Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Problems with mri_watershed: almost no skull stripping
by Úrsula Pérez Ramírez 28 Aug '14

28 Aug '14

Hello, I'm having troubles trying to obtain only the brain in T1-weighted RM images that contain metastases. First of all I have converted the DICOM images to mgz with "mri_convert /usr/local/freesurfer/subjects/A0D0C0.dcm /usr/local/freesurfer/subjects/case1.mgz" . Then, I have employed "mri_watershed -atlas /usr/local/freesurfer/subjects/case1.mgz /usr/local/freesurfer/subjects/brainmaskcase1.mgz" but as I see with freeview, I obtain the original images with a really bad or any skull stripping. For example, in one case, the left part is removed a lot and the right is intact. I have lowered the threshold but nothing changes. How could I solve it? I'm working in VirtualBox and I didn't find the ".license" file, so I haven't copied the three lines. Is it necessary? Thank you very much Regards, Úrsula

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error in pre-processing in TRACULA
by 渡辺杏里 28 Aug '14

28 Aug '14

Dear TRACULA experts Hello. I am running TRACULA, but it exited an error very early in pre-processing. My data is not a format in DICOM but .nii, does this cause the error? I set the dcmlist to .nii file (in attachment). Could anyone help me? This is the error log and I attached the configuration file. -error log- [watanabeanris-Mac-Pro:mybook/Anri/diffusion_tutorial] watanabeanri% trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/dmrirc.local -log /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.log -cmd /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Aug 22 11:03:45 JST 2014 mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii... TR=7175.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996496, -0.0735924, -0.0397398) j_ras = (-0.0756091, 0.995787, 0.0518831) k_ras = (-0.0357542, -0.0547061, 0.997862) writing to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz... cp /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs flip4fsl /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8 fslswapdim /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz x y z /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory Darwin watanabeanris-Mac-Pro.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Aug 22 11:03:46 JST 2014 Many thanks for your help. Best Wishes, Anri WATANABE ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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Obtaining volume measures based on T2 image
by Nobuko Kemmotsu 27 Aug '14

27 Aug '14

Dear Freesurfer experts, I have a project where I would like to compute volumes of the olfactory bulb. I understand olfactory bulb is currently not in the freesurfer atlases, so I would need to manually trace it for me to get the volume measures. Given that olfactory bulb appears easier to be seen on T2 scans, I am considering using T2 images for this purpose, but I also plan on obtaining high resolution T1 for reconstruction purposes. It may also be of my interest to try to automate this segmentation for future usage. How would I go about this process using FreeSurfer?

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FW: does Tracula correct for CSF contamination
by Laura Christine Anderson 27 Aug '14

27 Aug '14

Dear Tracula users, does anyone know whether or not Tracula uses any corrections for CSF contamination? Thanks for your time, Laura -- Laura Anderson, B.A. Graduate Student Clinical / Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112

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Re: [Freesurfer] problem with format of CT dicoms
by Borzello, Mia 27 Aug '14

27 Aug '14

Hi Freesurfers, Apologies, I've never used this format before. Here's the error: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri For additional information: 1. Neuropace2JB 2. mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz 3. UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped) Thanks so much, m ________________________________________ From: Borzello, Mia Sent: Friday, August 22, 2014 1:14 PM To: Freesurfer support list Subject: RE: [Freesurfer] problem with format of CT dicoms Hi Freesurfers, Apologies, I've never used this format before. Here's the error: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri For additional information: 1. Neuropace2JB 2. mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz 3. UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped) Thanks so much, m ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:43 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with format of CT dicoms Hi Mia, please follow the instructions on the web site below for submitting bug reports. thanks doug On 08/22/2014 12:37 PM, Borzello, Mia wrote: > Right, sorry. I was running a command with mri_convert in order to convert the ct dicoms to mgz format. The error I ran into was: > UseSliceScaleFactor 0 (slice 0: 1) > Segmentation fault (core dumped) > > Thanks, > m > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Friday, August 22, 2014 12:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] problem with format of CT dicoms > > Hi Mia, do you realize that your description of the problem is too vague > for us to help you? If you want help in a timely fashion, please include > more detail like the problem you ran, the command-line arguments, the > terminal output, etc. Please see the following web page for the types > information we are looking for: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > The easier you make it for us, the more likely you are to get help. > > thanks > doug > > > On 08/22/2014 12:17 PM, Borzello, Mia wrote: >> Hi Freesurfers, >> >> I'm in the process of creating the ct.mgz file, but it is erroring and >> saying there is a "segmentation fault (core dumped)." >> >> What can I do to remedy this? >> >> Thanks, >> m >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview: Creating and using a LUT with a single region
by Tamás Hauer 27 Aug '14

27 Aug '14

Hi, I am trying to use a LUT which picks out just one region of the segmentation, e.g.: $ cat HCOnlyColorLUT.txt #$Id: FreeSurferColorLUT.txt,v 1.70.2.7 2012/08/27 17:20:08 nicks Exp $ #No. Label Name: R G B A 0 Unknown 0 0 0 255 17 Left-Hippocampus 220 216 20 0 with which I expect the segmentation overlay to have only one yellow region corresponding to the left HC. I run the command line: $ freeview -v T1.mgz aseg.mgz:colormap=lut:lut=HCOnlyColorLUT.txt after which I am getting the overlay displayed as below. I must be doing something stupid, could you, please help me out? Thanks Tamás -- Tamás Hauer McMRI AG Neugasse 55 9000 St. Gallen, Switzerland Tel: (+41)-76-380-7379 Tel: (+41)-71-913-0580 Fax: (+41)-71-913-0589

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White matter lesions
by Elijah Mak 27 Aug '14

27 Aug '14

Dear Freesurfer Experts, I am hoping to do some WML analyses in some patient groups by using the measure of T1 hypointensities derived from the ASEG analyses. Is there a way to view and check the accuracy the WML mask for each subject? Also, how may I go about performing a voxelwise analyses of the WML masks between 2 groups? I am referring to the following paper: http://www.ncbi.nlm.nih.gov/pubmed/21518999 Any help and advice will be greatly appreciated. Thank you all for your time! Many Thanks, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Qdec Help
by Abrishamchi, Aurash David 27 Aug '14

27 Aug '14

Hello, I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the "find clusters and go to max" button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Apologies for the long e-mail, Let me know if you need any clarification. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 AAbrishamchi(a)mgh.harvard.edu<mailto:AAbrishamchi@mgh.harvard.edu>

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Cortical gray matter surface area
by will brown 27 Aug '14

27 Aug '14

Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 What about grey? Thanks, Will

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Individual commands in preproc-sess
by Reza Rajimehr 26 Aug '14

26 Aug '14

Hi, I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis of monkey data. To have a better control on the parameters of the analysis, I prefer to run the individual commands of preproc-sess one-by-one and check the output of each stage before proceeding with the rest of preproc-sess. Specifically I may manually edit the functional-anatomical registration, so I want to check the registration before moving on to the next step in preproc-sess. Also I need to skip the human-specific aspects of the analysis (e.g. Talairaching) if there are such things in preproc-sess. So is there a list of individual commends, in an appropriate order, that are used in preproc-sess? If someone has a routine for monkey data analysis with FreeSurfer v5.3, I would be happy to know about that as well. Thanks, Reza

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