Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

normal vector in gm
by Seok Lew 15 Mar '11

15 Mar '11

Hello users, My colleagues and I are trying to create a gray matter electric conduction model where a preferable conduction direction is aligned with the normal direction induced from the pial and white surface normals. Freesurfer reconstruction already gives pial and white matter surface normals and correspondences between them. Now I want to have the freesurfer surface normals projected on the mri volumes and interpolated for gray matter voxels (regions between the pial surface and the white surface), such that each voxel of gray matter can have a normal direction. Is it possible to do the job with freesurfer scripts ? If so, what scripts might work for this? Thanks in advance, Seok

2 5

Qdec - thickness-age correlation - Interpretation
by Alex Hanganu 15 Mar '11

15 Mar '11

Dear Freesurfer Experts, We have two groups at similar ages and the thickness-age correlation shows many cluster of significant values. Pointing to this maximum the plots present similar regressions coefficients for both groups. Actually it would be intresting to have the regions were the thickness – age correlation differ. Or what is the physiological meening of this kind of correlations ?? Sincerely, Sergiu, Alex.

2 2

mri_convert Siemens Allegra Dicom problem
by Myriam Siefert 14 Mar '11

14 Mar '11

Hi everybody, We're doing a structural VBM bicentric cross cultural study, using Freesurfer v5.0.0. on 2 computers : FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 9.8.0 i386 FREESURFER_HOME: /home/scnlab/Desktop/ freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Debian version: squeeze/sid Kernel info: Linux 2.6.32-29-generic i686 <freesurfer(a)nmr.mgh.harvard.edu> Successful reconstructions have been realized for some of the subjects from one of the 2 centers, using their DICOMS (Siemens Trio), but we seem to be unable to use any DICOM from the other center (Siemens Allegra). It seems that the same problem has already been submitted to the mailing list, without any available solution : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01354.html We get the following error messages (same on both computers): [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz mri_convert 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz file not found or unknown file type for file 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert --in_type siemens_dicom 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz mri_convert --in_type siemens_dicom 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm... ERROR (ScanSiemensSeries): /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL) [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert --in_type dicom 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgzmri_convert --in_type dicom 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm... Starting DICOMRead2() dcmfile = /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm dcmdir = /Users/SPLab/Desktop/OK-J-01/structural ERROR: /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm is not a dicom file [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert --in_type siemens --out_type mgz 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz mri_convert --in_type siemens --out_type mgz 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm... ERROR: could not parse /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm ERROR: siemensRead(): /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm - When trying to convert them with the MRI Convert software I get the following error message : "Unable to find series UID" - I can however convert them to nifti using SPM8 and MIPAV, and then successfully run mri_convert and auto-recon1. I also tried to "save as dicoms" in MIPAV, but it didn't change anything. Here are headers as given by MIPAV : Dimension 256 Dimension 256 Dimension 192 Type Unsigned Short Min 0.0 Max 1654.0 Orientation Axial Pixel resolution 0 0.75 Pixel resolution 1 0.75 Pixel resolution 2 1.0 Unit of measure Millimeters per pixel Transformation Matrix 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 (0002,0000) File Meta Information Group Length 206 (0002,0001) File Meta Information Version 1 (0002,0002) Media Storage SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0002,0003) Media Storage SOP Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322 (0002,0010) Transfer Syntax UID 1.2.840.10008.1.2 (0002,0012) Implementation Class UID 1.2.804.114118.3 (0002,0013) Implementation Version Name eFilm/UCDavisLib (0002,0016) Source Application Entity Title (0008,0005) Specific Character Set ISO_IR 100 (0008,0008) Image Type ORIGINAL, PRIMARY, M, ND (0008,0016) SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0008,0018) SOP Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322 (0008,0020) Study Date 20070308 (0008,0021) Series Date 20070308 (0008,0022) Acquisition Date 20070308 (0008,0023) Content (formerly Image) Date 20070308 (0008,0030) Study Time 142430.328000 (0008,0031) Series Time 153343.484000 (0008,0032) Acquisition Time 152244.074999 (0008,0033) Content (formerly Image) Time 153344.937000 (0008,0050) Accession Number 06H17 (0008,0060) Modality MAGNETIC_RESONANCE (0008,0064) Conversion Type Workstation (0008,0070) Manufacturer SIEMENS (0008,1010) Station Name MRC20409 (0008,1030) Study Description Research001^affiliates (0008,103E) Series Description MPRAGE_high_resolution (0008,1090) Manufacturer's Model Name Allegra (0008,1140) Referenced Image Sequence (0008,1140) (0008,1150): Referenced SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0008,1140) (0008,1155): Referenced SOP Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804425018700001053 (0008,1140) (0008,1150): Referenced SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0008,1140) (0008,1155): Referenced SOP Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804425018700001054 (0008,1140) (0008,1150): Referenced SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0008,1140) (0008,1155): Referenced SOP Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804425018700001055 (0018,0000) Acquisition Group Length 472 (0018,0020) Scanning Sequence IR, GR (0018,0021) Sequence Variant SP, MP (0018,0022) Scan Options IR (0018,0023) MR Acquisition Type 3D (0018,0024) Sequence Name *tfl3d1 (0018,0025) Angio Flag N (0018,0050) Slice Thickness 1 (0018,0080) Repetition Time 2500 (0018,0081) Echo Time 4.38 (0018,0082) Inversion Time 1100 (0018,0083) Number of Averages 1 (0018,0084) Imaging Frequency 123.075312 (0018,0085) Imaged Nucleus 1H (0018,0086) Echo Number(s) 0 (0018,0087) Magnetic Field Strength 2.8936200141907 (0018,0089) Number of Phase Encoding Steps 256 (0018,0091) Echo Train Length 1 (0018,0093) Percent Sampling 100 (0018,0094) Percent Phase Field of View 100 (0018,0095) Pixel Bandwidth 130 (0018,1000) Device Serial Number 20409 (0018,1012) Date of Secondary Capture 20110311 (0018,1014) Time of Secondary Capture 163150 (0018,1016) Secondary Capture Device Manufacturer National Institutes of Health, Center for Information Technology (0018,1018) Secondary Capture Device Manufacturer's Model Name Medical Image Processing, Analysis and Visualization (MIPAV) (0018,1019) Secondary Capture Device Software Version(s) 5.2.1 (0018,1020) Software Version(s) syngo MR 2004A 4VA25A (0018,1030) Protocol Name MPRAGE_high_resolution (0018,1200) Date of Last Calibration 20070216 (0018,1201) Time of Last Calibration 124353.000000 (0018,1251) Transmit Coil Name Head_3T (0018,1310) Acquisition Matrix 256, 0, 0, 256 (0018,1312) In-plane Phase Encoding Direction COL (0018,1314) Flip Angle 8 (0018,1315) Variable Flip Angle Flag N (0018,1316) SAR 0.01545061543584 (0018,1318) dB/dt 0 (0018,5100) Patient Position Head First-Supine (0020,0000) Relationship Group Length 336 (0020,000D) Study Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804422681200000004 (0020,000E) Series Instance UID 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002321 (0020,0010) Study ID 1 (0020,0011) Series Number 9 (0020,0012) Acquisition Number 1 (0020,0013) Instance (formerly Image) Number 95 (0020,0032) Image Position (Patient) -100.06779670715, -96.722891569138, 2.4289360046387 (0020,0037) Image Orientation (Patient) 1, 0, 0, 0, 1, 0 (0020,0052) Frame of Reference UID 1.3.12.2.1107.5.2.7.20409.20070308142804656.0.0.0 (0020,1040) Position Reference Indicator (0020,1041) Slice Location 2.4289360046387 (0028,0000) Image Presentation Group Length 166 (0028,0002) Samples per Pixel 1 (0028,0004) Photometric Interpretation MONOCHROME2 (0028,0010) Rows 256 (0028,0011) Columns 256 (0028,0030) Pixel Spacing 0.75, 0.75 (0028,0100) Bits Allocated 16 (0028,0101) Bits Stored 12 (0028,0102) High Bit 11 (0028,0103) Pixel Representation 0 (0028,0106) Smallest Image Pixel Value 0 (0028,0107) Largest Image Pixel Value 752 (0028,1050) Window Center 460 (0028,1051) Window Width 898 (0028,1055) Window Center & Width Explanation Algo1 (0029,0000) Private Tag -118 (0029,0010) Private Tag SIEMENS CSA HEADER (0029,0011) Private Tag SIEMENS MEDCOM HEADER (0029,0012) Private Tag SIEMENS MEDCOM HEADER2 (0029,1008) Private Tag IMAGE NUM 4 (0029,1009) Private Tag 20070308 (0029,1010) Private Tag SV10 8MEchoLinePositionB?a… (0029,1131) Private Tag 4.0.204078339 (0029,1132) Private Tag 131072 (0029,1133) Private Tag 0 (0029,1134) Private Tag DB TO DICOM (0029,1260) Private Tag com (0032,0000) Study Group Length 30 (0032,1060) Requested Procedure Description Research001 affiliates (0040,0000) Private Tag \ (0040,0244) Performed Procedure Step Start Date 20070308 (0040,0245) Performed Procedure Step Start Time 142430.328000 (0040,0253) Performed Procedure Step ID MR20070308142430 (0040,0254) Performed Procedure Step Description Research001^affiliates (7FE0,0000) Pixel Data Group Length 131080 So here are my questions : 1) Is there something wrong with the command lines I wrote? 2) Is there maybe something wrong in the files headers that I should edit so that Freesurfer would recognize them as dicoms? or any other solution in order to use those dicoms? 3) If we were to use the nifti files : - what would be the disadvantages? - is there a risk of orientation problems with single nifti files? with dual nifti files? should we check for L-R inversion for each subject after mri-convert? - are there any concerns with comparing these subjects to our other groups subjects (for whom we used the dicoms)? Thank you very much in advance, Myriam Siefert

2 1

question about the capability of qdec and using non normal distributed subjects
by Knut J Bjuland 14 Mar '11

14 Mar '11

Hi I am beginner in using Freesurfer. What can of statical analyze is Qdec cable of doing? Can I use data that are not normal distributed since my data sample contains subjects with neuronal damage? Cheers Knut J Bjuland DMV

2 1

cortical thickness and meaning of colored lines
by Angela Cosentino 13 Mar '11

13 Mar '11

2 1

I: I: Re: (no subject)
by Angela Cosentino 13 Mar '11

13 Mar '11

I've founded the answer at the second question. Please, tell me if my first sentence is ok. --- Dom 13/3/11, Angela Cosentino <cosentino_angela(a)yahoo.it> ha scritto: Da: Angela Cosentino <cosentino_angela(a)yahoo.it> Oggetto: [Freesurfer] I: Re: (no subject) A: fischl(a)nmr.mgh.harvard.edu Cc: freesurfer(a)nmr.mgh.harvard.edu Data: Domenica 13 marzo 2011, 09:21 Sorry. The 2 lines are red and yellow. But probably nothing changes. Sorry again! --- Dom 13/3/11, Angela Cosentino <cosentino_angela(a)yahoo.it> ha scritto: Da: Angela Cosentino <cosentino_angela(a)yahoo.it> Oggetto: Re: [Freesurfer] (no subject) A: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Data: Domenica 13 marzo 2011, 07:49 In this way, I see the cortical thickness' value near the "curvature" indication, voxel-by-voxel. It's ok? And, when I write the command line in tkmedit: "tkmedit SUBJECT_ID brainmask.mgz -surfs", I see the brainmask image and two colored line, a red one and a green one. The first one is th edge of cortical surface; the other one is the white and grey matter's edge. Between these 2 lines, the software calculates the cortical thickness. Is this ok?Have I understood well? Thanks. --- Sab 12/3/11, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> ha scritto: Da: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] (no subject) A: "Angela Cosentino" <hamtaro88(a)hotmail.it> Cc: freesurfer(a)nmr.mgh.harvard.edu Data: Sabato 12 marzo 2011, 22:06 you can load the lh.thickness (if you are viewing the left hemisphere surface) or rh.thickness (if you are viewing the right hemisphere surface) in tksurfer either using file->load curvature or file->load overlay cheers Bruce On Sat, 12 Mar 2011, Angela Cosentino wrote: > > Hi! > How can I view the cortical thickness' misure? > > _______________________________________________ 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. -----Segue allegato----- _______________________________________________ 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.

1 0

cortical thickness and significance of colored lines
by Angela Cosentino 13 Mar '11

13 Mar '11

To see cortical thickness I used "File"--> "Load Curvature" (rh.thick), as you have suggested. In this way, I see the cortical thickness' value near the "curvature" indication, voxel-by-voxel. It's ok? And, when I write the command line in tkmedit: "tkmedit SUBJECT_ID brainmask.mgz -surfs", I see the brainmask image and two colored line, a red one and a yellow one. The first one is th edge of cortical surface; the other one is the white and grey matter's edge. Between these 2 lines, the software calculates the cortical thickness. Is this ok?Have I understood well? Thanks.

1 0

I: Re: (no subject)
by Angela Cosentino 13 Mar '11

13 Mar '11

Sorry. The 2 lines are red and yellow. But probably nothing changes. Sorry again! --- Dom 13/3/11, Angela Cosentino <cosentino_angela(a)yahoo.it> ha scritto: Da: Angela Cosentino <cosentino_angela(a)yahoo.it> Oggetto: Re: [Freesurfer] (no subject) A: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Data: Domenica 13 marzo 2011, 07:49 In this way, I see the cortical thickness' value near the "curvature" indication, voxel-by-voxel. It's ok? And, when I write the command line in tkmedit: "tkmedit SUBJECT_ID brainmask.mgz -surfs", I see the brainmask image and two colored line, a red one and a green one. The first one is th edge of cortical surface; the other one is the white and grey matter's edge. Between these 2 lines, the software calculates the cortical thickness. Is this ok?Have I understood well? Thanks. --- Sab 12/3/11, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> ha scritto: Da: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] (no subject) A: "Angela Cosentino" <hamtaro88(a)hotmail.it> Cc: freesurfer(a)nmr.mgh.harvard.edu Data: Sabato 12 marzo 2011, 22:06 you can load the lh.thickness (if you are viewing the left hemisphere surface) or rh.thickness (if you are viewing the right hemisphere surface) in tksurfer either using file->load curvature or file->load overlay cheers Bruce On Sat, 12 Mar 2011, Angela Cosentino wrote: > > Hi! > How can I view the cortical thickness' misure? > > _______________________________________________ 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.

1 0

(no subject)
by Angela Cosentino 13 Mar '11

13 Mar '11

Hi! How can I view the cortical thickness' misure?

3 2

Surface region masking
by Mustafa, Nazahah 12 Mar '11

12 Mar '11

Hi all I used mri_annot2label and then mri_mergelabels to get frontal lobe region. Now I am going to get structures which lie under that frontal lobe. I was thinking to overlay between the lobe mask and the structures. I tried mri_label2vol but it was not completely masking the lobe areas. Is there any other way I can do? Thank you Regards; Naza The University of Aberdeen is a charity registered in Scotland, No SC013683.

1 0

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