Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Export freesurfer data
by ye tian 08 Apr '14

08 Apr '14

Dear Freesurfers, I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text? Thank you very much! Sincerely, Ye

3 7

tracula and libnetcdf
by Satrajit Ghosh 04 Apr '14

04 Apr '14

hi a.y., when running trac-preproc i'm getting this error (for dmri_motion and dmri_group), but it continues running: /software/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory what will this fail to do? also is libnetcdf now a dependency for freesurfer? the reason i ask is that i'm running this on a remote cluster for which i don't have admin privileges. cheers, satra

2 3

LGI in Qdec
by krista kelly 05 Mar '14

05 Mar '14

Hello, I followed instructions on how to incorporate the lgi_pial measure into QDec, however, it's not coming up when I go to choose this as a measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as to why this may be occurring? Thanks, Krista

2 8

QDEC bad fd number
by Mihaela Stefan 04 Mar '14

04 Mar '14

Hi freesurfers, I get this error when I load qdec.table.dat. Is it something wrong or should I ignore it? Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6027' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6209' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6243' in SUBJECTS_DIR . . . ERROR: QdecProject::VerifySubjects: Couldn't find subject '6052' in SUBJECTS_DIR Too many subjects not found! Someone else complained about the same problem but there was no reply: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html My qdec.table looks like this: fsid diagnosis Cage 6027 ABN -1.39 6209 ABN 2.61 . . Thanks! Mihaela

2 2

Compute DTI metrics in NAWM in Tracula
by Celine Louapre 04 Mar '14

04 Mar '14

Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

2 6

error at spmregister
by Borzello, Mia 04 Mar '14

04 Mar '14

Hi Freesurfers, I get an error when using spmregister saying "Maximum variable size allowed by the program is exceeded"- is that a problem with the number of dicoms? I can attach a screenshot of the error if that helps. Thanks, Mia

3 7

Re: [Freesurfer] Problematic dilated ventricles
by Victor Kovac 03 Mar '14

03 Mar '14

Dear Bruce, A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1. I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces. Could you please advise? Thank you. Victor On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz > > then run: > > recon-all -make all -s MPS1036-1 > > you should be all set > > Bruce > > > > On Mon, 9 Dec 2013, Victor Kovac wrote: > > I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you >> for looking into MPS2002-3 -- it is quite the brain. And somehow, with all >> those morphological abnormalities, this subject has an IQ of 130. Very >> strange. >> Thanks, >> Victor >> >> >> On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> which one? I'm still messing with MPS2002-3 in my spare time >> On Mon, 9 Dec 2013, Victor Kovac wrote: >> >> Hi Bruce, >> Is there a way for you to send the subject(s) you >> analyzed to me? I know >> it's too big for email, but could you possibly >> upload it to GoogleDrive? >> >> Thanks! >> Victor >> >> >> On Wed, Dec 4, 2013 at 3:40 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> p.s. the other thing I did was run the graph >> cut skull >> stripping, which removed a bunch of extraneous >> stuff >> On Wed, 4 Dec 2013, kovac081(a)umn.edu wrote: >> >> Hey! >> >> Victor Kovac (kovac081(a)umn.edu) has uploaded >> some files >> for you at the Martinos Center FileDrop: >> >> -> MPS2002-3.zip (292.12 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=55xjt9pflsi> >> -> MPS2017-1.zip (264.15 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=ak4v31bzu4p> >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here are the two subjects with ventriculomegaly that >> are causing >> the worst issues. The worst segmentation in >> MPS2002-3 is in the >> superior frontal (slices 150-180) and parietal >> (slices 50-95) >> cortical areas; this may be due to the numerous >> dilated >> Virchow-Robin spaces in his brain, which is another >> neuropathological feature of this disease. >> >> Thanks! >> Victor >> >> Please be aware, your upload will expire on December >> 31st. If >> you'd like to download these files, feel free to use >> the link >> below: >> >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep >> >> Cheers, >> The NMR Team >> >> >> >> >> >> 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. >> >> >> >> >> >> >>

3 6

Fw: Re: error in mri_glmfit-sim when using --bg and doss
by charujing123 03 Mar '14

03 Mar '14

Hi doug and others, I am sorry for pasting files in my first contrast directory, if it can help me desolve the question: cache.th23.abs.pdf.dat mc-z.abs.2.sig.cluster.summary mc-z.neg.3.sig.cluster.summary mc-z.pos.3.sig.cluster.summary cache.th23.abs.sig.cluster.mgh mc-z.abs.2.sig.masked.mgh mc-z.neg.3.sig.masked.mgh mc-z.pos.3.sig.masked.mgh cache.th23.abs.sig.cluster.summary mc-z.abs.2.sig.ocn.annot mc-z.neg.3.sig.ocn.annot mc-z.pos.3.sig.ocn.annot cache.th23.abs.sig.masked.mgh mc-z.abs.2.sig.ocn.mgh mc-z.neg.3.sig.ocn.mgh mc-z.pos.3.sig.ocn.mgh cache.th23.abs.sig.ocn.annot mc-z.abs.2.sig.voxel.mgh mc-z.neg.3.sig.voxel.mgh mc-z.pos.3.sig.voxel.mgh cache.th23.abs.sig.ocn.mgh mc-z.abs.3.pdf.dat mc-z.neg.3.y.ocn.dat mc-z.pos.3.y.ocn.dat cache.th23.abs.sig.voxel.mgh mc-z.abs.3.sig.cluster.mgh mc-z.neg.pdf.dat mc-z.pos.pdf.dat C.dat mc-z.abs.3.sig.cluster.summary mc-z.neg.sig.cluster.mgh mc-z.pos.sig.cluster.mgh cnr.mgh mc-z.abs.3.sig.masked.mgh mc-z.neg.sig.cluster.summary mc-z.pos.sig.cluster.summary F.mgh mc-z.abs.3.sig.ocn.annot mc-z.neg.sig.masked.mgh mc-z.pos.sig.masked.mgh gamma.mgh mc-z.abs.3.sig.ocn.mgh mc-z.neg.sig.ocn.annot mc-z.pos.sig.ocn.annot gammavar.mgh mc-z.abs.3.sig.voxel.mgh mc-z.neg.sig.ocn.mgh mc-z.pos.sig.ocn.mgh maxvox.dat mc-z.abs.3.y.ocn.dat mc-z.neg.sig.voxel.mgh mc-z.pos.sig.voxel.mgh mc-z.abs.2.pdf.dat mc-z.neg.3.pdf.dat mc-z.pos.3.pdf.dat mc-z.pos.y.ocn.dat mc-z.abs.2.sig.cluster.mgh mc-z.neg.3.sig.cluster.mgh mc-z.pos.3.sig.cluster.mgh sig.mgh Thanks. All the best. Rujing Zha 2014-02-22 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-22 10:18 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDF…, I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha 2014-02-22 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-02-21 23:49 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug On 2/21/14 5:47 AM, charujing123 wrote: Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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aligning/quality of CT
by Borzello, Mia 02 Mar '14

02 Mar '14

Hi Freesurfers, In general when aligning an MR and a CT, is a 32 slices CT sufficient? I've done a coregistration and am looking at it in tkmedit and the quality of the image isn't so good. Thanks, Mia

2 2

longitudinal process
by Anna Jonsson 02 Mar '14

02 Mar '14

Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna

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Freesurfer February 2014