Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 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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Freesurfer September 2012