Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

diffusion unpacksdcmdir error-wrong run!
by jake＠nmr.mgh.harvard.edu 03 Nov '08

03 Nov '08

Hi, Running the following command line : unpacksdcmdir -src /media/AJB_CERV1A/07311357 -targ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015 dti NII ajb_cerv_1a_dti.nii -unpackerr I encountered an error of the wrong run being unpacked. Instead of 15 as designated, 13 appears to have unpacked. This is data from our CD backup. This does not seems to be related to environment, because I originally tried to unpack in STD environment with same results, though all the original analysis was done in stable3 in 2004 when the scans were collected. The logfile is following after bugr. Thanks in advance! Jake BUGR: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti ------------------------------------------------ Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.12 2006/01/24 18:04:33 greve Exp $ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/unpack.log /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti Mon Nov 3 14:19:09 EST 2008 -src /media/AJB_CERV1A/07311357 -targ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015 dti NII ajb_cerv_1a_dti.nii -unpackerr dicomdir /media/AJB_CERV1A/07311357 Scanning source directory ... INFO: summary file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile INFO: status file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status INFO: scanning path to Siemens DICOM DIR: /media/AJB_CERV1A/07311357 INFO: Found 1758 files in /media/AJB_CERV1A/07311357 INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.13.2.1 2006/05/15 21:42:35 greve Exp $ cwd /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti cmdline --sortbyrun --d /media/AJB_CERV1A/07311357 --o /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile --status /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status sysname Linux hostname striatum machine i686 user jake INFO: found 1756 Siemens Files INFO: scanning info from Siemens Files INFO: status file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/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 INFO: found 1756 Siemens files syngo MR 2004A 4VA25A Sorting Assigning Run Numbers RunNo = 0 RunNo = 1 RunNo = 2 RunNo = 3 RunNo = 4 RunNo = 5 RunNo = 6 RunNo = 7 RunNo = 8 RunNo = 9 RunNo = 10 RunNo = 11 RunNo = 12 RunNo = 13 RunNo = 14 WARNING: Run 11 appears to be truncated Files Found: 78, Files Expected (lRep+1): 126 FileName /media/AJB_CERV1A/07311357/58851927 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime 130908.562000 AcqTime 130848.812487 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_functionals PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 30 InversionTime 30 RepetitionTime 2500 PhEncFOV 200 ReadoutFOV 200 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 384 NImageCols 384 NFrames 78 SliceArraylSize 30 IsMosaic 1 ImgPos 581.7606 607.9159 80.1682 VolRes 3.1250 3.1250 5.0000 VolDim 64 64 30 Vc -0.9896 -0.0181 -0.1426 Vr 0.0368 -0.9909 -0.1294 Vs -0.1389 -0.1333 0.9813 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: Run 15 appears to be truncated Files Found: 70, Files Expected (lRep+1): 1 FileName /media/AJB_CERV1A/07311357/58844259 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime 134037.953000 AcqTime 134005.220012 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 83 InversionTime 83 RepetitionTime 7900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 14 SeriesNo 15 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 64 IsMosaic 1 ImgPos 993.7068 1043.8300 171.7054 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9896 -0.0181 -0.1426 Vr 0.0300 -0.9962 -0.0813 Vs -0.1405 -0.0848 0.9864 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 Done scanning Mon Nov 3 14:24:42 EST 2008 ------------------------------------------ 1 circle_localizer ok 256 256 3 1 58867961 2 AAScout ok 128 128 128 2 58867988 3 t1_mprage_sag ok 256 256 128 1 58865756 4 t1_mprage_sag ok 256 256 128 1 58863603 5 ep2d_t1w ok 64 64 30 1 58859483 6 t2_HI_RES ok 448 444 30 1 58859933 7 AAScout ok 128 128 128 2 58860380 8 circle_localizer ok 256 256 3 1 58855710 9 ge_functionals ok 64 64 30 174 58855738 10 ge_functionals ok 64 64 30 174 58852366 11 ge_functionals err 64 64 30 78 58851927 12 ge_functionals ok 64 64 30 126 58850048 13 ge_functionals ok 64 64 30 126 58848889 14 ge_functionals ok 64 64 30 174 58844698 15 DIFFUSION_HighRes err 128 128 64 70 58844259 sortmethod fsfast unpacking config ------------------ {015 dti NII ajb_cerv_1a_dti.nii} ----------------------------------- --------------------------------------------------------- Run 015 ----------------------------------------- Mon Nov 3 14:24:43 EST 2008 015 dti NII ajb_cerv_1a_dti.nii Files In Run: --------------- 58848889 58848904 58848919 58848934 58848949 58848964 58848979 58848994 58849009 58849024 58849039 58849054 58849069 58849084 58846067 58846082 58846097 58846112 58846127 58846142 58846157 58846172 58846187 58846202 58846217 58846232 58846247 58846262 58846277 58846292 58846307 58846322 58846337 58846352 58846367 58846382 58846397 58846412 58846427 58846442 58846457 58846472 58846487 58846502 58846517 58846532 58846547 58846562 58846577 58846592 58846607 58846622 58846637 58846652 58846667 58846682 58846697 58846712 58846727 58846742 58846757 58846772 58846787 58846802 58846817 58846832 58846847 58846862 58846877 58846892 58846907 58846922 58846937 58846952 58846967 58846982 58846997 58847012 58847027 58847042 58847057 58847072 58847087 58847102 58847117 58847132 58847147 58847162 58847177 58847192 58847207 58847222 58847237 58847252 58847267 58847282 58847297 58847312 58847327 58847342 58847357 58847372 58847387 58847402 58847417 58847432 58847447 58847462 58847477 58847492 58847507 58847522 58847537 58847552 58844518 58844533 58844548 58844563 58844578 58844593 58844608 58844623 58844638 58844653 58844668 58844683 ----------------------------- VolRes: 3.125 3.125 4.9999980646632 ------- mri_convert ------------- mri_convert /media/AJB_CERV1A/07311357/58848889 /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii --sdcmlist /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ----------------------- mri_convert /media/AJB_CERV1A/07311357/58848889 /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii --sdcmlist /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom reading from /media/AJB_CERV1A/07311357/58848889... INFO: found 126 files in list file INFO: loading series header info. RunNo = 12 INFO: sorting. INFO: ( 64 64 30), nframes = 126, ismosaic=1 Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 2500, TR = 2500 ms FileName /media/AJB_CERV1A/07311357/58848889 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime 132256.718000 AcqTime 132234.949990 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_functionals PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 30 InversionTime 30 RepetitionTime 2500 PhEncFOV 200 ReadoutFOV 200 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows 384 NImageCols 384 NFrames 126 SliceArraylSize 30 IsMosaic 1 ImgPos 105.3537 103.3935 -55.8230 VolRes 3.1250 3.1250 5.0000 VolDim 64 64 30 Vc -0.9896 -0.0181 -0.1426 Vr 0.0368 -0.9909 -0.1294 Vs -0.1389 -0.1333 0.9813 VolCenter -0.3464 -7.5104 -9.4246 TransferSyntaxUID 1.2.840.10008.1.2.1 sagrev = 0, correv =0, trarev = 0 Vs = -0.138915 -0.133327 0.981288 INFO: no Siemens slice order reversal detected (good!). TR=2500.00, TE=30.00, TI=30.00, flip angle=90.00 i_ras = (-0.98962, -0.0181386, -0.142559) j_ras = (0.0368061, -0.990906, -0.129423) k_ras = (-0.138915, -0.133327, 0.981288) writing to /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii... StartTime: Mon Nov 3 14:19:09 EST 2008 EndTime: Mon Nov 3 14:24:54 EST 2008 unpacksdcmdir Done

2 1

Extraction mean curvature values
by Carl Schultz 02 Nov '08

02 Nov '08

Dear all, I compared the mean curvature between two groups using the mri_glmfit command and the Monte carlo simulation. Is there a possibility to extract the smoothed average curvature values of the significant clusters for all subjects? Thank you in advance Best regards Christoph Schultz University of Jena Department of Psychiatry Germany ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Walter Bauer-Wabnegg; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

2 1

Error Log
by Kellen Mobilia 01 Nov '08

01 Nov '08

Hi Would anyone happen to know the location where Freesurfer hides its error logs? Especially for the "medit tool. Are the located in the local Freesurfer directory or are they located somewhere else, like in the individual; subject folder? Any help would be awesome. Also what would be even better, if anyone knows of a command log that keeps a record of all the commands the medit tools is executing in the background, it probably doesn't exist but it is worth a shot. I am running Freesurfer on a Linux. Thanks Kellen

3 2

mris_calc
by Akram Bakkour 01 Nov '08

01 Nov '08

Hello, I have two thickness files I want to subtract one from the other, so I did: on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh #OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh \ and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' has wrong magic number." Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

2 2

Re: [Freesurfer] mris_calc
by rudolph＠nmr.mgh.harvard.edu 31 Oct '08

31 Oct '08

mris_calc currently only works with flat curvature files (eg ?h.curv, ?h.sulc, ?h.area, ?h.thickness, etc) and not on volumes. ------Original Message------ From: Akram Bakkour Sender: freesurfer-bounces(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] mris_calc Sent: Oct 31, 2008 20:13 Hello, I have two thickness files I want to subtract one from the other, so I did: on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \ -src_type w \ -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \ -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \ OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh #OAS1_????_MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \ 010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh \ and I get this weird error: "mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' has wrong magic number." Any ideas what this means, or if there is any way around this? I suppose I could do this in MATLAB, but I was curious about this magic number business. Thanks! Happy Halloween! A -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Sent via BlackBerry from T-Mobile

5 5

Re: [Freesurfer] Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 29 Oct '08

29 Oct '08

When I look in the contrast folder, there is only one gamma.mgh image, but I have two groups. I am assuming this is the mean thickness, or the mean difference in thickness between groups. How do I get it to save out one file for each group? Where is there a good explanation of the output files from qdec? Thanks Jen On Oct 28, 2008, at 4:30 PM, Doug Greve wrote: If you go into the qdec output directory, you will find a contrast for each group (class). In the contrast directory, you will find a file called gamma.mgh. This will be the average thickness for the group. You can load it into tksurfer, something like: tksurfer fsaverage lh inflated -overlay gamma.mgh doug Bramen, Jennifer E. wrote: Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

2 1

Viewing atlas?
by Ryan Scotton 29 Oct '08

29 Oct '08

Hi Freesurfers, Some associates of mine are working on a pipeline that generates cortical parcellations and we are looking to compare its measurements to some measurements generated by the freesurfer pipeline. However, our pipeline parcellates broader regions which include several labels generated by the FS cortical parcellation process within each of our labels. What we need is to get a general idea of where every label generated by FS fits within the context of our broader labeling scheme. SO, this may be an obvious question, but how might i be able to view an atlas image volume with the FS parcellation/labeling scheme applied to it in order to get a general idea of how the separate labeling schemes match up? Thanks! Ryan

3 3

Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 28 Oct '08

28 Oct '08

Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

2 1

FI and sulc -- how are they related?
by Rudolph Pienaar 28 Oct '08

28 Oct '08

> Dear Rudolph Pienaar, > could you please tell me if the Folding index and the sulc are in a way > correlated? > thank you Hi David - This question does not really have a simple yes or no answer, mostly because each measures different features. These features are both derived from the topology of the surface, but are not directly related. The 'sulc' measurement is the distance that a specific vertex is away from a hypothetical "mid-surface" that exists between the gyri and the sulci. This surface is chosen so that the "mean" of all the displacements is zero. The 'sulc' gives a indication then of linear *distance* and displacements: how "deep" and how "high" are the folds, but doesn't say much about how "sharply" folded they are, or in what manner are they folded (like cylinders, like spheres, etc). The FI is a *curvature* (not distance) measure. It uses the k1 and k2 principal curvatures at each vertex to calculate a value according to (per Van Essen/Drury 1997): FI_i = fabs(k1) * (fabs(k1) - fabs(k2)); Conceptually the FI tries to give a measure of how (relatively) tightly or sharply folded a gyrus is in a cylindrical sense. The more cylindrical a gyrus is, the more the FI increases along its length. For regions with spherical or saddle folding, k1 = k2 and the FI is zero. So it tells us more about how much like cylinders the folds are, but tell us nothing about how "deep" the folds extend. Essentially, the 'sulc' and the FI are related of course by the topology of the surface but they each measure conceptually different things. It is not possible to determine 'sulc' from the FI or vice versa. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

1 0

qdec patch
by Juranek, Jenifer 28 Oct '08

28 Oct '08

Nick, Just in case you're taking a head count, I would benefit from a patch for qdec which reads ?h.pial_lgi files as mentioned in response to Martin's posting yesterday. Cheers, Jenifer

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