Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

registration problem
by SHAHIN NASR 14 Nov '14

14 Nov '14

Hi, For one of my subjects, I have noticed a misalignment between sig.nii and orig.mgz when I try to show the sig map using either tkmedit (as below): cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45 or tkmedit-sess: cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Subjects tkmedit auil_anat orig.mgz -overlay auil2/bold/OriExp_TR3_1p5mm_PR/ANG_90_45/abs_sig.nii.gz -reg auil2/bold/register.dof6.dat~ I checked the registration file for this subjects and I don't see this problem there. tkregister2 --reg ../Subjects/auil2/bold/register.dof6.dat~ --mov ../Subjects/auil2/bold/template.nii.gz --surf I also checked the brain.mask and it covers the whole brain and looks fine to me. I also checked my other subjects and their results are fine. Do you have any idea why this is happening? P.S.: I process my data in in nmr-dev-env but I have also checked the above lines in nmr-stable53-env and problem is still there. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Prefrontal white matter
by Alshikho, Mohamad J. 14 Nov '14

14 Nov '14

Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and right prefrontal white matter areas. My plan is to derive a mask for that area from aseg.mgz then I will register this mask to the FA map to calculate the FA value. Is it possible to derive like this mask from aseg.mgz and can I control the dimensions of that mask? thanks a lot Mohamad

3 7

Cortex/volume parcellation
by Octavian Lie 14 Nov '14

14 Nov '14

Dear all, Is there a way to generate random or seed-based whole cortical (surface) or brain (volumetric) parcellations in freesurfer or plugins, generating n equal area (volume) scouts, where the user can select the n? Thank you, Octavian

2 1

Freesurfer YouTube lecture slide download link 404
by Alex Spedding 14 Nov '14

14 Nov '14

Hi, Sorry if this is the wrong place to put this - never used a mailing list before - but I've been watching the FreeSurfer lectures on Youtube. The link to download the slides in the Introduction Lecture ( https://www.youtube.com/watch?v=GywOKtfKZIU ) the only one I've watched so far is broken. If you could fix the link that would be appreciated. Thank you, Alex Spedding

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Data requirements
by will brown 13 Nov '14

13 Nov '14

Hi all, I have structural data that has a slice thickness of 5mm and spacing between slices of 5mm (there are around 30 dicom images). I ran it through recon-all but the output was bad. Is it possible to create surfaces from such data? Or is the bad output the answer to this question... Thanks, Will

2 1

Unpacking Siemens Functional Data: No DICOM files found
by Shady El Damaty 13 Nov '14

13 Nov '14

Hi freesurfers, I've been stuck on this problem for a while and couldn't find anything online to help me out so I've come to the mailing list as my last resort. I am trying to unpack my functional data into fsl format using the unpacksdcmdir command. However, I am not successful using this command and get the error message: "no dicom files found" This is the command I'm entering: unpacksdcmdir -src $DICOMDIR -targ ~/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log When I list the contents of $DICOMDIR, I find that there are about 800 or so files with enumerated names ending in *.ACQ (e.g.: 1.ACQ, 2.ACQ... 800.ACQ). Does anyone have any ideas why unpacksdcmdir isn't reading these files? The output after running the command appears below. Thanks in advance for your help! Shady El Damaty unpacksdcmdir -src $DICOMDIR -targ ~/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /glusterfs/mirror/cfmi/home/se394 -src /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER -targ /exports/home/se394/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log Thu Nov 13 12:59:20 EST 2014 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/11/13-17:59:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: se394 Machine: node020.cfmi.georgetown.edu Platform: Linux PlatformVersion: 3.10.0-123.9.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 node020.cfmi.georgetown.edu Linux node020.cfmi.georgetown.edu 3.10.0-123.9.2.el7.x86_64 #1 SMP Tue Oct 28 18:05:26 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thu Nov 13 12:59:20 EST 2014 Log File is /exports/home/se394/Ultimatum/sess01/unpack.log INFO: Logfile is /exports/home/se394/Ultimatum/sess01/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /exports/home/se394/Ultimatum/sess01/dicomdir.sumfile INFO: status file is /exports/home/se394/Ultimatum/sess01/parse.status Scanning directory Thu Nov 13 12:59:20 EST 2014 mri_parse_sdcmdir --sortbyrun --d /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER --o /exports/home/se394/Ultimatum/sess01/dicomdir.sumfile --status /exports/home/se394/Ultimatum/sess01/parse.status 0 Done scanning Thu Nov 13 12:59:24 EST 2014 ------------------------------------------ ERROR: no dicom files found in /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER

2 1

mri_cnr
by Jürgen Hänggi 13 Nov '14

13 Nov '14

Dear FS experts There is a reviewer question with respect to the voxels/vertices used to compute the SNR and CNR with FreeSurfer's mri_cnr function. Do we right that SNR/CNR computation is based only on the voxels that are located at the interface between the white and pial surface? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 2

mritotal failed
by will brown 12 Nov '14

12 Nov '14

Hi there, I am receiving the following error during recon-all: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7573/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/freesurfer/mni/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log Any ideas?

1 0

Missing 'recon edit' button in Freeview
by Zhang, Kunyu 12 Nov '14

12 Nov '14

Hi all, I seem to be missing the ‘recon edit’ button that is supposed to be next to ‘voxel edit’ in Freeview. I am using version 1.0 on Mac OS X 10.10 from the latest version (v5.3.0) of FreeSurfer. According to the FreeSurferWiki, if I check ‘recon edit’ within ‘voxel edit,’ it just locks the brush value to 255 and eraser value to 1, but for extended editing, Recon edit mode is needed. If anyone can please help me with this issue, I would greatly appreciate it! Thanks, Kunyu

1 0

FW: recon-all failure due to header
by Ashley Stillman 12 Nov '14

12 Nov '14

We are having issues running recon-all on our dicom files, as they are saved as a mosaic. When we open the original dicom file (attached) it lists out the rows, columns and slices. However, when we run mriparsesdcmdir, it just posts 0’s for the rows and columns (screen shot attached). We are able to recreate the output file necessary to run recon-all (basically fill in the missing 0’s). Is there a way to tell recon-all to call on this file to retrieve the missing data manually? Thank you, Ashley Ashley N. Stillman Clinical Psychology Graduate Research Assistant University of Tulsa, T.R.A.P.T. Lab Laureate Institute for Brain Research email: anstillman(a)laureateinstitute.org<mailto:anstillman@laureateinstitute.org> | ashley-stillman(a)utulsa.edu<mailto:ashley-stillman@utulsa.edu>

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