Freesurfer

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Re: [Freesurfer] Multiple frame error with recon-all
by ye tian 26 Jun '13

26 Jun '13

Hello Bruce, Sorry! The first email was too big and the mailing list rejected me. My image was already in Jpeg though. Sincerely, Ye On Wed, Jun 26, 2013 at 5:17 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Ye, > > can you cc the list so that others can help you? 787 would usually be too > many files for an anatomical. Something on the order of 170-256 is more > typical. If you visualize them the white matter should be bright, the gray > matter darker and the CSF very dark > > > Bruce > > > On Wed, 26 Jun 2013, ye tian wrote: > > Dear Bruce, >> I just confirmed a few hours ago that I indeed have structural MRI data >> though. I have attached an example of the last 787 files from my data >> below. >> In fact, I tried to use only those to reconstruct my volumes and surfaces. >> >> Do they serve as inputs to freesurfer? >> >> Thank you very much! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 5:04 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> no, once they have been acquired you can't change anything. You >> have to hope that they also acquired structural data in addition >> to the functional data (which is quite common). You can't change >> the way your images were formed posthoc... >> >> On Wed, 26 Jun 2013, ye tian wrote: >> >> Dear Bruce, >> If I understand correctly, I should bring these >> images back to the scanner >> and change some settings. Am I right? >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:59 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> you need to know what different scan types >> were acquired. The >> ones you showed were the fMRI time-series and >> designed to >> hilight changes in blood oxygenation level, >> which is an indirect >> marker of changes in neural firing, not >> anatomy >> >> On Wed, 26 Jun 2013, ye tian wrote: >> >> Dear Bruce, >> I inherited the data from a previous >> graduate >> student. I sent out a message >> to learn more information about the >> scanner a few >> days ago. >> What information do I need to know about >> the >> scanner? >> >> Thank you so much for your time and >> effort! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:41 PM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Ye >> >> you can't convert it, you have to >> acquire it >> that way. Where did >> you get your data? >> >> Bruce >> On Wed, 26 Jun 2013, ye tian >> wrote: >> >> Dear Bruce, >> Sorry for my lack of >> knowledge. I looked >> online, but >> couldn't find how to >> convert MRI data to >> T1-weighted >> anatomical. Would >> you please shine some >> light on it? >> >> Thank you very much! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:21 >> PM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Ye >> >> you need to give >> recon-all a >> T1-weighted >> anatomical (e.g. >> mprage, SPGR/FLASH, >> etc...), not >> the fMRI >> data. >> >> cheers >> Bruce >> On Wed, 26 Jun 2013, >> ye tian >> wrote: >> >> Dear Bruce, >> >> Recon-all exits >> with the >> following error >> >> ERROR: input(s) >> cannot have >> multiple >> frames! >> >> >> >> $SUBJECTS_DIR/Barba50527_2/**mri/orig/001.mgz has 439 >> frames >> >> If I open >> 001.mgz using >> freeview, I >> obtain the image >> in the >> attachment saved >> as freeview >> 001.mgz.png. >> >> >> >> In order to make >> sure that >> my problem >> does not come >> from further >> upstream, I >> am including the >> major steps >> that I took >> to get to >> this error. >> >> MAJOR STEPS >> >> STEP0: >> My inherited >> data has names >> >> >> >> BARBA50527.MR.MEDITATE_**MEDITATION.#.#.year.month.day.** >> #.#.#.#.#.IMA >> where each # is >> a string of >> numbers. >> >> >> STEP1: >> The images can >> be grouped >> into five >> categories, >> according to the >> numbers in >> the names that >> occupy the >> positions of >> the red #: >> 1.1-1.3, >> 2.1, >> 3.1-3.160, >> 4.1-4.439, >> 5.1-5.439 >> >> [1] Note: Images >> from groups >> 4 & 5 are >> very >> different from >> the images of >> groups 1, 2 and >> 3. A link to >> a youtube >> video of all >> the images can >> be seen >> in note[1]. >> >> >> STEP2: >> recon-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148038.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> recon-all >> completes without >> error. >> >> [2] Note: other >> attempts >> leads to >> different errors. >> See note [2] for >> details. >> >> >> STEP3: >> recon-all -s >> Barba50527_2 >> -autorecon1 >> >> Exits with the >> error message >> at the >> beginning of the >> email. The >> number 439 >> seems to come >> from the >> number of files >> in each >> group. >> >> >> USEFUL COMMENTS >> >> >> >> >> http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.** >> edu/msg23764.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html> >> >> I will do it for >> 001.mgz and >> 002.mgz and >> will let >> you know how it >> goes. >> >> >> QUESTIONS >> 1. Do I really >> need to >> manually parse >> the sequence >> of images? If >> so, how? >> 2. I don't >> really need to >> mri_convert my >> files into >> other formats, >> e.g., >> .dcm, do I? >> 3. Each file >> from groups 4 >> and 5 have >> multiple >> images. Do I >> need to cut >> them >> into sub-images, >> each with >> one brain? >> >> Thank you very >> much! >> >> Sincerely, >> Ye >> >> >> >> >> >> NOTES: >> Note [1] >> A video of the >> data can be >> found at >> >> >> >> http://www.youtube.com/watch?**v=W8ZFGvGvHVc&list=** >> UUfGdQq3j1gqPAc4z6Spmu2g<http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g> >> >> On the top left >> corner: >> the white text >> is: >> current frame >> number / total >> frame number >> the yellow text >> is: the >> name of the >> frame >> >> Note[2] >> recon-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.** >> 07.27.10.52.51 >> >> .437500.56141898.IMA >> Completes >> without error >> recon-all -s >> Barba50527_2 >> -autorecon1 >> Warning: only >> one run found >> Error: >> MRIsample(): source >> matrix has >> zero >> determinant; >> matrix is: >> EOF >> >> econ-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.** >> 07.27.10.52.51 >> >> .437500.56141898.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.2.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.3.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148038.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> error.log: >> matrix >> dimensionality >> >> >> >> >> >> 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<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. >> >> >> >> >> >> >> >> >> >>

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Re: [Freesurfer] Multiple frame error with recon-all
by Bruce Fischl 26 Jun '13

26 Jun '13

Hi Ye you need to give recon-all a T1-weighted anatomical (e.g. mprage, SPGR/FLASH, etc...), not the fMRI data. cheers Bruce On Wed, 26 Jun 2013, ye tian wrote: > Dear Bruce, > > Recon-all exits with the following error > > ERROR: input(s) cannot have multiple frames! > $SUBJECTS_DIR/Barba50527_2/mri/orig/001.mgz has 439 frames > > If I open 001.mgz using freeview, I obtain the image in the attachment saved > as freeview 001.mgz.png. > > > > In order to make sure that my problem does not come from further upstream, I > am including the major steps that I took to get to this error. > > MAJOR STEPS > > STEP0: > My inherited data has names > BARBA50527.MR.MEDITATE_MEDITATION.#.#.year.month.day.#.#.#.#.#.IMA > where each # is a string of numbers. > > > STEP1: > The images can be grouped into five categories, according to the numbers in > the names that occupy the positions of the red #: 1.1-1.3, 2.1, > 3.1-3.160, 4.1-4.439, 5.1-5.439 > > [1] Note: Images from groups 4 & 5 are very different from the images of > groups 1, 2 and 3. A link to a youtube video of all the images can be seen > in note[1]. > > > STEP2: > recon-all -s Barba50527_2 > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51 > .437500.56148038.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51 > .437500.56148502.IMA > recon-all completes without error. > > [2] Note: other attempts leads to different errors. See note [2] for > details. > > > STEP3: > recon-all -s Barba50527_2 -autorecon1 > > Exits with the error message at the beginning of the email. The number 439 > seems to come from the number of files in each group. > > > USEFUL COMMENTS > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html > > I will do it for 001.mgz and 002.mgz and will let you know how it goes. > > > QUESTIONS > 1. Do I really need to manually parse the sequence of images? If so, how? > 2. I don't really need to mri_convert my files into other formats, e.g., > .dcm, do I? > 3. Each file from groups 4 and 5 have multiple images. Do I need to cut them > into sub-images, each with one brain? > > Thank you very much! > > Sincerely, > Ye > > > > > > NOTES: > Note [1] > A video of the data can be found at > http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g > > On the top left corner: > the white text is: current frame number / total frame number > the yellow text is: the name of the frame > > Note[2] > recon-all -s Barba50527_2 > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51 > .437500.56141898.IMA > Completes without error > recon-all -s Barba50527_2 -autorecon1 > Warning: only one run found > Error: MRIsample(): source matrix has zero determinant; matrix is: EOF > > econ-all -s Barba50527_2 > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51 > .437500.56141898.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.2.1.2010.07.27.10.52.51 > .437500.56148502.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.3.1.2010.07.27.10.52.51 > .437500.56148502.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51 > .437500.56148038.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51 > .437500.56148502.IMA > error.log: matrix dimensionality > > >

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libboost_program_options.so.5 issue
by Hoptman, Matthew 26 Jun '13

26 Jun '13

Hi all, Any news on the libboost_program_options.so.5 issue, as relates to mri_cvs_register? I've encountered it using mris_resample (as part of mri_cvs_register) using. When I run: qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V ${FREESURFER_HOME}/bin/mri_cvs_register --mov ${subject} where ${subject} was found by looping through all of my subjects I get the error: mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory bugr gives me: ---------------------------------------------------------------- FREESURFER_HOME: /home/hoptman/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0beta Debian version: 6.0.4 Kernel info: Linux 2.6.32-5-amd64 x86_64 Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Substantia Nigra
by Ata Akh 26 Jun '13

26 Jun '13

Hello Dear Freesurfers, is there a possibility, a way, to visualize the substantia nigra in Freesurfer like using 3DSlicer!? Thanks Ata

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SPM ROI to Cortical Thickness
by Ozranov-Palchik, Ola 26 Jun '13

26 Jun '13

Dear FreeSurfer Experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Thank you in advance for your help! Ola Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov(a)childrens.harvard.edu<mailto:olga.ozranov@childrens.harvard.edu> phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab

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[FreeSurfer] Corpus Callosum tracts
by Teodorescu, Roxana 26 Jun '13

26 Jun '13

Dear FreeSurfers, I would like to get the tracts in Corpus Callosum body, not just the forceps major and forceps minor given by tracula. Is there a way to get that with Tracula? Thank you. Roxana. ------------------------------------------------------------------------------------------- Roxana O. Teodorescu, PhD Postdoctoral Fellow Department of Neurology Mount Sinai School of Medicine

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Re: [Freesurfer] Freesurfer 5.3 error
by Salil Soman 25 Jun '13

25 Jun '13

Dear Bruce, I apologize, I misread your last message. My fsaverage folder is now empty. We had some issues with storage space for our output files and I am rerunning a number of patients for a different study from the ones I had done previously (but acquired with the same protocol). I guess these files got lost. Is there a way I can reset my freesurfer install to function as though I am running cases for the first time / get things working again? Best wishes, Sal On Tue, Jun 25, 2013 at 6:25 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > those are the contents of /mnt/glusterfs/salsoman/** > output/FS/fsaverage/label/lh.**BA1.label? > > I've attached our current one so that you can compare > > cheers > Bruce > On Tue, 25 Jun 2013, Salil Soman wrote: > > Thank you Doug, >> >> Here are the file contents. >> >> -Sal >> >> Sun Jun 23 22:25:24 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS >> /mnt/glusterfs/salsoman/**freesurfer/bin/recon-all >> -i SPGR/2536_21_1.nii.gz -s GK_2536_FS -nuintensitycor-3T -nocanorm >> -openmp >> 50 -all >> subjid GK_2536_FS >> setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/**output/FS >> FREESURFER_HOME /mnt/glusterfs/salsoman/**freesurfer >> Actual FREESURFER_HOME /mnt/glusterfs/salsoman/**freesurfer >> build-stamp.txt: freesurfer-Linux-centos6_x86_**64-stable-pub-v5.2.0 >> Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18 >> 16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >> cputime unlimited >> filesize unlimited >> datasize unlimited >> stacksize unlimited >> coredumpsize unlimited >> memoryuse unlimited >> vmemoryuse unlimited >> descriptors 1024 >> memorylocked 64 kbytes >> maxproc 772831 >> maxlocks unlimited >> maxsignal 772831 >> maxmessage 819200 >> maxnice 0 >> maxrtprio 0 >> maxrttime unlimited >> >> total used free shared buffers cached >> Mem: 99005808 49579412 49426396 0 1598396 37801604 >> -/+ buffers/cache: 10179412 88826396 >> Swap: 10485756 459696 10026060 >> >> ##############################**########## >> program versions used >> $Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ >> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ >> mri_convert -all-info >> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:24-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 >> mreuter Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> FLIRT version 5.5 >> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ >> mri_convert --version >> stable5 >> ProgramName: tkregister2_cmdl ProgramArguments: --all-info >> ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:25-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 >> greve >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> Program nu_correct, built from: >> Package MNI N3, version 1.10, compiled by nicks@minerva >> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 >> ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:25-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: >> stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013 >> 00:28:02 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ >> User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks >> Exp >> $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 >> greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> >> >> ======= NUMBER OF OPENMP THREADS = 50 ======= >> ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_ca_normalize ProgramArguments: -all-info >> ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 >> nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks >> Exp >> $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: >> stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013 >> 00:28:02 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ >> User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mri_concatenate_lta ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_concatenate_lta.c,v >> 1.10 >> 2011/03/16 21:23:48 nicks Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_normalize_tp2 ProgramArguments: -all-info >> ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 >> nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks >> Exp >> $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks >> Exp >> $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks >> Exp >> $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_fix_topology ProgramArguments: -all-info >> ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 >> nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_euler_number ProgramArguments: -all-info >> ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 >> greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: >> Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_make_surfaces ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_make_surfaces.c,v >> 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_anatomical_stats ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_anatomical_stats.c,v >> 1.72 2011/03/02 00:04:26 nicks Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:33-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks >> Exp >> $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ProgramName: mris_curvature_stats ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:33-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_curvature_stats.c,v >> 1.64 2011/03/02 00:04:30 nicks Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: >> $Name: >> stable5 $ TimeStamp: 2013/06/24-05:25:34-GMT BuildTimeStamp: Feb 26 2013 >> 00:28:02 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp >> $ >> User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ >> >> ProgramName: mri_robust_register ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_robust_register.cpp,v >> 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ >> >> ProgramName: mri_robust_template ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_robust_template.cpp,v >> 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: >> stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 >> 00:28:02 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: >> salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: >> 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: >> stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 >> 00:28:02 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: >> salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: >> 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_fuse_segmentations ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT >> BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_fuse_segmentations.c,v >> 1.8 2011/03/02 00:04:15 nicks Exp $ User: salsoman Machine: >> barley13.stanford.edu Platform: Linux PlatformVersion: >> 3.2.0-33-generic >> CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2013/06/24-05:25:36-GMT BuildTimeStamp: Feb >> 26 >> 2013 00:28:02 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 >> greve >> Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux >> PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: >> 40400 >> ##############################**######### >> GCADIR /mnt/glusterfs/salsoman/**freesurfer/average >> GCA RB_all_2008-03-26.gca >> GCASkull RB_all_withskull_2008-03-26.**gca >> AvgCurvTif average.curvature.filled.**buckner40.tif >> GCSDIR /mnt/glusterfs/salsoman/**freesurfer/average >> GCS curvature.buckner40.filled.**desikan_killiany.2010-03-25.**gcs >> ##############################**######### >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS >> >> mri_convert /mnt/glusterfs/salsoman/SRC/**GK_2536/SPGR/2536_21_1.nii.gz >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig/**001.mgz >> >> mri_convert /mnt/glusterfs/salsoman/SRC/**GK_2536/SPGR/2536_21_1.nii.gz >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig/**001.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /mnt/glusterfs/salsoman/SRC/**GK_2536/SPGR/2536_21_1.nii.gz. >> **.. >> TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, -1, 0) >> k_ras = (0, 0, 1) >> writing to /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig/** >> 001.mgz... >> #-----------------------------**--------------- >> #@# MotionCor Sun Jun 23 22:25:47 PDT 2013 >> Found 1 runs >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig/**001.mgz >> Checking for (invalid) multi-frame inputs... >> WARNING: only one run found. This is OK, but motion >> correction cannot be performed on one run, so I'll >> copy the run to rawavg and continue. >> >> cp /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig/**001.mgz >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/**rawavg.mgz >> >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS >> >> mri_convert /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/** >> rawavg.mgz >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig.**mgz --conform >> >> mri_convert /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/** >> rawavg.mgz >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig.**mgz --conform >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/** >> rawavg.mgz... >> TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, -1, 0) >> k_ras = (0, 0, 1) >> Original Data has (0.8594, 0.8594, 1) mm size and (256, 256, 156) voxels. >> Data is conformed to 1 mm size and 256 voxels for all directions >> changing data type from float to uchar (noscale = 0)... >> MRIchangeType: Building histogram >> Reslicing using trilinear interpolation >> writing to /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig.** >> mgz... >> >> mri_add_xform_to_header -c >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/** >> transforms/talairach.xfm >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig.**mgz >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/orig.**mgz >> >> INFO: extension is mgz >> #-----------------------------**--------------- >> #@# Talairach Sun Jun 23 22:26:10 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale >> --i >> orig.mgz --o orig_nu.mgz >> >> >> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm >> >> >> cp transforms/talairach.auto.xfm transforms/talairach.xfm >> >> #-----------------------------**--------------- >> #@# Talairach Failure Detection Sun Jun 23 22:38:56 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> >> talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6134, >> pval=0.2817 >= threshold=0.0050) >> >> awk -f /mnt/glusterfs/salsoman/**freesurfer/bin/extract_** >> talairach_avi_QA.awk/mnt/**glusterfs/salsoman/output/FS/** >> GK_2536_FS/mri/transforms/**talairach_avi.l >> og >> >> >> tal_QC_AZS/mnt/glusterfs/**salsoman/output/FS/GK_2536_FS/** >> mri/transforms/talairach_avi.l >> og >> >> TalAviQA: 0.97859 >> z-score: 0 >> TalAviQA2: 3.3941 >> #-----------------------------**--------------- >> #@# Nu Intensity Correction Sun Jun 23 22:39:05 PDT 2013 >> >> mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar >> transforms/talairach.xfm >> --proto-iters 1000 --distance 50 --n 1 >> >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> /mnt/glusterfs/salsoman/**freesurfer/bin/mri_nu_correct.**mni >> --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters >> 1000 >> --distance 50 --n 1 >> nIters 1 >> $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ >> Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18 >> 16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >> Sun Jun 23 22:39:06 PDT 2013 >> Program nu_correct, built from: >> Package MNI N3, version 1.10, compiled by nicks@minerva >> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 >> tmpdir is ./tmp.mri_nu_correct.mni.7330 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7330/**nu0.mnc -odt float >> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7330/**nu0.mnc -odt float >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from orig.mgz... >> TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 0, -1) >> k_ras = (0, 1, 0) >> changing data type from uchar to float (noscale = 0)... >> writing to ./tmp.mri_nu_correct.mni.7330/**nu0.mnc... >> >> ------------------------------**-------------------------- >> Iteration 1 Sun Jun 23 22:39:17 PDT 2013 >> nu_correct -clobber ./tmp.mri_nu_correct.mni.7330/**nu0.mnc >> ./tmp.mri_nu_correct.mni.7330/**nu1.mnc -tmpdir >> ./tmp.mri_nu_correct.mni.7330/**0/ -iterations 1000 -distance 50 >> [salsoman@barley13.stanford.**edu:/mnt/glusterfs/salsoman/** >> output/FS/GK_2536_F >> S/mri/] [2013-06-23 22:39:18] running: >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/nu_**estimate_np_and_em >> -parzen >> -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask >> -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp >> -tmpdir ./tmp.mri_nu_correct.mni.7330/**0/ >> ./tmp.mri_nu_correct.mni.7330/**nu0.mnc ./tmp.mri_nu_correct.mni.7330/** >> nu1.imp >> >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Use of ?PATTERN? without explicit operator is deprecated at >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/sharpen_**volume line 153. >> Processing:...................**..............................** >> ............... >> .Done >> Number of iterations: 109 >> CV of field change: 0.000986757 >> [salsoman@barley13.stanford.**edu:/mnt/glusterfs/salsoman/** >> output/FS/GK_2536_F >> S/mri/] [2013-06-23 22:46:39] running: >> /mnt/glusterfs/salsoman/**freesurfer/mni/bin/make_**template -quiet >> -shrink 3 >> ./tmp.mri_nu_correct.mni.7330/**nu0.mnc >> ./tmp.mri_nu_correct.mni.7330/**0//template.mnc >> >> Transformingslices:...........**..............................** >> ........................... >> ..................Done >> Transformingslices:...........**..............................** >> ........................... >> ..............................**..............................** >> ............... >> ..............................**..............................** >> ............... >> ..............................**........Done >> >> >> >> mri_binarize --i ./tmp.mri_nu_correct.mni.7330/**nu1.mnc --min -1 --o >> ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> >> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ >> cwd /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.7330/**nu1.mnc --min >> -1 --o >> ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> sysname Linux >> hostname barley13.stanford.edu >> machine x86_64 >> user salsoman >> >> input ./tmp.mri_nu_correct.mni.7330/**nu1.mnc >> frame 0 >> nErode3d 0 >> nErode2d 0 >> output ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> Binarizing based on threshold >> min -1 >> max +infinity >> binval 1 >> binvalnot 0 >> Found 16777216 values in range >> Counting number of voxels >> Found 16777216 voxels in final mask >> mri_binarize done >> mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/**ones.mgz --i >> orig.mgz --sum ./tmp.mri_nu_correct.mni.7330/**sum.junk --avgwf >> ./tmp.mri_nu_correct.mni.7330/**input.mean.dat >> >> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >> cwd >> cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> --i >> orig.mgz --sum ./tmp.mri_nu_correct.mni.7330/**sum.junk --avgwf >> ./tmp.mri_nu_correct.mni.7330/**input.mean.dat >> sysname Linux >> hostname barley13.stanford.edu >> machine x86_64 >> user salsoman >> UseRobust 0 >> Loading ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> Loading orig.mgz >> Voxel Volume is 1 mm^3 >> Generating list of segmentation ids >> Found 1 segmentations >> Computing statistics for each segmentation >> 0 1 ** 16777216 16777216.000 >> >> Reporting on 1 segmentations >> Computing spatial average of each frame >> 0 >> Writing to ./tmp.mri_nu_correct.mni.7330/**input.mean.dat >> mri_segstats done >> mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/**ones.mgz --i >> ./tmp.mri_nu_correct.mni.7330/**nu1.mnc --sum >> ./tmp.mri_nu_correct.mni.7330/**sum.junk --avgwf >> ./tmp.mri_nu_correct.mni.7330/**output.mean.dat >> >> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >> cwd >> cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> --i >> ./tmp.mri_nu_correct.mni.7330/**nu1.mnc --sum >> ./tmp.mri_nu_correct.mni.7330/**sum.junk --avgwf >> ./tmp.mri_nu_correct.mni.7330/**output.mean.dat >> sysname Linux >> hostname barley13.stanford.edu >> machine x86_64 >> user salsoman >> UseRobust 0 >> Loading ./tmp.mri_nu_correct.mni.7330/**ones.mgz >> Loading ./tmp.mri_nu_correct.mni.7330/**nu1.mnc >> Voxel Volume is 1 mm^3 >> Generating list of segmentation ids >> Found 1 segmentations >> Computing statistics for each segmentation >> 0 1 ** 16777216 16777216.000 >> >> Reporting on 1 segmentations >> Computing spatial average of each frame >> 0 >> Writing to ./tmp.mri_nu_correct.mni.7330/**output.mean.dat >> mri_segstats done >> mris_calc -o ./tmp.mri_nu_correct.mni.7330/**nu1.mnc >> ./tmp.mri_nu_correct.mni.7330/**nu1.mnc mul .90527967007596602086 >> Saving result to './tmp.mri_nu_correct.mni.**7330/nu1.mnc' (type = MINC >> ) [ ok ] >> mri_convert ./tmp.mri_nu_correct.mni.7330/**nu1.mnc nu.mgz --like >> orig.mgz >> mri_convert ./tmp.mri_nu_correct.mni.7330/**nu1.mnc nu.mgz --like >> orig.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from ./tmp.mri_nu_correct.mni.7330/**nu1.mnc... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 0, -1) >> k_ras = (0, 1, 0) >> INFO: transform src into the like-volume: orig.mgz >> writing to nu.mgz... >> mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz >> type change took 0 minutes and 13 seconds. >> mapping (11, 68) to ( 3, 110) >> >> >> Sun Jun 23 22:48:17 PDT 2013 >> mri_nu_correct.mni done >> >> mri_add_xform_to_header -c >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri/** >> transforms/talairach.xfm >> nu.mgz nu.mgz >> >> INFO: extension is mgz >> #-----------------------------**--------------- >> #@# Intensity Normalization Sun Jun 23 22:48:19 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> mri_normalize -g 1 nu.mgz T1.mgz >> >> using max gradient = 1.000 >> reading from nu.mgz... >> normalizing image... >> talairach transform >> 1.097 -0.025 -0.058 1.356; >> 0.020 1.037 0.488 -12.228; >> 0.025 -0.377 1.099 4.862; >> 0.000 0.000 0.000 1.000; >> processing without aseg, no1d=0 >> MRInormInit(): >> INFO: Modifying talairach volume c_(r,a,s) based on average_305 >> MRInormalize(): >> MRIsplineNormalize(): npeaks = 15 >> Starting OpenSpline(): npoints = 15 >> building Voronoi diagram... >> performing soap bubble smoothing, sigma = 8... >> >> Iterating 2 times >> ------------------------------**--- >> 3d normalization pass 1 of 2 >> white matter peak found at 111 >> white matter peak found at 109 >> gm peak at 76 (76), valley at 58 (58) >> csf peak at 38, setting threshold to 63 >> building Voronoi diagram... >> performing soap bubble smoothing, sigma = 8... >> ------------------------------**--- >> 3d normalization pass 2 of 2 >> white matter peak found at 111 >> white matter peak found at 110 >> gm peak at 76 (76), valley at 58 (58) >> csf peak at 38, setting threshold to 63 >> building Voronoi diagram... >> performing soap bubble smoothing, sigma = 8... >> Done iterating ------------------------------**--- >> writing output to T1.mgz >> 3D bias adjustment took 4 minutes and 10 seconds. >> #-----------------------------**--------------- >> #@# Skull Stripping Sun Jun 23 22:52:31 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> mri_em_register -skull nu.mgz >> /mnt/glusterfs/salsoman/**freesurfer/average/RB_all_** >> withskull_2008-03-26.gca >> transforms/talairach_with_**skull.lta >> >> >> >> ======= NUMBER OF OPENMP THREADS = 50 ======= >> aligning to atlas containing skull, setting unknown_nbr_spacing = 5 >> reading 1 input volumes... >> logging results to talairach_with_skull.log >> reading'/mnt/glusterfs/**salsoman/freesurfer/average/** >> RB_all_withskull_2008-03-26.**gca >> '... >> average std = 23.1 using min determinant for regularization = 53.4 >> 0 singular and 5702 ill-conditioned covariance matrices regularized >> reading 'nu.mgz'... >> freeing gibbs priors...done. >> bounding unknown intensity as < 20.2 or > 943.7 >> total sample mean = 92.0 (1443 zeros) >> ************************************************** >> spacing=8, using 3481 sample points, tol=1.00e-05... >> ************************************************** >> register_mri: find_optimal_transform >> find_optimal_transform: nsamples 3481, passno 0, spacing 8 >> resetting wm mean[0]: 117 --> 126 >> resetting gm mean[0]: 74 --> 74 >> input volume #1 is the most T1-like >> using real data threshold=15.0 >> skull bounding box = (49, 48, 35) --> (207, 208, 231) >> using (102, 101, 133) as brain centroid... >> mean wm in atlas = 126, using box (83,81,109) --> (121, 120,157) to find >> MRI >> wm >> before smoothing, mri peak at 109 >> after smoothing, mri peak at 109, scaling input intensities by 1.156 >> scaling channel 0 by 1.15596 >> initial log_p = -4.8 >> ************************************************** >> First Search limited to translation only. >> ************************************************** >> max log p = -4.714732 @ (-9.091, -9.091, -27.273) >> max log p = -4.622298 @ (13.636, -4.545, 4.545) >> max log p = -4.568388 @ (-2.273, -2.273, 2.273) >> max log p = -4.567887 @ (-3.409, 1.136, -1.136) >> max log p = -4.554366 @ (-0.568, -5.114, 0.568) >> max log p = -4.554366 @ (0.000, 0.000, 0.000) >> Found translation: (-1.7, -19.9, -21.0): log p = -4.554 >> ****************************************** >> Nine parameter search. iteration 0 nscales = 0 ... >> ****************************************** >> Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.6 >> (thresh=-4.5) >> 1.064 0.000 0.000 -9.830; >> 0.000 1.194 0.320 -71.787; >> 0.000 -0.320 1.194 -0.574; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 1 nscales = 0 ... >> ****************************************** >> Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 >> (thresh=-4.1) >> 1.064 0.000 0.000 -9.830; >> 0.000 1.270 0.340 -84.084; >> 0.000 -0.296 1.105 7.422; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 2 nscales = 0 ... >> ****************************************** >> Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 >> (thresh=-4.1) >> 1.064 0.000 0.000 -9.830; >> 0.000 1.270 0.340 -84.084; >> 0.000 -0.296 1.105 7.422; >> 0.000 0.000 0.000 1.000; >> reducing scale to 0.2500 >> ****************************************** >> Nine parameter search. iteration 3 nscales = 1 ... >> ****************************************** >> Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 >> (thresh=-4.1) >> 1.082 -0.052 0.020 -7.974; >> 0.036 1.306 0.390 -99.503; >> -0.033 -0.327 1.073 19.471; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 4 nscales = 1 ... >> ****************************************** >> Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 >> (thresh=-4.1) >> 1.082 -0.052 0.020 -7.974; >> 0.036 1.306 0.390 -99.503; >> -0.033 -0.327 1.073 19.471; >> 0.000 0.000 0.000 1.000; >> reducing scale to 0.0625 >> ****************************************** >> Nine parameter search. iteration 5 nscales = 2 ... >> ****************************************** >> Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 >> (thresh=-4.1) >> 1.084 -0.052 0.020 -8.295; >> 0.035 1.296 0.416 -101.760; >> -0.034 -0.358 1.062 25.483; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 6 nscales = 2 ... >> ****************************************** >> Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 >> (thresh=-4.1) >> 1.084 -0.052 0.020 -8.295; >> 0.035 1.296 0.416 -101.760; >> -0.034 -0.358 1.062 25.483; >> 0.000 0.000 0.000 1.000; >> min search scale 0.025000 reached >> ************************************************* >> Computing MAP estimate using 3481 samples... >> ************************************************* >> dt = 5.00e-06, momentum=0.80, tol=1.00e-05 >> l_intensity = 1.0000 >> Aligning input volume to GCA... >> Transform matrix >> 1.08441 -0.05186 0.02026 -8.29545; >> 0.03508 1.29640 0.41613 -101.75975; >> -0.03396 -0.35825 1.06199 25.48265; >> 0.00000 0.00000 0.00000 1.00000; >> nsamples 3481 >> Quasinewton: input matrix >> 1.08441 -0.05186 0.02026 -8.29545; >> 0.03508 1.29640 0.41613 -101.75975; >> -0.03396 -0.35825 1.06199 25.48265; >> 0.00000 0.00000 0.00000 1.00000; >> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR >> RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE >> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = >> -0.0 tol 0.000010 >> Resulting transform: >> 1.084 -0.052 0.020 -8.295; >> 0.035 1.296 0.416 -101.760; >> -0.034 -0.358 1.062 25.483; >> 0.000 0.000 0.000 1.000; >> >> pass 1, spacing 8: log(p) = -4.1 (old=-4.8) >> transform before final EM align: >> 1.084 -0.052 0.020 -8.295; >> 0.035 1.296 0.416 -101.760; >> -0.034 -0.358 1.062 25.483; >> 0.000 0.000 0.000 1.000; >> >> **************************************************** >> EM alignment process ... >> Computing final MAP estimate using 382743 samples. >> **************************************************** >> dt = 5.00e-06, momentum=0.80, tol=1.00e-07 >> l_intensity = 1.0000 >> Aligning input volume to GCA... >> Transform matrix >> 1.08441 -0.05186 0.02026 -8.29545; >> 0.03508 1.29640 0.41613 -101.75975; >> -0.03396 -0.35825 1.06199 25.48265; >> 0.00000 0.00000 0.00000 1.00000; >> nsamples 382743 >> Quasinewton: input matrix >> 1.08441 -0.05186 0.02026 -8.29545; >> 0.03508 1.29640 0.41613 -101.75975; >> -0.03396 -0.35825 1.06199 25.48265; >> 0.00000 0.00000 0.00000 1.00000; >> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR >> RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE >> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = >> 4.4 tol 0.000000 >> final transform: >> 1.084 -0.052 0.020 -8.295; >> 0.035 1.296 0.416 -101.760; >> -0.034 -0.358 1.062 25.483; >> 0.000 0.000 0.000 1.000; >> >> writing output transformation to transforms/talairach_with_**skull.lta... >> registration took 69 minutes and 47 seconds. >> >> mri_watershed -T1 -brain_atlas >> /mnt/glusterfs/salsoman/**freesurfer/average/RB_all_** >> withskull_2008-03-26.gca >> transforms/talairach_with_**skull.lta T1.mgz brainmask.auto.mgz >> >> >> Mode: T1 normalized volume >> Mode: Use the information of atlas (default parms, --help for >> details) >> >> *********************************************************** >> The input file is T1.mgz >> The output file is brainmask.auto.mgz >> Weighting the input with atlas information before watershed >> >> ***************************WATERSHED**************************** >> Sorting... >> first estimation of the COG coord: x=126 y=122 z=125 r=70 >> first estimation of the main basin volume: 1445912 voxels >> Looking for seedpoints >> 2 found in the cerebellum >> 14 found in the rest of the brain >> global maximum in x=105, y=117, z=92, Imax=255 >> CSF=21, WM_intensity=110, WM_VARIANCE=5 >> WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 >> preflooding height equal to 10 percent >> done. >> Analyze... >> >> main basin size=10816010181 voxels, voxel volume =1.000 >> = 10816010181 mmm3 = 10816010.240 cm3 >> done. >> PostAnalyze...Basin Prior >> 12 basins merged thanks to atlas >> ***** 0 basin(s) merged in 1 iteration(s) >> ***** 0 voxel(s) added to the main basin >> done. >> Weighting the input with prior template >> >> ****************TEMPLATE DEFORMATION**************** >> >> second estimation of the COG coord: x=128,y=129, z=122, r=9758 >> iterations >> ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ >> >> GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 45874 >> RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1030067734 >> LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1060864313 >> RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=41 , nb = -1082494987 >> LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = -1100073048 >> OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=24 , nb = 1081747772 >> >> CSF_MAX TRANSITION GM_MIN GM >> GLOBAL >> before analyzing : 32, 43, 52, 73 >> after analyzing : 32, 49, 52, 55 >> RIGHT_CER >> before analyzing : 14, 19, 40, 85 >> after analyzing : 14, 33, 40, 46 >> LEFT_CER >> before analyzing : 15, 23, 44, 76 >> after analyzing : 15, 37, 44, 46 >> RIGHT_BRAIN >> before analyzing : 41, 48, 52, 74 >> after analyzing : 41, 50, 52, 56 >> LEFT_BRAIN >> before analyzing : 34, 45, 52, 71 >> after analyzing : 34, 49, 52, 54 >> OTHER >> before analyzing : 24, 40, 66, 87 >> after analyzing : 24, 57, 66, 64 >> mri_strip_skull: done peeling brain >> highly tesselated surface with 10242 vertices >> matching...60 iterations >> >> ***********************VALIDATION*********************** >> curvature mean = -0.014, std = 0.013 >> curvature mean = 65.084, std = 6.593 >> >> No Rigid alignment: -atlas Mode Off (basic atlas / no registration) >> before rotation: sse = 4.44, sigma = 7.78 >> after rotation: sse = 4.44, sigma = 7.78 >> Localization of inacurate regions: Erosion-Dilation steps >> the sse mean is 5.53, its var is 11.13 >> before Erosion-Dilatation 3.50% of inacurate vertices >> after Erosion-Dilatation 4.66% of inacurate vertices >> Validation of the shape of the surface done. >> Scaling of atlas fields onto current surface fields >> >> ********FINAL ITERATIVE TEMPLATE DEFORMATION******** >> Compute Local values csf/gray >> Fine Segmentation...46 iterations >> >> mri_strip_skull: done peeling brain >> >> Brain Size = 1439142 voxels, voxel volume = 1.000 mm3 >> = 1439142 mmm3 = 1439.142 cm3 >> >> >> ****************************** >> Saving brainmask.auto.mgz >> done >> >> cp brainmask.auto.mgz brainmask.mgz >> >> #-----------------------------**-------- >> #@# EM Registration Mon Jun 24 00:03:10 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> mri_em_register -uns 3 -mask brainmask.mgz nu.mgz >> /mnt/glusterfs/salsoman/**freesurfer/average/RB_all_**2008-03-26.gca >> transforms/talairach.lta >> >> >> >> ======= NUMBER OF OPENMP THREADS = 50 ======= >> aligning to atlas containing skull, setting unknown_nbr_spacing = 3 >> using MR volume brainmask.mgz to mask input volume... >> reading 1 input volumes... >> logging results to talairach.log >> reading >> '/mnt/glusterfs/salsoman/**freesurfer/average/RB_all_**2008-03-26.gca'... >> average std = 6.9 using min determinant for regularization = 4.7 >> 0 singular and 1812 ill-conditioned covariance matrices regularized >> reading 'nu.mgz'... >> freeing gibbs priors...done. >> bounding unknown intensity as < 14.9 or > 790.2 >> total sample mean = 84.4 (994 zeros) >> ************************************************** >> spacing=8, using 2772 sample points, tol=1.00e-05... >> ************************************************** >> register_mri: find_optimal_transform >> find_optimal_transform: nsamples 2772, passno 0, spacing 8 >> resetting wm mean[0]: 102 --> 107 >> resetting gm mean[0]: 64 --> 64 >> input volume #1 is the most T1-like >> using real data threshold=25.1 >> skull bounding box = (61, 67, 54) --> (194, 197, 206) >> using (105, 110, 130) as brain centroid... >> mean wm in atlas = 107, using box (89,94,111) --> (121, 125,148) to find >> MRI >> wm >> before smoothing, mri peak at 109 >> after smoothing, mri peak at 109, scaling input intensities by 0.982 >> scaling channel 0 by 0.981651 >> initial log_p = -4.3 >> ************************************************** >> First Search limited to translation only. >> ************************************************** >> max log p = -4.046112 @ (-9.091, -9.091, -27.273) >> max log p = -3.926434 @ (4.545, -4.545, 4.545) >> max log p = -3.926434 @ (0.000, 0.000, 0.000) >> max log p = -3.911584 @ (3.409, -1.136, -5.682) >> max log p = -3.897925 @ (-2.841, 2.841, 5.114) >> max log p = -3.897925 @ (0.000, 0.000, 0.000) >> Found translation: (-4.0, -11.9, -23.3): log p = -3.898 >> ****************************************** >> Nine parameter search. iteration 0 nscales = 0 ... >> ****************************************** >> Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9 >> (thresh=-3.9) >> 1.064 0.000 0.000 -12.315; >> 0.000 1.148 0.453 -81.971; >> 0.000 -0.432 0.988 42.250; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 1 nscales = 0 ... >> ****************************************** >> Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 >> (thresh=-3.5) >> 1.055 -0.150 -0.059 15.090; >> 0.128 1.052 0.415 -82.117; >> 0.000 -0.464 1.062 37.519; >> 0.000 0.000 0.000 1.000; >> reducing scale to 0.2500 >> ****************************************** >> Nine parameter search. iteration 2 nscales = 1 ... >> ****************************************** >> Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 >> (thresh=-3.5) >> 1.081 -0.059 0.014 -8.838; >> 0.025 1.116 0.400 -76.717; >> -0.035 -0.415 1.056 32.599; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 3 nscales = 1 ... >> ****************************************** >> Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 >> (thresh=-3.3) >> 1.101 -0.061 0.014 -11.382; >> 0.025 1.116 0.400 -78.592; >> -0.034 -0.407 1.036 33.963; >> 0.000 0.000 0.000 1.000; >> reducing scale to 0.0625 >> ****************************************** >> Nine parameter search. iteration 4 nscales = 2 ... >> ****************************************** >> Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 >> (thresh=-3.3) >> 1.098 -0.079 0.007 -7.337; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 5 nscales = 2 ... >> ****************************************** >> Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 >> (thresh=-3.3) >> 1.101 -0.079 0.007 -7.651; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> ****************************************** >> Nine parameter search. iteration 6 nscales = 2 ... >> ****************************************** >> Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 >> (thresh=-3.3) >> 1.101 -0.079 0.007 -7.651; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> min search scale 0.025000 reached >> ************************************************* >> Computing MAP estimate using 2772 samples... >> ************************************************* >> dt = 5.00e-06, momentum=0.80, tol=1.00e-05 >> l_intensity = 1.0000 >> Aligning input volume to GCA... >> Transform matrix >> 1.10052 -0.07872 0.00715 -7.65093; >> 0.04280 1.10969 0.41752 -81.72749; >> -0.03428 -0.42408 1.02550 37.91086; >> 0.00000 0.00000 0.00000 1.00000; >> nsamples 2772 >> Quasinewton: input matrix >> 1.10052 -0.07872 0.00715 -7.65093; >> 0.04280 1.10969 0.41752 -81.72749; >> -0.03428 -0.42408 1.02550 37.91086; >> 0.00000 0.00000 0.00000 1.00000; >> 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 TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = >> -0.0 tol 0.000010 >> Resulting transform: >> 1.101 -0.079 0.007 -7.651; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> >> pass 1, spacing 8: log(p) = -3.3 (old=-4.3) >> transform before final EM align: >> 1.101 -0.079 0.007 -7.651; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> >> **************************************************** >> EM alignment process ... >> Computing final MAP estimate using 312841 samples. >> **************************************************** >> dt = 5.00e-06, momentum=0.80, tol=1.00e-07 >> l_intensity = 1.0000 >> Aligning input volume to GCA... >> Transform matrix >> 1.10052 -0.07872 0.00715 -7.65093; >> 0.04280 1.10969 0.41752 -81.72749; >> -0.03428 -0.42408 1.02550 37.91086; >> 0.00000 0.00000 0.00000 1.00000; >> nsamples 312841 >> Quasinewton: input matrix >> 1.10052 -0.07872 0.00715 -7.65093; >> 0.04280 1.10969 0.41752 -81.72749; >> -0.03428 -0.42408 1.02550 37.91086; >> 0.00000 0.00000 0.00000 1.00000; >> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR >> RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE >> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = >> 3.9 tol 0.000000 >> final transform: >> 1.101 -0.079 0.007 -7.651; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> >> writing output transformation to transforms/talairach.lta... >> registration took 56 minutes and 24 seconds. >> #-----------------------------**--------- >> #@# CA Normalize Mon Jun 24 00:59:34 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz >> /mnt/glusterfs/salsoman/**freesurfer/average/RB_all_**2008-03-26.gca >> transforms/talairach.lta norm.mgz >> >> writing control point volume to ctrl_pts.mgz >> using MR volume brainmask.mgz to mask input volume... >> reading 1 input volume >> reading atlas from >> '/mnt/glusterfs/salsoman/**freesurfer/average/RB_all_**2008-03-26.gca'... >> reading transform from 'transforms/talairach.lta'... >> reading input volume from nu.mgz... >> resetting wm mean[0]: 102 --> 107 >> resetting gm mean[0]: 64 --> 64 >> input volume #1 is the most T1-like >> using real data threshold=25.1 >> skull bounding box = (61, 67, 54) --> (194, 197, 206) >> using (105, 110, 130) as brain centroid... >> mean wm in atlas = 107, using box (89,94,111) --> (121, 125,148) to find >> MRI >> wm >> before smoothing, mri peak at 109 >> after smoothing, mri peak at 109, scaling input intensities by 0.982 >> scaling channel 0 by 0.981651 >> using 244171 sample points... >> INFO: compute sample coordinates transform >> 1.101 -0.079 0.007 -7.651; >> 0.043 1.110 0.418 -81.727; >> -0.034 -0.424 1.025 37.911; >> 0.000 0.000 0.000 1.000; >> INFO: transform used >> finding control points in Left_Cerebral_White_Matter.... >> found 41584 control points for structure... >> bounding box (129, 73, 57) --> (191, 176, 203) >> Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 230.0 >> 0 of 209 (0.0%) samples deleted >> finding control points in Right_Cerebral_White_Matter...**. >> found 40735 control points for structure... >> bounding box (70, 73, 57) --> (130, 171, 203) >> Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 230.0 >> 0 of 240 (0.0%) samples deleted >> finding control points in Left_Cerebellum_White_Matter..**.. >> found 3012 control points for structure... >> bounding box (133, 151, 89) --> (179, 188, 135) >> Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 230.0 >> 1 of 12 (8.3%) samples deleted >> finding control points in Right_Cerebellum_White_Matter.**... >> found 2764 control points for structure... >> bounding box (92, 151, 85) --> (133, 189, 136) >> Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 230.0 >> 0 of 15 (0.0%) samples deleted >> finding control points in Brain_Stem.... >> found 3520 control points for structure... >> bounding box (117, 139, 115) --> (147, 197, 144) >> Brain_Stem: limiting intensities to 90.0 --> 230.0 >> 0 of 9 (0.0%) samples deleted >> using 485 total control points for intensity normalization... >> bias field = 1.019 +- 0.065 >> 1 of 484 control points discarded >> finding control points in Left_Cerebral_White_Matter.... >> found 41584 control points for structure... >> bounding box (129, 73, 57) --> (191, 176, 203) >> Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 233.0 >> 0 of 250 (0.0%) samples deleted >> finding control points in Right_Cerebral_White_Matter...**. >> found 40735 control points for structure... >> bounding box (70, 73, 57) --> (130, 171, 203) >> Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 233.0 >> 0 of 268 (0.0%) samples deleted >> finding control points in Left_Cerebellum_White_Matter..**.. >> found 3012 control points for structure... >> bounding box (133, 151, 89) --> (179, 188, 135) >> Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 233.0 >> 0 of 60 (0.0%) samples deleted >> finding control points in Right_Cerebellum_White_Matter.**... >> found 2764 control points for structure... >> bounding box (92, 151, 85) --> (133, 189, 136) >> Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 233.0 >> 0 of 62 (0.0%) samples deleted >> finding control points in Brain_Stem.... >> found 3520 control points for structure... >> bounding box (117, 139, 115) --> (147, 197, 144) >> Brain_Stem: limiting intensities to 75.0 --> 233.0 >> 0 of 79 (0.0%) samples deleted >> using 719 total control points for intensity normalization... >> bias field = 1.010 +- 0.067 >> 0 of 719 control points discarded >> finding control points in Left_Cerebral_White_Matter.... >> found 41584 control points for structure... >> bounding box (129, 73, 57) --> (191, 176, 203) >> Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 238.0 >> 0 of 301 (0.0%) samples deleted >> finding control points in Right_Cerebral_White_Matter...**. >> found 40735 control points for structure... >> bounding box (70, 73, 57) --> (130, 171, 203) >> Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 238.0 >> 0 of 377 (0.0%) samples deleted >> finding control points in Left_Cerebellum_White_Matter..**.. >> found 3012 control points for structure... >> bounding box (133, 151, 89) --> (179, 188, 135) >> Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 238.0 >> 0 of 82 (0.0%) samples deleted >> finding control points in Right_Cerebellum_White_Matter.**... >> found 2764 control points for structure... >> bounding box (92, 151, 85) --> (133, 189, 136) >> Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 238.0 >> 0 of 65 (0.0%) samples deleted >> finding control points in Brain_Stem.... >> found 3520 control points for structure... >> bounding box (117, 139, 115) --> (147, 197, 144) >> Brain_Stem: limiting intensities to 73.0 --> 238.0 >> 0 of 147 (0.0%) samples deleted >> using 972 total control points for intensity normalization... >> bias field = 1.007 +- 0.053 >> 2 of 972 control points discarded >> writing normalized volume to norm.mgz... >> writing control points to ctrl_pts.mgz >> freeing GCA...done. >> normalization took 2 minutes and 55 seconds. >> #-----------------------------**--------- >> #@# CA Reg Mon Jun 24 01:02:30 PDT 2013 >> /mnt/glusterfs/salsoman/**output/FS/GK_2536_FS/mri >> >> mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after >> -mask brainmask.mgz norm.mgz >> /mnt/glusterfs/salsoman/**freesurfer/average/RB_all_**2008-03-26.gca >> transforms/talairach.m3z >> >> not handling expanded ventricles... >> using previously computed transform transforms/talairach.lta >> renormalizing sequences with structure alignment, equivalent to: >> -renormalize >> -regularize_mean 0.500 >> -regularize 0.500 >> using MR volume brainmask.mgz to mask input volume... >> reading 1 input volumes... >> logging results to talairach.log >> >> >> ======= NUMBER OF OPENMP THREADS = 50 ======= >> reading input volume 'norm.mgz'... >> reading GCA >> '/mnt/glusterfs/salsoman/**freesurfer/average/RB_all_**2008-03-26.gca'... >> label assignment complete, 0 changed (0.00%) >> det(m_affine) = 1.45 (predicted orig area = 5.5) >> label assignment complete, 0 changed (0.00%) >> freeing gibbs priors...done. >> average std[0] = 5.0 >> **************** pass 1 of 1 ************************ >> setting smoothness coefficient to 0.039 >> blurring input image with Gaussian with sigma=2.000... >> 0000: dt=0.000, rms=0.806, neg=0, invalid=96777 >> 0001: dt=129.472000, rms=0.728 (9.599%), neg=0, invalid=96777 >> 0002: dt=92.480000, rms=0.712 (2.226%), neg=0, invalid=96777 >> 0003: dt=129.472000, rms=0.699 (1.800%), neg=0, invalid=96777 >> 0004: dt=129.472000, rms=0.693 (0.860%), neg=0, invalid=96777 >> 0005: dt=129.472000, rms=0.687 (0.887%), neg=0, invalid=96777 >> 0006: dt=129.472000, rms=0.684 (0.413%), neg=0, invalid=96777 >> 0007: dt=129.472000, rms=0.680 (0.585%), neg=0, invalid=96777 >> 0008: dt=110.976000, rms=0.679 (0.242%), neg=0, invalid=96777 >> 0009: dt=110.976000, rms=0.676 (0.391%), neg=0, invalid=96777 >> 0010: dt=110.976000, rms=0.673 (0.464%), neg=0, invalid=96777 >> 0011: dt=110.976000, rms=0.669 (0.563%), neg=0, invalid=96777 >> 0012: dt=110.976000, rms=0.666 (0.489%), neg=0, invalid=96777 >> 0013: dt=110.976000, rms=0.661 (0.684%), neg=0, invalid=96777 >> 0014: dt=110.976000, rms=0.658 (0.493%), neg=0, invalid=96777 >> 0015: dt=110.976000, rms=0.655 (0.439%), neg=0, invalid=96777 >> 0016: dt=110.976000, rms=0.653 (0.321%), neg=0, invalid=96777 >> 0017: dt=110.976000, rms=0.651 (0.311%), neg=0, invalid=96777 >> 0018: dt=110.976000, rms=0.649 (0.263%), neg=0, invalid=96777 >> 0019: dt=110.976000, rms=0.648 (0.202%), neg=0, invalid=96777 >> 0020: dt=110.976000, rms=0.647 (0.218%), neg=0, invalid=96777 >> 0021: dt=110.976000, rms=0.646 (0.148%), neg=0, invalid=96777 >> 0022: dt=110.976000, rms=0.644 (0.166%), neg=0, invalid=96777 >> 0023: dt=110.976000, rms=0.644 (0.139%), neg=0, invalid=96777 >> 0024: dt=110.976000, rms=0.642 (0.173%), neg=0, invalid=96777 >> 0025: dt=110.976000, rms=0.641 (0.153%), neg=0, invalid=96777 >> 0026: dt=110.976000, rms=0.640 (0.164%), neg=0, invalid=96777 >> 0027: dt=110.976000, rms=0.640 (0.146%), neg=0, invalid=96777 >> 0028: dt=110.976000, rms=0.639 (0.135%), neg=0, invalid=96777 >> 0029: dt=110.976000, rms=0.638 (0.119%), neg=0, invalid=96777 >> 0030: dt=110.976000, rms=0.637 (0.137%), neg=0, invalid=96777 >> 0031: dt=110.976000, rms=0.636 (0.126%), neg=0, invalid=96777 >> 0032: dt=110.976000, rms=0.636 (0.090%), neg=0, invalid=96777 >> 0033: dt=110.976000, rms=0.635 (0.063%), neg=0, invalid=96777 >> 0034: dt=129.472000, rms=0.635 (0.051%), neg=0, invalid=96777 >> 0035: dt=129.472000, rms=0.635 (0.000%), neg=0, invalid=96777 >> 0036: dt=129.472000, rms=0.635 (0.030%), neg=0, invalid=96777 >> 0037: dt=129.472000, rms=0.634 (0.062%), neg=0, invalid=96777 >> 0038: dt=129.472000, rms=0.634 (0.034%), neg=0, invalid=96777 >> 0039: dt=129.472000, rms=0.634 (0.027%), neg=0, invalid=96777 >> blurring input image with Gaussian with sigma=0.500... >> 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 >> 0040: dt=295.936000, rms=0.632 (0.322%), neg=0, invalid=96777 > >

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Freesurfer 5.3 error
by Salil Soman 25 Jun '13

25 Jun '13

Dear Freesurfer experts, I had been running freesurfer 5.3 without trouble on a sungrid cluster of ubuntu servers. Recently, however, I am now getting a new error: Loading source label. Invalid argument ERROR reading /mnt/glusterfs/salsoman/output/FS/fsaverage/label/lh.BA1.label Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18 16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s GK_2536_FS exited with ERRORS at Mon Jun 24 13:55:21 PDT 2013 Any suggestions on how I can fix this problem would be a great help. The log file is attached. Best wishes, Sal

2 1

Difficulty Visualizing Hippo-Subfields
by Mike Strupp-Levitsky 25 Jun '13

25 Jun '13

Hi All, I'm having a problem related to that of Ed Gronensch (see below) with viewing the hippocampal subfields overlaid on the nu.mgz mri in Freeview. I recently installed the most recent version for FreeSurfer (lion for MAC). When I use the command listed on the website ( cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt) It says in the command console history "Can not find index for color name posterior_left_CA1". When I manually load the subfields through the GUI (by loading them as subsequent volumes), they load just fine, however there is no suitable color pallet this way because the subfield.mgz files are, as you know probabilistic and therefore even when I choose the Lookup Table color map, are shown in rainbow colors. It is clear that these colors are a reflection of the fact that the subfields are probabilistic, not labels. In other words, the value of the image varies on the 0-255 scale and the colors reflect these, rather than the subfields being different discrete colors due to all being part of a mask or something like that. I hope this makes sense. Any help you could provide would be incredibly appreciated. Thanks SO much. Best, Mike ----------------------------------------------------------------------- Mike Strupp-Levitsky, BA Data Manager & Image Analyst Molecular Imaging & Neuropathology Division Columbia University, Department of Psychiatry New York State Psychiatric Institute, Suite 3920 (W): 212-543-5016 (C): 607-227-8811 Email: ms4637(a)columbia.edu

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Re: [Freesurfer] A segmentation estimation?
by Bruce Fischl 25 Jun '13

25 Jun '13

for the aseg it's these lines: . . . pass 1: 89966 changed. image ll: -2.224, PF=1.000 pass 2: 15019 changed. image ll: -2.221, PF=1.000 pass 3: 5116 changed. pass 4: 2124 changed. writing labeled volume to aseg.auto_noCCseg.mgz... although I guess I only compute it for the first couple of iterations of ICM cheers Bruce On Tue, 25 Jun 2013, Dov Sadan wrote: > This ?Computing Initial Surface Statistics > -face loglikelihood: -8.0702 (-4.0351) > -vertex loglikelihood: -6.6450 (-3.3225) > -normal dot loglikelihood: -3.4961 (-3.4961) > -quad curv loglikelihood: -6.1619 (-3.0810) > Total Loglikelihood : -24.3732 > > > > On Tue, Jun 25, 2013 at 10:34 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > No, not that. That is the density reestimation. Later on it > should write out the log posterior > > > > On Jun 25, 2013, at 3:32 PM, Dov Sadan <dov.sadan.19(a)gmail.com> wrote: > > Dear Buche, > Thank you very much for your quick reply. > > Do you mean those lines: (from recon-all. log) > ================== > . > . > . > gca peak = 0.27536 (62) > mri peak = 0.11940 (97) > Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, > overlap=0.000) > Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, > peak = 96), gca=96.1 > . > . > > =================== > > If this is what you meant, can you shed some light on this log. > What "gca peak" / "mri peak" means? And what the number > insight the parentheses represent ? > > Thanks in advance, > Assaf > > > > > On Tue, Jun 25, 2013 at 9:49 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Dov > > I think it writes out the log posterior at each > iteration of the aseg (mri_ca_label) > > cheers > Bruce > On Tue, 25 Jun 2013, Dov Sadan wrote: > > Hi there, > > I'm wondering if there's any parameter > which can assess the correctness of > the freesurfer's segmentation ( > the aparc.a2009s+aseg.mgz file). > > --> Assuming the freesurfer's algorithm > fitting/minimizing an objective > function, right ? If so, where I can > find the value of this > fitted function ? (or RMS value ?) > > Thanks in advance, > Dov > > > > > 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. > > > > >

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