Freesurfer

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30132 discussions

QDEC Interaction of Two Covariates
by David S Lee 19 Apr '18

19 Apr '18

External Email - Use Caution Hi FreeSurfer Experts, I want to test the relationship between cortical thickness and two continuous covariates (interaction) while controlling for one categorical variable. In QDEC, I can only choose one covariate, so I created a new variable that is a dot product (covariate1*covariate2) of the two to represent interaction. After analyzing, when I look at the data points at a single voxel, there is no visual indication of interaction. There also is no fitted line. Am I utilizing QDEC correctly? Thank you for your help! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Recon-all with custom atlas
by Ting Li 19 Apr '18

19 Apr '18

External Email - Use Caution Hi Freesurfer Experts, We want to run recon-all with a custom atlas which is generated from ANTs multivariate template construction. What is the right procedure to run recon-all? Run recon-all to my atlas itself first and them use this output as a template or I use the custom template directly. I looked up your email database to search related topic and got lost. I have sent another email to your group and no response received. Please help me. Thanks for you time. I look forward to hearing from you. Best, Ting

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Re: [Freesurfer] recon all error mpr2mni305
by Hoopes, Andrew 19 Apr '18

19 Apr '18

Hi Richard, it seems this was caused by a minor update to our mac build machine. These libraries should be correctly linked now in the most recent dev build (updated a few minutes ago). Let me know if you still have issues best, Andrew On 4/19/18, 2:39 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Jones, Richard" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of richard.jones(a)choa.org> wrote: How does the input image look, ie, orig.mg> The images the look the same as the input DICOM images, no scaling or other problems. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon all error mpr2mni305
by Jones, Richard 19 Apr '18

19 Apr '18

External Email - Use Caution Message: 1 Date: Thu, 19 Apr 2018 12:05:03 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305 To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <0b445a3f-8fde-d23e-dab6-442a773c9965(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252"; format=flowed How does the input image look, ie, orig.mg> The images the look the same as the input DICOM images, no scaling or other problems.

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Re: [Freesurfer] LGI for the lobar annotation
by Douglas N. Greve 19 Apr '18

19 Apr '18

What is your command line? Also, please remember to post to the list On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote: > Dear Douglas, > > thank you. > > The code worked, but I didn't understand the result very well. What > means intensity? The area, is the ara from the piall_lgi surface > (outer surface)? > > Thank you again > > On Tue, Apr 17, 2018 at 1:07 PM Douglas Greve <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> wrote: > > If you run it with --help you will see an example > > > On 4/16/18 7:16 AM, Fernanda Hansen P. de Moraes wrote: >> Thank you, Douglas, >> >> do you have any suggestions on how to make you work? >> >> Fernanda >> >> >> >> On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve >> <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: >> >> that should work, except the command line is not quite right >> >> >> On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes wrote: >>> Good night, >>> >>> does anyone know if it is possible to calculate the lGI for >>> the ?h.lobesStrict.annot? And if it yes, how can I do it? >>> >>> I've already tried to use: >>> >>> /mri_segstats --annot subjxx/label/lh.lobesStrict.annot --i >>> $SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum >>> lh.lobesStrict.annot.pial_lgi.stats/ >>> >>> Thank you! >>> -- >>> Fernanda Hansen P. de Moraes >>> Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede >>> D'Or São Luiz >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the >> person to whom it is >> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> -- >> Fernanda Hansen P. de Moraes >> Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or >> São Luiz >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Fernanda Hansen P. de Moraes > Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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unable to open freeview
by Darko Komnenić 19 Apr '18

19 Apr '18

Dear experts, I encountered a problem when trying to open freeview. I am using FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply freeview in the terminal, as described in this link: http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewQui… but the feedback I get is: freeview.bin: Command not found. Am I missing something? When searching for freeview on my computer, "freesurfer" and "freesurfer.bin" appear in my bin subfolder, but for some reason they seem not to be recognized. Any help is appreciated! Best, Darko

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Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness
by Arsenije Subotic 19 Apr '18

19 Apr '18

Hi Doug, I am able to get up to the mrs_glmfit step of the Surface Based Group fMRI Analysis, but it does not indicate how a comparison should be made between the two groups that I have. It only gives information on how to perform a one sample group mean test (osgm). In addition, when you mention using a mrs_glmfit-sim command, does this also generate cerebrovascular reactivity values, or does it only provide cortical thickness values? I was also hoping that I could potentially visualize an average area of low BOLD CVR for both groups. Is that possible? Thanks, Arsenije

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How FDR was used to correct for multiple comparisons
by Livia Liu 19 Apr '18

19 Apr '18

Dear FS experts, I'd like to know that how FDR was used to correct for multiple comparisons. I do FDR correction in two way in FreeSurfer. 1, Do the FDR correction in the qdec tool. And the page of “False Discovery Rate” in the page “Multiple-Comparisons Correction in Qdec” was lost. 2, Use “lme_mass_FDR.m” to do the FDR correction in LME model, which was based on Tom's FDR.m in the github, however the page was also lost. Would help to provide more details as to how FDR in the two way was used to correct for multiple comparisons? Thank you very much, and looking forward to reply. Kind regards, Livia

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Freesurfer dev version : recon all error mpr2mni305
by Jones, Richard 19 Apr '18

19 Apr '18

I ran the command shown below to do recon-all on DICOM images from a Philips Ingenia scanner using the development version of freesurfer on a Mac running high Sierra. recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject HOPE_SS020 -all The program crashed with the error "ERROR: mpr2mni305 failed, see transforms/talairach_avi.log" The talairach_avi.log file is shown below, followed by the log file. As a test I ran the same command, on the same data, using Freesurfer 6 and that ran without problems (except that it didn't handle the diffusion tags in the Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a problem in the development version). Any suggestions as to what may be causing the problems with the library in the development version? Thanks, Richard /Applications/freesurfer_dev/subjects/HOPE_SS020/mri /Applications/freesurfer_dev/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Thu Apr 19 08:45:01 EDT 2018 mri_convert.bin orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig_nu.mgz... TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (-1, 7.45058e-09, 0) j_ras = (3.72529e-09, -4.88944e-09, -1) k_ras = (0, 1, 4.88944e-09) writing to talsrcimg.img... Analyze Output Matrix -1.00000 0.00000 0.00000 128.15305; 0.00000 -0.00000 1.00000 -116.15433; 0.00000 -1.00000 0.00000 128.60870; 0.00000 0.00000 0.00000 1.00000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Thu Apr 19 08:45:02 EDT 2018 /Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Thu Apr 19 08:45:02 2018 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp Reason: image not found Abort ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 ERROR: mpr2mni305 execution aborted Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499 Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499 INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects Actual FREESURFER_HOME /Applications/freesurfer_dev Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 /Applications/freesurfer_dev/subjects/HOPE_SS020 \n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm... Starting DICOMRead2() dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat Ref Series No = 301 Found 202 files, checking for dicoms Found 200 dicom files in series. First Sorting Computing Slice Direction Vs: -0.897217 -0.0611658 0.0354633 Vs: -0.996909 -0.0679621 0.0394038 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 200 ndcmfiles = 200 PE Dir = ROW (dicom read) Loading pixel data TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (0.0644896, -0.994415, 0.0835493) j_ras = (0.0448617, -0.08075, -0.995724) k_ras = (0.996909, 0.0679621, 0.0394038) writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Apr 19 08:44:06 EDT 2018 Found 1 runs /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. \n cp /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz \n /Applications/freesurfer_dev/subjects/HOPE_SS020 \n mri_convert /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz --conform \n mri_convert.bin /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz... TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (0.0644896, -0.994415, 0.0835493) j_ras = (0.0448617, -0.08075, -0.995724) k_ras = (0.996909, 0.0679621, 0.0394038) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/transforms/talairach.xfm /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Apr 19 08:44:12 EDT 2018 /Applications/freesurfer_dev/subjects/HOPE_SS020/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Applications/freesurfer_dev/subjects/HOPE_SS020/mri /Applications/freesurfer_dev/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Thu Apr 19 08:44:12 EDT 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks(a)gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9696 /Applications/freesurfer_dev/subjects/HOPE_SS020/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9696/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9696/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig.mgz... TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (-1, 7.45058e-09, 0) j_ras = (3.72529e-09, -4.88944e-09, -1) k_ras = (0, 1, 4.88944e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9696/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Apr 19 08:44:14 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.9696/nu0.mnc ./tmp.mri_nu_correct.mni.9696/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9696/0/ -iterations 1000 -distance 50 [fsdev@meshuga.choa.org:/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/] [2018-04-19 08:44:14] running: /Applications/freesurfer_dev/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9696/0/ ./tmp.mri_nu_correct.mni.9696/nu0.mnc ./tmp.mri_nu_correct.mni.9696/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 55 CV of field change: 0.000965325 mri_convert ./tmp.mri_nu_correct.mni.9696/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9696/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from ./tmp.mri_nu_correct.mni.9696/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.45058e-09, 0) j_ras = (3.72529e-09, -4.88944e-09, -1) k_ras = (0, 1, 4.88944e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Apr 19 08:45:01 EDT 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

2 1

SLURM - speed processing
by Alexandre Obert 19 Apr '18

19 Apr '18

External Email - Use Caution Hi all, I'm definitively a noob with both freesurfer and SLURM processes and I wonder if anyone could give me some advice. I tried processing a subject (including hippocampal segmentation) using the following command (freesurfer 6.0.0): recon-all -all -s s03 -hippocampal-subfields-T1 It took nearly 12h to process. I then submit this job to a supercomputer (using slurm) and I asked for nearly 30Go RAM It took nearly 7h to process. That seems good but I wonder if it's possible to speed it up a little more? Regards, Alex

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