Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

stuck on step to create surface
by Jane Qu 18 Jun '13

18 Jun '13

Hi freesurfers! I am new to freesurfer and have encountered a problem with surface generation. I am working with a non-human primate anatomical volume. I finished segmenting the white matter and am on this next step. I think, however, that the step where the surface is generated from wm.mgz is crashing (I started the process last night and it has not finished and does not appear to be moving forward). Does anybody know why this might be happening? How long should I expect this step to take? I have attached below some of the messages I'm receiving. Thanks in advance! Jane

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Mapping annotation files from one subject to another
by Peter Savadjiev 18 Jun '13

18 Jun '13

Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where <file> and <output> are some file names) and that executed without any problems. Then I ran mris_ca_label <subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here <subject_id> is some subjects' name, and <output> and <newfile> are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter

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ct.anat.nii file
by Borzello, Mia 18 Jun '13

18 Jun '13

Hi Freesurfers, I'm wondering if there is a way to figure out if a ct.anat.nii file is corrupt or not. I'm using MRICro as a viewer, and the file doesn't look right. Thanks, Mia

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medial wall crossing surface
by celine＠nmr.mgh.harvard.edu 18 Jun '13

18 Jun '13

Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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Temporal Lobe Problem
by LIOR ZWANZIGER 18 Jun '13

18 Jun '13

Hi, I have scans of around 60 participants and about 75% percent of these have significant portions of their temporal lobe excluded. I have attached different slices from four different subjects to give you an idea of the typical scan I've been encountering, [though there are problems in minimally 10 slices for each participant and some exclusions can be found in more than 50 slices.] We are using FreeSurfer version 5.1.0. What is your advice, since there are so many slices for a large number of participants that would need to be edited? Extension of the watershed parameters, adding control points, or something else I haven't considered? I am hesitant to add control points for such a great number of participants. Thank you! Lior Zwanziger

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Group Analysis
by Nooshin Zadeh 18 Jun '13

18 Jun '13

Dear Freesurfer group I am interested to do group analysis on my data. If I want to do inter-individual group analysis, what is the minimum number of subjects I need to have? Also if I want to do intra-individual analysis, what is the best way in FS? I appreciate your time and your help. Thanks a lot, Nooshin

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recon-all error: mri_watershed (picture include)
by Sudhin A. Shah 18 Jun '13

18 Jun '13

Hi, This is the error I get: ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=96, z=161, r=9988 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 42408 RIGHT_CER CSF_MIN=1, CSF_intensity=17, CSF_MAX=27 , nb = 1512 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=20 , nb = 2142 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=29 , nb = 17010 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 15750 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 5994 mri_watershed Error: GLOBAL region of the brain empty ! Please find attached a screenshot of the MRI Please advice, S

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Re: [Freesurfer] Tracula bbr errors
by Douglas Greve 18 Jun '13

18 Jun '13

Hi Matt, was I supposed to get back to you on this? I generally leave these types of questions to Nick and Zeke. doug ps. Please post to the list instead of us indivudally. thanks! On 6/16/13 12:46 PM, Matthew Hoptman wrote: > Hi Dr. Greve, > Any news on the libboost_program_options.so.5 issue? I've encountered > it using mris_resample (as part of mri_cvs_register) using Linux Mint 14 > Best, > Matt

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problem downloading Xhemi files
by amirhossein manzouri 18 Jun '13

18 Jun '13

Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir

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Fwd: DICOM unpacking error
by Luc Amdahl 18 Jun '13

18 Jun '13

---------- Forwarded message ---------- From: Luc Amdahl <luc.amdahl(a)gmail.com> Date: Mon, Jun 17, 2013 at 3:45 PM Subject: Re: [Freesurfer] DICOM unpacking error To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Thanks for responding. Here is the command line and screen output: [Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdcmdir -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /Users/lab/MRI/Solar_System -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii Fri Jun 14 09:47:20 EDT 2013 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/14-13:47:20-GMT BuildTimeStamp: May 13 2013 16:45:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: lab Machine: Sheinberg-Lab-MRI-iMac.local Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 Sheinberg-Lab-MRI-iMac.local Darwin Sheinberg-Lab-MRI-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 Fri Jun 14 09:47:20 EDT 2013 Log File is subj_4/unpack.log INFO: Logfile is subj_4/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is subj_4/dicomdir.sumfile INFO: status file is subj_4/parse.status Scanning directory Fri Jun 14 09:47:20 EDT 2013 mri_parse_sdcmdir --sortbyrun --d DICOM --o subj_4/dicomdir.sumfile --status subj_4/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Fri Jun 14 09:48:46 EDT 2013 ------------------------------------------ 1 localizer ok 512 512 3 1 59198979 2 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59199008 3 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59187534 4 T1_MEMPRAGE_freesurfer ok 256 256 176 1 59175542 5 ep_TR2500_128 ok 64 64 42 128 59175096 6 ep_TR2500_128 ok 64 64 42 128 59170659 7 ep_TR2500_128 ok 64 64 42 128 59169456 8 ep_TR2500_128 ok 64 64 42 128 59168253 9 ep_TR2500_128 ok 64 64 42 128 59167050 10 ep_TR2500_128 ok 64 64 42 128 59162613 11 ep_TR2500_113 ok 64 64 42 113 59299072 12 t2_3DFLAIR ok 256 240 176 1 59297629 unpacking config ------------------ {5 bold nii f.nii} {6 bold nii f.nii} {7 bold nii f.nii} {8 bold nii f.nii} {9 bold nii f.nii} {10 bold nii f.nii} ----------------------------------- --------------------------------------------------------- Run 5 ----------------------------------------- Fri Jun 14 09:48:46 EDT 2013 5 bold nii f.nii ERROR: reading DICOM/59175096 tag 28 30 Here is the version of FS I'm using: freesurfer-i386-apple-darwin10.8.0-stable5-20130513 What exactly do you mean when you ask where the DICOM's are from? I receive them from Brown's MRF facility, and we've been successful in converting them on other iMac's using the same version of FS. Thanks, Luc On Mon, Jun 17, 2013 at 2:36 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you send the complete command line and screen output, and tell us what > version of FS you are using and where the dicoms are from? > > On Mon, 17 Jun 2013, Luc Amdahl wrote: > > Hi Freesurfers, >> I am trying to use Freesurfer to convert DICOM files to nii f.nii files. >> Freesurfer is able to find all the DICOM files but always gives me an >> error: >> "ERROR: reading DICOM/59175096 tag 28 30". >> >> Can anyone help? >> >> Thanks, >> >> Luc >> >> -- >> Luc Amdahl >> Brown University '14 >> Sc.B. Neuroscience >> 69 Brown St., #6137 >> Providence, RI 02912 >> 603.252.4441 >> >> >> > > 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<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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Freesurfer June 2013