Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

Concatenate surfaces
by MCLAREN, Donald 29 Sep '11

29 Sep '11

Is there a way to concatenate surfaces for use with mri_segstats? The surfaces are already in fsaverage space. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Error for Patients Abnormal Side Right
by Antonella Kis 29 Sep '11

29 Sep '11

Dear Doug, Seems that this will never end...It is so painful already. I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left. Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I was running: mri_glmfit-sim \ --glmdir lh_qdec_AbnormalSide_R.glmdir \ --cache 2 neg \ --cwpvalthresh .99 \ --overwrite and the ERROR: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/june2011/_orig_ FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/y.mgh --fsgd /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/qdec.fsgd dods --glmdir /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir --surf fsaverage lh --label /usr/local/freesurfer/subjects/june2011/_orig_/fsaverage/label/lh.aparc.label --C /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /usr/local/freesurfer/subjects/june2011/_orig_/qdec/lh_qdec_AbnormalSide_R.glmdir/contrasts/lh-Diff-Class1-Class2-Intercept-thickness.mat DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 31.843147 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm32/neg/th20/mc-z.csd PLEASE HELP! THANKS! AK

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aparc2feat and using Freesurfer Lookup Table
by Michelle Umali 29 Sep '11

29 Sep '11

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+ aseg.nii.gz -thr 433v uthr 433 \ featdir/reg/freesurfer/Visual_V3d_l.nii.gz The resulting image was empty. I was able to use aseg2feat for all subcortical regions, so then i used aparc2feat. However, this uses a different color table which is missing many of the regions present in the Freesurfer Color Lookup table that I would like to use. How can I get area 433 (Visual_V3d_l) from the Freesurfer Color Lookup Table so I can later run fslmaths to generate a mask? Thanks. Michelle

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Error with Clusters Summary (ASAP)
by Antonella Kis 29 Sep '11

29 Sep '11

Dear Doug, Sorry, I am coming up with the same problem. I am running the mri_glmfit_sim on the QDEC results to get the text file with the cortical thickness average and cluster summary but unfortunately I see for one side the --sim is not give me any clusters even if I can see 5 in QDEC after choosing the threshold 2. How can I correct this so --sim can cache my clusters from QDEC? If there is no way to correct this what should be my contrast vector if I want to eliminate AGE so I want to see the differences only between groups. In QDEC I did not choose age as covariant so I had only the discrete variable = Class. Should I take the contrast vector if I want to eliminate AGE to be equal with [1 -1] and my fsgd will not include the Age variable? MANY THANKS! AK

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unpacking error:: "exited abnormally"
by swoodman＠nmr.mgh.harvard.edu 29 Sep '11

29 Sep '11

Hello, I'm trying to unpack a diffusion run and getting this error, "child process excited abnormally". Anyone encounter this before? Here are the details: [purkinje:pat08_sess2_dti] (nmr-stable3-env) unpacksdcmdir -src /space/archive/181/siemens/TrioTim-35162-20080921-182835-474000 -targ /cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti -run 6 dti NII pat08_sess2_dti.nii -unpackerr Thu Sep 29 10:56:17 EDT 2011 INFO: Logfile is /cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti/unpack.log Scanning source directory ... INFO: summary file is /cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti/dicomdir.sumfile INFO: status file is /cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_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 Done scanning Thu Sep 29 11:03:30 EDT 2011 ------------------------------------------ 1 localizer ok 512 512 3 1 474000-000001-000002.dcm 2 AAScout ok 128 128 128 2 474000-000002-000001.dcm 3 T1_MPRAGE_sag ok 256 256 128 1 474000-000003-000001.dcm 4 T1_MPRAGE_sag ok 256 256 128 1 474000-000004-000001.dcm 5 DIFFUSION_HighRes err 128 128 64 24 474000-000005-000001.dcm 6 DIFFUSION_HighRes err 128 128 64 70 474000-000006-000001.dcm 7 DIFFUSION_HighRes ok 128 128 64 1 474000-000007-000001.dcm 8 DIFFUSION_HighRes ok 128 128 64 1 474000-000008-000001.dcm 9 DIFFUSION_HighRes ok 128 128 64 1 474000-000009-000001.dcm 10 DIFFUSION_HighRes ok 128 128 64 1 474000-000010-000001.dcm 11 DIFFUSION_HighRes ok 128 128 64 1 474000-000011-000001.dcm 12 DIFFUSION_HighRes ok 128 128 1 64 474000-000012-000001.dcm 13 ep2d_t1w ok 64 64 30 1 474000-000013-000001.dcm 14 PASL ok 64 64 16 133 474000-000014-000001.dcm 15 PASL err 64 64 16 1 474000-000015-000001.dcm 16 PASL err 64 64 16 1 474000-000016-000001.dcm 17 PASL ok 64 64 16 133 474000-000017-000001.dcm 18 PASL err 64 64 16 1 474000-000018-000001.dcm 19 PASL err 64 64 16 1 474000-000019-000001.dcm 20 ge_functionals ok 64 64 30 126 474000-000020-000001.dcm 21 ge_functionals ok 64 64 30 174 474000-000021-000001.dcm 22 ge_functionals ok 64 64 30 174 474000-000022-000001.dcm 23 ge_functionals ok 64 64 30 128 474000-000023-000001.dcm 24 ge_functionals ok 64 64 30 126 474000-000024-000001.dcm 25 ge_functionals ok 64 64 30 174 474000-000025-000001.dcm 26 T2_TSE_Axial_HiRes ok 256 256 30 1 474000-000026-000001.dcm unpacking config ------------------ {6 dti NII pat08_sess2_dti.nii} ----------------------------------- --------------------------------------------------------- Run 6 ----------------------------------------- Thu Sep 29 11:03:30 EDT 2011 6 dti NII pat08_sess2_dti.nii INFO: this run has an error, but trying anyway ERROR: mri_convert child process exited abnormally [purkinje:pat08_sess2_dti] (nmr-stable3-env) bugr Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.32.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat08_sess2_dti Thank you for any help!! Sandra

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problems unpacking diffusion runs
by swoodman＠nmr.mgh.harvard.edu 29 Sep '11

29 Sep '11

Hello all, I'm trying to unpack some old data and for a couple of sessions it is unpacking the wrong run. I just want to unpack the diffusion run. I give it the correct run number, it see's that number is the diffusion run, but unpacks another run instead. Here is the command I used: [purkinje:pat09_sess1_dti] (nmr-stable5.1-env) unpacksdcmdir -src /space/archive/25/siemens/Allegra-20401-20040831-134936-640000 -targ /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -run 021 dti NII pat09_sess1_dti.nii -unpackerr Here is what is spits out: $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -src /space/archive/25/siemens/Allegra-20401-20040831-134936-640000 -targ /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti -run 021 dti NII pat09_sess1_dti.nii -unpackerr Thu Sep 29 10:12:31 EDT 2011 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/09/29-14:12:31-GMT BuildTimeStamp: Sep 27 2011 05:57:44 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: swoodman Machine: purkinje Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 purkinje Linux purkinje 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 29 10:12:31 EDT 2011 Log File is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/unpack.log INFO: Logfile is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dicomdir.sumfile INFO: status file is /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/parse.status Scanning directory Thu Sep 29 10:12:31 EDT 2011 mri_parse_sdcmdir --sortbyrun --d /space/archive/25/siemens/Allegra-20401-20040831-134936-640000 --o /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dicomdir.sumfile --status /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_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 Done scanning Thu Sep 29 10:20:13 EDT 2011 ------------------------------------------ 1 circle_localizer ok 256 256 3 1 640000-1-2.dcm 2 AAScout ok 128 128 128 2 640000-2-1.dcm 3 t1_mprage_sag ok 256 256 128 1 640000-3-1.dcm 4 t1_mprage_sag ok 256 256 128 1 640000-4-1.dcm 5 ep2d_t1w ok 64 64 30 1 640000-5-1.dcm 6 t2_HI_RES ok 448 444 30 1 640000-6-1.dcm 7 ge_functionals_PACE ok 64 64 30 174 640000-7-1.dcm 8 ge_functionals_PACE ok 64 64 30 174 640000-8-1.dcm 9 ge_functionals_PACE err 64 64 30 10 640000-9-1.dcm 10 ge_functionals_PACE err 64 64 30 10 640000-10-1.dcm 11 ge_functionals_PACE ok 64 64 30 174 640000-11-1.dcm 12 ge_functionals_PACE ok 64 64 30 174 640000-12-1.dcm 13 ge_functionals_PACE ok 64 64 30 174 640000-13-1.dcm 14 ge_functionals_PACE ok 64 64 30 174 640000-14-1.dcm 15 ge_functionals_PACE ok 64 64 30 174 640000-15-1.dcm 16 ge_functionals_PACE ok 64 64 30 174 640000-16-1.dcm 17 ge_functionals_PACE ok 64 64 30 174 640000-17-1.dcm 18 ge_functionals_PACE ok 64 64 30 174 640000-18-1.dcm 19 ge_functionals_PACE ok 64 64 30 174 640000-19-1.dcm 20 ge_functionals_PACE ok 64 64 30 174 640000-20-1.dcm 21 DIFFUSION_HighRes err 128 128 64 70 640000-21-1.dcm 22 DIFFUSION_VeryHighRes err 128 128 30 84 640000-22-1.dcm unpacking config ------------------ {021 dti NII pat09_sess1_dti.nii} ----------------------------------- --------------------------------------------------------- Run 021 ----------------------------------------- Thu Sep 29 10:20:13 EDT 2011 021 dti NII pat09_sess1_dti.nii mri_convert /space/archive/25/siemens/Allegra-20401-20040831-134936-640000/640000-17-1.dcm /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017/pat09_sess1_dti.nii --sdcmlist /cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom StartTime: Thu Sep 29 10:12:31 EDT 2011 EndTime: Thu Sep 29 10:20:32 EDT 2011 unpacksdcmdir Done **and as you see if has decided to copy to run 017 and in that directory the output files are not correct. [purkinje:pat09_sess1_dti] (nmr-stable5.1-env) ls dicomdir.sumfile dti unpack.log [purkinje:pat09_sess1_dti] (nmr-stable5.1-env) cd dti [purkinje:dti] (nmr-stable5.1-env) ls 017 seq.info [purkinje:dti] (nmr-stable5.1-env) cd 017/ [purkinje:017] (nmr-stable5.1-env) ls flf pat09_sess1_dti.nii pat09_sess1_dti.nii-infodump.dat The bugreport: FREESURFER_HOME: /usr/local/freesurfer/stable5_1_0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.32.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017 ssh purkinje setenv SUBJECTS_DIR /space/sake/3/users/inverse/subjects cd /autofs/cluster/ablood/1/cervBTXDTI2011/data/pat09_sess1_dti/dti/017 Any advice/help is much appreciated. Thank you!! Sandra

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Bug in freesurfer_read_surf.m & a quick fix
by Matti Stenroos 29 Sep '11

29 Sep '11

Hi, In FreeSurfer 4.3.0, the Matlab routine "freesurfer_read_surf.m" crashes, when run with one output argument: function [vertices, faces] = freesurfer_read_surf(fname) The function help says: % Note that reading the faces of a quad file can take a long % time due to their compact storage format. In this case, the return of % vertices can be faster if the face output variable is not specified; in % this case, the faces are not read. However, when the function is called in the form vertices = freesurfer_read_surf(fname), it crashes on line 152 faces = faces + 1; because the variable "faces" is not defined. A quick fix: wrap line 152 inside an if clause: If nargin>1 faces=faces+1; end Unfortunately I don't know, how to check, whether this has been fixed in later releases. Cheers, Matti

2 2

missing lh.thickness.fwhm10.fsaverage.mgh in some subjects
by Rajagopalan, Venkateswaran 29 Sep '11

29 Sep '11

Dear All, I was trying to run "mris_preproc" after completing all autorecon steps in some of my subjects folder under "surf" I see "lh.thickness.fwhm10.fsaverage.mgh" whereas in others it is missing. I ran autorecon 1, 2 and 3 the same way in all the subjects so I am wondering what might be the problem why it is not generated only in some subjects. How to generate these files in order to run stats. Thanks Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

aseg2feat and aparc2feat
by Michelle Umali 29 Sep '11

29 Sep '11

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+aseg.nii.gz -thr 433v uthr 433 \ featdir/reg/freesurfer/Visual_V3d_l.nii.gz The resulting image was empty. I was able to use aseg2feat for all subcortical regions, so then i used aparc2feat. However, this uses a different color table which is missing many of the regions present in the Freesurfer Color Lookup table that I would like to use. How can I get area 433 (Visual_V3d_l) from the Freesurfer Color Lookup Table so I can later run fslmaths to generate a mask? Thanks. Michelle

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Re: [Freesurfer] Mcsrch error during recon-all
by Nick Schmansky 28 Sep '11

28 Sep '11

the log does not indicate that mri_em_register exited with an error. it appears that it produced its output correctly and continued through to nearly the end of the stream. the IFLAG messages can be ignored. the log indicates that mri_label2label is exiting with an error when trying to load the label from the fsaverage directory. the fsaverage subject is symlinked to the users SUBJECTS_DIR (to save space), but sometimes this seems to cause problems on some systems. i would try copying it to your subjects dir: cd $SUBJECTS_DIR rm fsaverage cp -r $FREESURFER_HOME/subjects/fsaverage . then you just need to run the last two stages of recon-all: recon-all -s <subjid> -balabels -label-exvivo-ec or if you dont care about the Brodmann or exvivo EC labels, you dont need to run anything. for reference: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable n. On Wed, 2011-09-28 at 17:36 -0400, Warren Winter wrote: > Hi Nick, > > > Thanks for your help. > > > The first set of errors (of the kind I described) follows the command > " mri_em_register -skull > nu.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta " > > > The next follows the command " mri_em_register -uns 3 -mask > brainmask.mgz > nu.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_2008-03-26.gca transforms/talairach.lta" > > > The next follows the command " mri_em_register -skull -t > transforms/talairach.lta > nu_noneck.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta " > > > I've attached the log if you could use it for reference. > > > Best, > > > Warren > > > > > > On Sep 28, 2011, at 4:18 PM, Nick Schmansky wrote: > > > the IFLAG messages can be ignored if mri_em_register is not exiting > > with > > error. which command is running that is exiting with error? can > > you > > send that command line from the recon-all.log file? > > > > n. > > > > On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote: > > > Hi, > > > > > > > > > Each time I have run recon-all on our subjects, I end up with the > > > same > > > slew of error messages underneath "Computing MAP estimate using [x > > > number of] samples" and underneath "EM alignment process": > > > > > > > > > "IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE > > > MCSRCH > > > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > > > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES" > > > > > > > > > At the very end of the log file I see: > > > > > > > > > "Loading source label. > > > Abort > > > Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 > > > x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > > recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011" > > > > > > > > > Any help on this would be greatly appreciated. > > > > > > > > > Best, > > > > > > > > > Warren > > > > > > -- > > > Warren Winter > > > Lab Coordinator > > > Children's Hospital Boston > > > Division of Developmental Medicine > > > 1 Autumn Street, AU 650 > > > Boston, MA 02215 > > > 857-218-5224 > > > > > > > > > _______________________________________________ > > > 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. > > > > > > > -- > Warren Winter > Lab Coordinator > Children's Hospital Boston > Division of Developmental Medicine > 1 Autumn Street, AU 650 > Boston, MA 02215 > 857-218-5224 > >

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Freesurfer September 2011