record and removed most poll record. Basically, > our Mac workstation polled once for every 10 seconds. > > 2012/8/20 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> Can you send us your command line and screen out? Really, two months? >> Bruce >> >> >> >> On Aug 19, 2012, at 11:39 PM, lordowen <lordowentu(a)gmail.com> wrote: >> >>> Dear experts: >>> >>> We performed permutation analysis (with -sim perm) for our thickness >>> data. After 2 month calculation, the process completed but the CSD >>> folder only contained an empty folder named "poll". No CSD file in >>> them. So I wonder if the CSD file has been stored in another place or >>> something wrong with them? Please advise us. >>> >>> -- >>> Best regards >>> -- >>> 杜政昊 >>> >>> Cheng-Hao Tu, PhD >>> Post Doctoral Research Fellow >>> Integrated Brain Research Unit >>> Department of Medical Research and Education >>> Taipei Veterans General Hospital >>> No.201, Sect.2, Shih-Pai Rd. >>> Taipei >>> Taiwan >>> Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com >>> Tel: +886-2-28712121 ext 3474 >>> Fax: +886-2-28745182 >>> >>> _______________________________________________ >>> 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. > > > > -- > Best regards > -- > 杜政昊 > > Cheng-Hao Tu, PhD > Post Doctoral Research Fellow > Integrated Brain Research Unit > Department of Medical Research and Education > Taipei Veterans General Hospital > No.201, Sect.2, Shih-Pai Rd. > Taipei > Taiwan > Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com > Tel: +886-2-28712121 ext 3474 > Fax: +886-2-28745182 -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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how i can compute volume of a VOI
by Eustratios Karavasilis 03 Sep '12

03 Sep '12

Dear all, i am new Freesurfer user (Freesurfer 5.0 installed). I want to calculate the volume of a VOI that is not calculated from recon all. I ll decribe you the steps that were followed. Using tkmedit and tkmedit tools i created ROIs in many slices. Every ROI i saved it as label, then i merge all the labels using the mri_mergelabels. I am trying create a volume from this "final" label using mri_label2vol, using as label the new "final" label, as template volume the origin volume (orig.mgz) but i don't have the register.dat file. How i can create it? The above way is the appropriate way to calculate a VOI? Thank you in advance!

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cortical volume and ortical jacobian_whitematter
by Knut J Bjuland 03 Sep '12

03 Sep '12

Hi,I have looked into cortical surface volume and cortical jacobian_whitematter. Can I use these measure a in similar way as cortical thickness? Do jacobian_whitematter represent the whitematter thickness in the cortex? How reliable are cortical volumes compared to cortical thickness?Best regardKnut J

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Freesurfer-Error message
by Varghese Chikku 03 Sep '12

03 Sep '12

Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012 My image files, in dcm format, are at /media/sf_freesurferstudys/raw/raw_scr/T1pre : /media/sf_freesurferstudys/raw/raw_scr/T1pre> ls Image00001 Image00010 Image00019 Image00028 Image00037 Image00046 Image00002 Image00011 Image00020 Image00029 Image00038 Image00047 Image00003 Image00012 Image00021 Image00030 Image00039 Image00048 Image00004 Image00013 Image00022 Image00031 Image00040 Image00049 Image00005 Image00014 Image00023 Image00032 Image00041 Image00050 Image00006 Image00015 Image00024 Image00033 Image00042 Image00007 Image00016 Image00025 Image00034 Image00043 Image00008 Image00017 Image00026 Image00035 Image00044 Image00009 Image00018 Image00027 Image00036 Image00045 Many thanks for your help. chikku

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Fwd: Command line to get BA stats with the thresholds
by _andreia_＠sapo.pt 31 Aug '12

31 Aug '12

Hi! I'm reposting my question: Is there a command line to obtain the BA values with the recommended thresholds (e.g. 0.9 for V1) from all subjects at once? At least for each area at once for all subjects? Thank you, Andreia Pereira

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(no subject)
by Ryan 31 Aug '12

31 Aug '12

Hello all, I'm analyzing the data for a training study our research group conducted, and I'm looking to see if there are changes in cortical thickness as a result of training. We have pre- and post-training scans, so I followed the longitudinal tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#In…) There are 4 measures listed on the website (average, rate, pc1, and spc) - which do I choose if I simply want to see if there is a difference in cortical thickness for pre vs. post? Also, do I need to run anything afterwards such as cluster corrections? Best, -W. Ryan McGarry

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Loading nifti overlays with TCL script
by Sid Kundu 31 Aug '12

31 Aug '12

Hello Freesurfers, I have a basic question as I'm just getting into scripting, but I'm trying to write a script that loads overlays from multiple contrasts and takes images. However, I can't figure out how to properly load nifti files as overlays. I'm attempting to load .nii volumes from group level analysis (which should need no registration file), so when I use sclv_read_from_volume setting the argument for registration type to 1 or 2 (look for register.dat, or calculate identity) both fail. Any help on this would be much appreciated. Thanks in advance. _________________________________ Sid Kundu Biomedical Engineering Boston University

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scale bar shrink/grow problem if fsaverage is displayed
by Jörg Pfannmöller 31 Aug '12

31 Aug '12

Dear freesurfers, if I display fsaverage in tksurfer (tksurfer fsaverage rh pial) and switch on the scale bar it appears to have a length of approximately 1 cm. However, If I start to zoom into the brain the color bar shrinks until a certain scale-up is reached. After it has completely vanished it starts to grow if I further scale-up the image. If I use a subject from our investigations this problem does not ocur. Can someone give my a hint about the cause of this problem? Cheers pfannmoe

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I: hippocampal subfield segmentation
by lorenzo pasquini 30 Aug '12

30 Aug '12

hello carolina to me it took about 5-6 hours. greets, lorenzo ________________________________ Da: Carolina Valencia <cvalencia(a)linkdx.com.co> A: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Inviato: Giovedì 30 Agosto 2012 20:37 Oggetto: [Freesurfer] hippocampal subfield segmentation Hi Freesurfer community, A quick question, how long takes to run the hippocampal subfield segmentation for a subject that has already run the typical recon-all pipeline? Thank you, -- -- Carolina Valencia M _______________________________________________ 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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how to convert .vtk surface meshes with labels to .annot format?
by Arno Klein 30 Aug '12

30 Aug '12

what is the best way to convert a .vtk surface mesh (with labels as scalars) to freesurfer .annot format? i am currently converting the vtk file to freesurfer .label files, then using freesurfer to consolidate these into an .annot file, which is slow, roundabout, and generates a lot of files. cheers, @rno

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