Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Re: [Freesurfer] epidewarp.fsl for FSL 5.x
by Douglas Greve 22 Mar '16

22 Mar '16

It is there again. I don't know what the status if it is in terms of the version. Try it and let me know doug On 11/25/14 4:34 PM, Morgan Hough wrote: > Hi Doug, > > Could you put the epidewarp.fsl script back on your ftp site? I don’t > see it at the link in the archives: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl > > BTW, is the script updated in some way for 5.x or can I can the old > script just be changed to accept 5.x version numbers. > > Cheers, > > -Morgan

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Re: [Freesurfer] 3_group_comparison
by Lee Tirrell 15 Mar '16

15 Mar '16

Hi Dusan, setenv is used when you are using tcsh. since you are using bash, you can run this command to set your language: export LANG=en_US.UTF-8 Hope this helps. Best, Lee On Tue, 29 Sep 2015, Dusan Hirjak wrote: > Thank you very much for your suggestion. Now it has worked well. > However, I am having trouble running the simulation via: > > mri_glmfit-sim --glmdir NSS_3_GR.glmdir --cache 4 abs --cwp 0.05 --2spaces > > ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > > Where can I set up the EN language with "setenv LANG en_US.UTF-8"? > > > I am getting this message: > > > bash-3.2$ setenv LANG en_US.UTF-8 > > bash: setenv: command not found > > > How can I change the language? > > > Many thanks! > > Dusan > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: rpwang(a)nmr.mgh.harvard.edu > Date: Mon, 28 Sep 2015 19:35:12 -0400 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 3_group_comparison > > Was the path of the overlay file correct? It looks like it can’t find the file. Try providing the full path of the overlay file in the freeview command. > > Best, > Ruopeng > > On Sep 28, 2015, at 6:46 PM, Dusan Hirjak <dusanhirjak(a)hotmail.com> wrote: > > Many thanks!!!, yes, freeview has opened, but I am still not seeing any results, just the "lh.inflated" > It says: "Failed to load surface overlay" > > and than I got the following message: > > bash-3.2$ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d > 2015-09-29 00:41:53.887 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.905 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.906 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.921 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.922 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > Did not find any volume geometry information in the surface > ø;C 8Íÿ¿ø;C È+’Àá > > reading colortable from annotation file... > colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > could not read overlay data from /users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > 2015-09-29 00:42:02.445 Freeview[22049:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: > > I dont understand the problem. Do you have any ideas??? > > Thank you! > > Dusan > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > From: greve(a)nmr.mgh.harvard.edu > > Date: Mon, 28 Sep 2015 18:33:50 -0400 > > Subject: Re: [Freesurfer] 3_group_comparison > > > > I think it needs a -f before the surface > > > > On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > > > Many thanks, yes, it did work well. > > > > > > But, than I ran "freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d" > > > > > > and got the following message: > > > > > > bash-3.2$ freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d > > > > > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable > > > > > > Unrecognized sub-option flag 'annot=aparc.annot'. > > > > > > > > > Freeview has opened, but it showed no results at all:-( > > > > > > > > > What should I do? I read that one has to upgrade the newest > > > freeview-version? Is it possible to get the newest version without > > > installing freesurfer again? > > > > > > Many thanks! > > > > > > Dusan > > > > > > > > > ------------------------------------------------------------------------ > > > Date: Mon, 28 Sep 2015 11:35:50 -0400 > > > From: greve(a)nmr.mgh.harvard.edu > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] 3_group_comparison > > > > > > Did you include the back slashes in your command? If so, remove them > > > and retry. > > > > > > On 9/25/15 7:11 PM, Dusan Hirjak wrote: > > > > > > Dear Freesurfer experts, > > > > > > I am trying to compare 3 groups (aut, sch, ges) according to > > > thickness, area and LGI at once (omnibus test). > > > > > > I did run the following command: > > > > > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in > > > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out > > > lh.NSS_3_GR.thickness.15.mgh > > > > > > > > > This step did work properly:-) > > > > > > > > > > > > Now, Im trying to run the following command, but it does not work: > > > > > > > > > mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd > > > NSS_3_GR.fsgd dods\ --C contrasts.mtx \ --surf fsaverage lh \ > > > --cortex \ --glmdir NSS_3_GR.glmdir > > > > > > > > > I got this message: "ERROR: Option--y unknown" > > > > > > > > > What am I doing wrong? > > > > > > > > > Thank you for your help! > > > > > > > > > > > > Best regards > > > > > > > > > Dusan > > > > > > > > > _______________________________________________ > > > 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 > > > 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. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you > in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. > >

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Re: [Freesurfer] Tracula_weighted dti metrics values
by Anastasia Yendiki 09 Feb '16

09 Feb '16

Hi John - The values are weighted (multiplied) by the probability distribution (path.pd.nii.gz) at the same voxel. So they are the expected values, from a probabilistic standpoint. The distribution is thresholded at 20% of its maximum by default (this is a parameter in dmri_pathstats). Best, a.y On Wed, 16 Sep 2015, John Anderson wrote: > Hi Anastasia, > How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD > values? > I checked the command "dmri_pathstats" inside the file "trac-all.log" but I > was unable to figure out how this weighting is working. Is it by multiplying > the mean DTI metrics by the number of voxel? > > If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map > for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA > value using the command "fslstats" like: > > fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m ==== >This command will > output the mean FA for the probabilistic distribution map. How can I weight > this FA value using the previous command line? > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > >

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Gray matter intensity
by Sabrina Yu 08 Feb '16

08 Feb '16

Hello, I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html> And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity. 1) Does the wmparc.stats contain mean white matter intensity values for each ROI? 2) Is it possible to extract these same mean intensity values for gray matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data. Thank you, Sabrina Yu

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HSF in 5.3
by Alan Francis 29 Jan '16

29 Jan '16

Hi Eugenio: I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message. [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields ERROR: Flag -hippocampal-subfields unrecognized. -s Smoke_d004 -hippocampal-subfields Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I tried adding the -hippocampal-subfields-T1 but that did not work too. thanks, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Cannot open FreeSurfer application zipped file
by Meirelles, Osorio (NIH/NIA/IRP) [E] 27 Jan '16

27 Jan '16

Dear experts, I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file” Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated. Thanks, Osorio -----Original Message----- From: Meirelles, Osorio (NIH/NIA/IRP) [E] Sent: Thursday, December 24, 2015 12:23 PM To: Freesurfer support list Cc: Matthew Glasser Subject: RE: [Freesurfer] hello freesurfer developer~ Dear experts, I tried to unzip the file “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. I entered on my command prompt: “gunzip freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the message after a few minutes: “gzip: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of file” Perhaps this might be a version issue. Anyway, any help into getting the correct installation file would be greatly appreciated. Thanks, Osorio -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2015 12:16 PM To: Freesurfer support list Cc: Matthew Glasser Subject: Re: [Freesurfer] hello freesurfer developer~ Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: > hello experts!my name is areum. > i have some question to you. > a few days ago i was down load HCP(human connectom project) data. > but.. how can i use these HCP format. > i have never seen before these format(fig.1.png) > I want to see HCP data subjects's cortical thickness using qdec. > how can i to do? > plz answer me > > 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah(a)gmail.com>: > Hello experts! > I have some question to you.. > > I don't need to show up so small blue regions(fig.1 blue region) > > How can i control these? > > 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > Hi, please create a new thread since this is a new topic. > Also, I don't > understand your question so please elaborate. > > On 11/09/2015 05:34 AM, A-reum Min wrote: > > Hello experts! > > > > i have some question to you.. > > > > How can i control the cluster size? > > > > My cluster threshold is 1. > > > > then, too many blue regions (as shown fig.1). > > > > so, i want to control cluster threshold 1--> cluster > threshold 5. > > > > 2015-11-08 20:44 GMT+09:00 A-reum Min > <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com>>: > > > > Hello bruce! > > > > I solve the problem for your answer. > > > > And.. i have some question to you.. > > > > How can i control the cluster size? > > > > My cluster threshold is 1. > > > > then, too many blue regions (as shown fig.1). > > > > so, i want to control cluster threshold 1--> cluster > threshold 5. > > > > How can i to do? > > > > > > > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>: > > > > are > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > and > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > images from *different* series or from the > *same* series? If > > they are in the same series than that explains > what is > > happening. You should only give recon-all a > single file from > > any one acquisition - it will figure out the > rest of the files > > that are part of it. > > > > cheers > > Bruce > > > > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > > > hello experts. > > i have some question to you... > > > > when i enter the recon-all -i /paht~ > > > > error showed up.... like below one.. > > > > how can i to fix it? > > > > [areum@localhost 0165766_1]# recon-all -i > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > -i > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > -all -s sub002 > > Subject Stamp: > > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > Current Stamp: > > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is > > /usr/local/freesurfer/subjects/OSA/0165766_1 > > Actual FREESURFER_HOME /usr/local/freesurfer > > Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP > > Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter > > Exp $ > > reading from > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > > Starting DICOMRead2() > > dcmfile = > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > > dcmdir = > /usr/local/freesurfer/subjects/OSA/0165766_1 > > Ref Series No = 3 > > Found 247 files, checking for dicoms > > Found 244 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.8 0 0 > > Vs: -1 0 0 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 244 > > ndcmfiles = 244 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, -0, 0) > > writing to > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > > > > mri_convert > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter > > Exp $ > > reading from > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > > Starting DICOMRead2() > > dcmfile = > > > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > > dcmdir = > /usr/local/freesurfer/subjects/OSA/0165766_1 > > Ref Series No = 3 > > Found 247 files, checking for dicoms > > Found 244 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.8 0 0 > > Vs: -1 0 0 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 244 > > ndcmfiles = 244 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, -0, 0) > > writing to > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > > > #-------------------------------------------- > > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > > Found 2 runs > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > Checking for (invalid) multi-frame inputs... > > Checking for (invalid) multi-frame inputs... > > > #----------------------------------------------- > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > > > mri_robust_template --mov > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > --average 1 --template > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > > --satit > > --inittp 1 --fixtp --noit --iscale > > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/00 > 1-iscale.txt > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx > t > > --subsample 200 --lta > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > > > > $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 > > 19:59:06 mreuter Exp $ > > > > --mov: Using > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > as > > movable/source volume. > > --mov: Using > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > as > > movable/source volume. > > Total: 2 input volumes > > --average: Using method 1 for template > computation. > > --template: Using > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > > as > > template output volume. > > --satit: Will estimate SAT iteratively! > > --inittp: Using TP 1 as target for > initialization > > --fixtp: Will map everything to init TP! > > --noit: Will output only first template (no > iterations)! > > --iscale: Enableing intensity scaling! > > --iscaleout: Will perform intensity scaling > and output results > > --subsample: Will subsample if size is > larger than 200 on > > all axes! > > --lta: Will output LTA transforms > > reading source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > > converting source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > > to > > bspline ... > > MRItoBSpline degree 3 > > reading source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > > converting source > > > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > > to > > bspline ... > > MRItoBSpline degree 3 > > > > MultiRegistration::initializing Xforms (init > 1 , maxres 0 > > , iterate 5 , > > epsit 0.01 ) : > > > > [init] ========================= TP 2 to TP > 1 > > ============================== > > Register TP 2 ( > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > ) > > to TP 1 ( > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > ) > > > > -- Original : (0.4688, 0.4688, > 0.800001) mm size > > and (512, 512, 244) > > voxels. > > -- Resampled: (0.4688, 0.4688, > 0.4688) mm size and > > (512, 512, 417) > > voxels. > > -- Reslicing using cubic bspline > > MRItoBSpline degree 3 > > -- Original : (0.4688, 0.4688, > 0.800001) mm size > > and (512, 512, 244) > > voxels. > > -- Resampled: (0.4688, 0.4688, > 0.4688) mm size and > > (512, 512, 417) > > voxels. > > -- Reslicing using cubic bspline > > MRItoBSpline degree 3 > > > > - Max Resolution used: 3 > > -- gpS ( 64 , 64 , 52 ) > > -- gpT ( 64 , 64 , 52 ) > > - running loop to estimate saturation > parameter: > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Killed > > Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP > > Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s sub002 exited with ERRORS at > Thu Nov 5 > > 02:37:57 PST 2015 > > > > For more details, see the log file > > > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > 2015-10-19 11:05 GMT+09:00 A-reum Min > <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com>>: > > hello experts. > > i have a question to you.. > > > > i'm doing recon-all stage, but errors show up like > this > > > > > > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 > --template > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > > --satit > > --inittp 1 --fixtp --noit --iscale --iscaleout > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > > --subsample 200 --lta > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > > > / > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > > 19:59:06 mreuter > > Exp $ > > > > --mov: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > > as > > movable/source volume. > > --mov: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > as > > movable/source volume. > > Total: 2 input volumes > > --average: Using method 1 for template > computation. > > --template: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > > as > > template output volume. > > --satit: Will estimate SAT iteratively! > > --inittp: Using TP 1 as target for initialization > > --fixtp: Will map everything to init TP! > > --noit: Will output only first template (no > iterations)! > > --iscale: Enableing intensity scaling! > > --iscaleout: Will perform intensity scaling and > output results > > --subsample: Will subsample if size is larger than > 200 on > > all axes! > > --lta: Will output LTA transforms > > reading source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > > converting source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > > to > > bspline ... > > MRItoBSpline degree 3 > > reading source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > > converting source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > > to > > bspline ... > > MRItoBSpline degree 3 > > > > MultiRegistration::initializing Xforms (init 1 , > maxres 0 > > , iterate 5 > > , epsit 0.01 ) : > > > > [init] ========================= TP 2 to TP 1 > > ============================== > > Register TP 2 ( > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > ) > > to TP 1 ( > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > > ) > > > > -- Original : (0.4688, 0.4688, 0.800001) mm > size > > and (512, 512, > > 244) voxels. > > -- Resampled: (0.4688, 0.4688, 0.4688) mm > size and > > (512, 512, > > 417) voxels. > > -- Reslicing using cubic bspline > > MRItoBSpline degree 3 > > -- Original : (0.4688, 0.4688, 0.800001) mm > size > > and (512, 512, > > 244) voxels. > > -- Resampled: (0.4688, 0.4688, 0.4688) mm > size and > > (512, 512, > > 417) voxels. > > -- Reslicing using cubic bspline > > MRItoBSpline degree 3 > > > > - Max Resolution used: 3 > > -- gpS ( 64 , 64 , 52 ) > > -- gpT ( 64 , 64 , 52 ) > > - running loop to estimate saturation > parameter: > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Sigma too small: 0 (identical images?) > > Killed > > [areum@localhost 14]# > > > > [areum@localhost 14]# $Id: > mri_robust_template.cpp,v 1.37.2.2 > > 2012/10/10 19:59:06 mreuter Exp $ > > c > > Bad : modifier in $ ( ). > > [areum@localhost 14]# > > [areum@localhost 14]# --mov: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > > as > > movable/source volume. > > --mov:: Too many arguments. > > [areum@localhost 14]# --mov: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > as > > movable/source volume. > > --mov:: Too many arguments. > > [areum@localhost 14]# Total: 2 input volumes > > Total:: Too many arguments. > > b > > [areum@localhost 14]# --average: Using method 1 > for template > > computation. > > --average:: Too many arguments. > > [areum@localhost 14]# --template: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > > as > > template output volume. > > --template:: Too many arguments. > > [areum@localhost 14]# --satit: Will estimate SAT > iteratively! > > i > > --satit:: Too many arguments. > > [areum@localhost 14]# --inittp: Using TP 1 as > target for > > initialization > > --inittp:: Too many arguments. > > [areum@localhost 14]# --fixtp: Will map everything > to init TP! > > --fixtp:: Too many arguments. > > [areum@localhost 14]# --noit: Will output only > first > > template (no > > iterations)! > > Badly placed ()'s. > > [areum@localhost 14]# --iscale: Enableing > intensity scaling! > > --iscale:: Too many arguments. > > [areum@localhost 14]# --iscaleout: Will perform > intensity > > scaling and > > output results > > --iscaleout:: Too many arguments. > > [areum@localhost 14]# --subsample: Will subsample > if size > > is larger > > than 200 on all axes! > > --subsample:: Too many arguments. > > [areum@localhost 14]# --lta: Will output LTA > transforms > > --lta:: Too many arguments. > > [areum@localhost 14]# reading source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > > - > > reading: Command not found. > > [areum@localhost 14]# converting source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > > to > > bspline ... > > b > > converting: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > r > > MRItoBSpline: Command not found. > > [areum@localhost 14]# reading source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > > n > > reading: Command not found. > > [areum@localhost 14]# converting source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > > to > > bspline ... > > > > converting: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > p > > MRItoBSpline: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# > MultiRegistration::initializing > > Xforms (init 1 , > > maxres 0 , iterate 5 , epsit 0.01 ) : > > / > > Badly placed ()'s. > > [areum@localhost 14]# > > [areum@localhost 14]# [init] > ========================= TP > > 2 to TP 1 > > ============================== > > a > > [init]: No match. > > [areum@localhost 14]# Register TP 2 ( > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > ) > > Badly placed ()'s. > > e > > [areum@localhost 14]# to TP 1 ( > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > > ) > > n > > Badly placed ()'s. > > [areum@localhost 14]# > > [areum@localhost 14]# -- Original : > (0.4688, > > 0.4688, 0.800001) > > mm size and (512, 512, 244) voxels. > > Badly placed (. > > [areum@localhost 14]# -- Resampled: > (0.4688, > > 0.4688, 0.4688) mm > > size and (512, 512, 417) voxels. > > Badly placed (. > > [areum@localhost 14]# -- Reslicing using > cubic bspline > > a > > --: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > T > > MRItoBSpline: Command not found. > > [areum@localhost 14]# -- Original : > (0.4688, > > 0.4688, 0.800001) > > mm size and (512, 512, 244) voxels. > > Badly placed (. > > [areum@localhost 14]# -- Resampled: > (0.4688, > > 0.4688, 0.4688) mm > > size and (512, 512, 417) voxels. > > Badly placed (. > > [areum@localhost 14]# -- Reslicing using > cubic bspline > > a > > --: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > u > > MRItoBSpline: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# - Max Resolution used: 3 > > i > > -: Command not found. > > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > > Badly placed ()'s. > > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > > Badly placed ()'s. > > [areum@localhost 14]# - running loop to > estimate saturation > > parameter: > > l > > -: Command not found. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > 4 > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Killed > > . > > Killed: Command not found. > > [areum@localhost 14]# Linux localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 > UTC 2014 > > x86_64 > > x86_64 x86_64 GNU/Linux > > > > Linux: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# recon-all -s subj014 exited > with > > ERRORS at Sat > > Oct 17 07:50:15 PDT 2015 > > a > > ERROR: Flag exited unrecognized. > > -s subj014 exited with ERRORS at Sat Oct 17 > 07:50:15 PDT 2015 > > Linux localhost.localdomain 2.6.32-504.el6.x86_64 > #1 SMP > > Wed Oct 15 > > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s subj014 exited with ERRORS at Sat Oct > 17 > > 08:35:33 PDT > > 2015 > > > > For more details, see the log file > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > [areum@localhost 14]# > > [areum@localhost 14]# For more details, see the > log file > > > /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > > > For: Command not found. > > [areum@localhost 14]# To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > e > > To: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# [areum@localhost 14]# > recon-all -i > > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm > -i > > /usr/local/ > > > > [areum@localhost: Command not found. > > [areum@localhost 14]# Subject Stamp: > > freesurfer-Linux-centos6_x86_6 > > i > > Subject: Command not found. > > [areum@localhost 14]# Current Stamp: > > freesurfer-Linux-centos6_x8 > > 2 > > Current: Command not found. > > [areum@localhost 14]# INFO: SUBJEC > > INFO:: Too many arguments. > > [areum@localhost 14]# Actual FREESURFER_HOME > > /usr/local/freesurfer > > 8 > > Actual: Command not found. > > [areum@localhost 14]# Linux localhost.l > > s > > Linux: Command not found. > > [areum@localhost 14]# > > /usr/local/freesurfer/subjects/OSA/14/subj014 > > g > > /usr/local/freesurfer/subjects/OSA/14/subj014: > Permission > > denied. > > [areum@localhost 14]# > > [areum@localhost 14]# mri_convert /u > > mri_convert /u > > > > mri_convert: missing output volume name > > > > type mri_convert -u for usage > > > > [areum@localhost 14]# > > [areum@localhost 14]# mri_convert > > /usr/local/freesurfer/subjects/ > > mri_convert /usr/local/freesurfer/subjects/ > > > > mri_convert: missing output volume name > > > > type mri_convert -u for usage > > > > [areum@localhost 14]# $Id: mri_convert.c,v > 1.179.2.7 > > 2012/09/05 > > 21:55:16 mreuter Exp $ > > Bad : modifier in $ ( ). > > [areum@localhost 14]# reading from > > > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... > > reading: Command not found. > > [areum@localhost 14]# Startin > > Startin: Command not found. > > [areum@localhost 14]# dcmfile = > > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm > > dcmfile: Command not found. > > [areum@localhost 14]# dcmdir = > > /usr/local/freesurfer/subjects/OSA/14 > > dcmdir: Command not found. > > [areum@localhost 14]# Ref Series No = 3 > > Ref: Command not found. > > [areum@localhost 14]# Found 247 files, checking > for dicoms > > Found: Command not found. > > [areum@localhost 14]# Found 244 dicom files in > series. > > Found: Command not found. > > [areum@localhost 14]# First Sorting > > First: Command not found. > > [areum@localhost 14]# Computing Slice Direction > > Computing: Command not found. > > [areum@localhost 14]# Vs: -0.8 0 0 > > Vs:: Too many arguments. > > [areum@localhost 14]# Vs: -1 0 0 > > Vs:: Too many arguments. > > [areum@localhost 14]# Second Sorting > > Second: Command not found. > > [areum@localhost 14]# Counting frames > > Counting: Command not found. > > [areum@localhost 14]# nframes = 1 > > nframes: Command not found. > > [areum@localhost 14]# nslices = 244 > > nslices: Command not found. > > [areum@localhost 14]# ndcmfiles = 244 > > ndcmfiles: Command not found. > > [areum@localhost 14]# PE Dir = ROW (dicom read) > > Badly placed ()'s. > > [areum@localhost 14]# TransferSyntaxUID: > > --1.2.840.10008.1.2.1-- > > TransferSyntaxUID:: Too many arguments. > > [areum@localhost 14]# Loading pixel data > > Loading: Command not found. > > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, > flip > > angle=12.00 > > TR=7.70,: Command not found. > > [areum@localhost 14]# i_ras = (0, -1, 0) > > Badly placed ()'s. > > [areum@localhost 14]# j_ras = (0, 0, -1) > > Badly placed ()'s. > > [areum@localhost 14]# k_ras = (1, -0, 0) > > Badly placed ()'s. > > [areum@localhost 14]# writing to > > /usr/local/freesurfer/subjects/OSA/14/subj014/ > > writing: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# > > [areum@localhost 14]# mri_convert > > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/loc > > mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > > /usr/loc > > mri_convert: can't determine type of output volume > > [areum@localhost 14]# > > [areum@localhost 14]# mri_convert > > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > > > mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter > > Exp $ > > reading from > > > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... > > Starting DICOMRead2() > > dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > > dcmdir = /usr/local/freesurfer/subjects/OSA/14 > > Ref Series No = 3 > > Found 247 files, checking for dicoms > > Found 244 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.8 0 0 > > Vs: -1 0 0 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 244 > > ndcmfiles = 244 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > > i_ras = (0, -1, 0) > > j_ras = (0, 0, -1) > > k_ras = (1, -0, 0) > > writing to > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > > [areum@localhost 14]# $Id: mri_convert.c,v > 1.179.2.7 > > 2012/09/05 > > 21:55:16 mreuter Exp $ > > Bad : modifier in $ ( ). > > [areum@localhost 14]# reading from > /usr/local/freesurfer/sub > > reading: Command not found. > > [areum@localhost 14]# Starting DICOMRead2() > > Badly placed ()'s. > > [areum@localhost 14]# dcmfile = > > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > > dcmfile: Command not found. > > [areum@localhost 14]# dcmdir = > > /usr/local/freesurfer/subjects/OSA/14 > > dcmdir: Command not found. > > [areum@localhost 14]# Ref Series No = 3 > > Ref: Command not found. > > [areum@localhost 14]# Found 247 files, checking > for dicoms > > Found: Command not found. > > [areum@localhost 14]# Found 244 di > > Found: Command not found. > > [areum@localhost 14]# First Sorting > > First: Command not found. > > [areum@localhost 14]# Computing Slice Direction > > Computing: Command not found. > > [areum@localhost 14]# Vs: -0.8 0 0 > > Vs:: Too many arguments. > > [areum@localhost 14]# Vs: -1 0 0 > > Vs:: Too many arguments. > > [areum@localhost 14]# Second Sorting > > Second: Command not found. > > [areum@localhost 14]# Counting frames > > Counting: Command not found. > > [areum@localhost 14]# nframes = 1 > > nframes: Command not found. > > [areum@localhost 14]# nslices = 244 > > nslices: Command not found. > > [areum@localhost 14]# ndcmfiles = 244 > > ndcmfiles: Command not found. > > [areum@localhost 14]# PE Dir = ROW (dicom read) > > Badly placed ()'s. > > [areum@localhost 14]# TransferSyntaxUID: > > --1.2.840.10008.1.2.1-- > > TransferSyntaxUID:: Too many arguments. > > [areum@localhost 14]# Loading pixel data > > Loading: Command not found. > > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, > flip > > angle=12.00 > > TR=7.70,: Command not found. > > [areum@localhost 14]# i_ras = (0, -1, 0) > > Badly placed ()'s. > > [areum@localhost 14]# j_ras = (0, 0, -1) > > Badly placed ()'s. > > [areum@localhost 14]# k_ras = (1, -0, 0) > > Badly placed ()'s. > > [areum@localhost 14]# writing to > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > > writing: Command not found. > > [areum@localhost 14]# > #---------------------------- > > #----------------------------: Command not found. > > [areum@localhost 14]# #@# MotionCor Sat Oct 17 > 08:09:23 > > PDT 2015 > > #@#: Command not found. > > [areum@localhost 14]# Found 2 runs > > Found: Command not found. > > [areum@localhost 14]# > > /usr/local/freesurfer/subjects/OSA/14/sub > > /usr/local/freesurfer/subjects/OSA/14/sub: Command > not found. > > [areum@localhost 14]# /usr/local/freesurfer > > /usr/local/freesurfer: Permission denied. > > [areum@localhost 14]# Checking for (invalid) > multi-frame > > inputs... > > Badly placed ()'s. > > [areum@localhost 14]# Checking for (invalid) > multi-frame in > > Badly placed ()'s. > > [areum@localhost 14]# > > #----------------------------------------------- > > #-----------------------------------------------: > Command > > not found. > > [areum@localhost 14]# > > /usr/local/freesurfer/subjects/OSA/14/subj014 > > /usr/local/freesurfer/subjects/OSA/14/subj014: > Permission > > denied. > > [areum@localhost 14]# > > [areum@localhost 14]# > > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_temp > > Bad : modifier in $ ( ). > > [areum@localhost 14]# > > [areum@localhost 14]# --mov: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > > as > > movable/ > > --mov:: Too many arguments. > > [areum@localhost 14]# --mov: Using > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > a > > --mov:: Too many arguments. > > [areum@localhost 14]# Total: 2 input volumes > > Total:: Too many arguments. > > [areum@localhost 14]# --average: Using method 1 > for template > > computation. > > --average:: Too many arguments. > > [areum@localhost 14]# --template > > --template: Command not found. > > [areum@localhost 14]# --satit: Will estimate SAT > iteratively! > > --satit:: Too many arguments. > > [areum@localhost 14]# --inittp: Using TP 1 as > target for > > initialization > > --inittp:: Too many arguments. > > [areum@localhost 14]# --fixtp: Will map everything > to init TP! > > --fixtp:: Too many arguments. > > [areum@localhost 14]# --noit: Will output only > first > > template (no > > iterations)! > > Badly placed ()'s. > > [areum@localhost 14]# --iscale: Enableing > intensity scaling! > > --iscale:: Too many arguments. > > [areum@localhost 14]# --iscaleout: Will perform > intensity > > scaling and > > output results > > --iscaleout:: Too many arguments. > > [areum@localhost 14]# --subsa > > --subsa: Command not found. > > [areum@localhost 14]# --lta: Will output LT > > --lta:: Too many arguments. > > [areum@localhost 14]# reading source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > > reading: Command not found. > > [areum@localhost 14]# converting source > > > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > > to > > bspline ... > > converting: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > MRItoBSpline: Command not found. > > [areum@localhost 14]# rea > > rea: Command not found. > > [areum@localhost 14]# converting source '/u > > Unmatched '. > > [areum@localhost 14]# MRItoBSpline degree 3 > > MRItoBSpline: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# Multi > > Multi: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# [init] > ========================= TP > > 2 to TP 1 > > ============================== > > [init]: No match. > > [areum@localhost 14]# Register TP 2 ( > /usr/l > > Too many ('s. > > [areum@localhost 14]# to TP 1 ( > > > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > > ) > > Badly placed ()'s. > > [areum@localhost 14]# > > [areum@localhost 14]# -- Original : > (0.4688, > > 0.4688, 0.800001) > > mm size and (512, 512, 244) voxels. > > Badly placed (. > > [areum@localhost 14]# -- Resampled: > (0.4688, > > 0.4688, 0.4688) mm > > size and (512, 512, 4 > > Too many ('s. > > [areum@localhost 14]# -- Reslicing using > cubic bspline > > --: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > MRItoBSpline: Command not found. > > [areum@localhost 14]# -- Original : > (0.4688, > > 0.4688, 0.800001) > > mm size and (512, 512, 244) voxels. > > Badly placed (. > > [areum@localhost 14]# -- Resampled: (0. > > Too many ('s. > > [areum@localhost 14]# -- Reslicing using > cubic bspline > > --: Command not found. > > [areum@localhost 14]# MRItoBSpline degree 3 > > MRItoBSpline: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# - Max Resolution used: 3 > > -: Command not found. > > [areum@localhost 14]# -- gpS ( 64 , 64 , > > Too many ('s. > > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > > Badly placed ()'s. > > [areum@localhost 14]# - running loop to > estimate > > saturation pa > > -: Command not found. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > > Sigma: Command not found. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical image > > Too many ('s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Sigma too small: > > Sigma: Command not found. > > [areum@localhost 14]# Sigma too small: 0 > (identical images?) > > Badly placed ()'s. > > [areum@localhost 14]# Si > > Si: Command not found. > > [areum@localhost 14]# Killed > > Killed: Command not found. > > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32 > > Linux: Command not found. > > [areum@localhost 14]# > > [areum@localhost 14]# recon-all -s subj014 exited > with > > ERRORS at Sat > > Oct 17 08 > > ERROR: Flag exited unrecognized. > > -s subj014 exited with ERRORS at Sat Oct 17 08 > > Linux localhost.localdomain 2.6.32-504.el6.x86_64 > #1 SMP > > Wed Oct 15 > > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s subj014 exited with ERRORS at Sat Oct > 17 > > 08:35:53 PDT > > 2015 > > > > For more details, see the log file > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > > > > > how can i to do? > > > > plz help me.. > > > > 2015-10-18 0:11 GMT+09:00 Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>: > > Hi A-reum > > > > can you please follow the bug-reporting > procedures in: > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > also, don't include a snapshot of text - > cutting and > > pasting the actual text in is far more > useful, but in > > addition we need a lot of other information > if we are to > > be able to help you > > > > cheers > > Bruce > > > > On Sun, 18 Oct 2015, A-reum Min wrote: > > > > hello experts. > > I have a question to you... > > > > I'm doing recon-all stage... but errors > showed up > > (fig.1) > > > > how can i to do? > > > > plz, help me > > > > > > 2015-09-16 23:56 GMT+09:00 Douglas Greve > > <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use .hdr. When you have a > .hdr/.img > > pair, just use the .img file. > > > > On 9/16/15 10:51 AM, A-reum Min wrote: > > hello, experts > > I have some question. > > > > I want to use analyze format instead of > DICOM file. > > > > So, i type this sentence > > > > recon-all -i > > > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > > -i > > > /usr/local/freesurfer/subjects/test_han/I0071579.img > > -all -s han001 > > > > > > and then error occured.... > > > > ERROR: cannot determine file type for > > > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > > Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 > GNU/Linux > > > > recon-all -s han001 exited with ERRORS at > Wed Sep 16 > > 06:35:02 PDT 2015 > > > > For more details, see the log file > > > /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > How can i to do using analyze format? > > > > > > 2015-08-27 23:55 GMT+09:00 Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>: > > Specify something for --seg. It just > needs to > > be a surface > > overlay of > > the same size as the input. > > > > On 08/27/2015 01:49 AM, A-reum Min > wrote: > > > Hello doug > > > > > > i enter the ' mri_segstats --i y.mgh > --vox > > 33 0 0 --avgwf > > out.dat' > > > then, error occured --> ERROR: must > specify > > a segmentation > > volume > > > > > > > > > 2015-08-27 12:50 GMT+09:00 Douglas > Greve > > <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > > > > > don't use "vertexno", just put > the > > vertex number, eg, > > --vox 33 0 0 > > > > > > > > > On 8/26/15 9:22 PM, A-reum Min > wrote: > > >> Hello developer, > > >> > > >> I have some question to you. > > >> > > >> How can i get the significant > vertices > > value using Qdec > > result? > > >> > > >> When i enter the 'mri_segstats > --i > > y.mgh --vox vertexno > > 33 0 0 > > >> --avgwf out.dat', then error > ouccured > > --> ERROR : > > Option out.dat > > >> unknown. > > >> > > >> So, i enter the 'mri_segstats > --i y.mgh > > --vox vertexno > > 33 0 0 > > >> --avgwf out.dat', then error > occured > > --> ERROR : Option > > 0 unkown. > > >> > > >> How can i fix it? > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> 2015-08-25 23:41 GMT+09:00 > Douglas > > Greve > > >> <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > >> > > >> > > >> > > >> On 8/25/15 9:35 AM, A-reum > Min > > wrote: > > >>> Hello developers > > >>> > > >>> I have some question to > you. > > >>> > > >>> 1.In fig.png, how many > vertices > > were composed of > > cluster at > > >>> least? > > >> I'm not sure what you mean. > it does > > not look like > > there are > > >> any clusters there > > >>> > > >>> 2. How to change Area > > Threshold(fig.png)? > > >> The area is controlled by > the > > clusterwise threshold > > (--cwp) > > >> to mri_glmfit-sim > > >>> > > >>> 3. How to change CSD > > thresh(fig.png)? > > >> That is controlled by the > threshold > > when specifying > > "--cache > > >> threshold sign" to > mri_glmfit-sim > > >>> > > >>> 4. What is the difference > between > > two words(Area > > Threshold, > > >>> CSD thresh)? > > >> One is the cluster-pvalue > and the > > other is the > > >> cluster-forming thershold > > >>> > > >>> 5. What is the exactly > mean two > > words(Area > > Threshold, CSD > > >>> thresh)? > > >> See above > > >> > > >>> > > >>> Thank you > > >>> > > >>> 2015-08-12 23:23 GMT+09:00 > Douglas > > N Greve > > >>> <greve(a)nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > >>> > > >>> > > >>> > > >>> On 08/10/2015 10:06 > PM, A-reum > > Min wrote: > > >>> > HI expert ! > > >>> > > > >>> > My name is Areum. I > have > > some question to > > you. > > >>> > > > >>> > 1. Does FreeSurfer > offer a > > effect size? if > > that offer, > > >>> how can i use > > >>> > effect size? > > >>> > > > >>> If you're doing a > group > > analysis, you can > > compute > > >>> fscalc > > glmdir/contrast/gamma.mgh div > > glmdir/rstd.mgh -o > > >>> glmdir/contrast/effectsize.mgh > > >>> > > > >>> > 2. I was wondering > about the > > stats.dat file > > in > > >>> stats_table (in Qdec > > >>> > folder). > > >>> > > > >>> > Stats.dat file’s > value mean > > that each area’s > > average > > >>> (include whole > > >>> > vertex) or each > > >>> > > > >>> > area’s average (only > > significant vertex)? > > >>> > > > >>> what stats.dat? if > > subject/stats/lh.aparc.stats, then > > >>> the area is the > > >>> total area for the ROI > > >>> > > > >>> > 3. Can I get whole > vertex > > value or > > significant vertex > > >>> value? Because, > > >>> > I want to > > >>> > > > >>> > compare two groups > > correlation using SPSS. In > > >>> addition, I want to > compare > > >>> > > > >>> > thickness, volume > and > > surface area > > correlation within > > >>> the one group > > >>> > using SPSS. > > >>> > > > >>> You can extract a > given vertex > > with > > >>> mri_segstats --i y.mgh --crs > > vertexno 0 0 > > --avgwf > > >>> vertexno.dat > > >>> vertexno.dat will be a text > > file with number of > > rows > > >>> equalt to thge > > >>> number of subjects > where the > > value is the data > > from the > > >>> given (0-based) > > >>> vertex no. y.mgh is > the input > > to mri_glmfit > > >>> > > > >>> > 4. I currently use > the > > default cluster > > >>> size(significant area > > threshold > > >>> > is 0mm^2). So, I > > >>> > > > >>> > want to control > cluster size > > larger than > > default > > >>> cluster size. How can > > >>> > I control the > > >>> > > > >>> > cluster size? > > >>> > > > >>> I don't know what you > mean. > > >>> > > > >>> > 5. In FreeSurfer > manual, GLM > > and Qdec have a > > same > > >>> results. But when I > > >>> > use the > > >>> > > > >>> > both(GLM, Qdec) > group > > analysis program > > results are not > > >>> same. What is > > >>> > differences > > >>> > > > >>> > between two analysis > > program? How can I get > > same > > >>> result while GLM and > > >>> > Qdec? > > >>> > > > >>> No way to know unless > you tell > > us the specifics > > of what > > >>> you did > > >>> > > > >>> > 6. How can I get > surface > > area and volume > > using > > >>> GLM(group analysis > > >>> > program)? > > >>> > > > >>> surface area and > volume are > > outputs of > > recon-all, not glm > > >>> > > > >>> > > > >>> > plz reply to me > > >>> > > > >>> > > > >>> > 2015-08-10 21:35 > GMT+09:00 > > A-reum Min > > >>> <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com>> > > >>> > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>: > > >>> > > > >>> > Hello developer~ > > >>> > > > >>> > I have some questions > to you. > > >>> > > > >>> > 1. Does FreeSurfer > offer a > > effect size? if that > > >>> offer, how can i > > >>> > use effect size? > > >>> > > > >>> > 2. I was wondering > about the > > stats.dat file in > > >>> stats_table (in > > >>> > Qdec folder). > > >>> > > > >>> > Stats.dat file’s value > mean > > that each area’s > > >>> average (include > > >>> > whole vertex) or each > > >>> > > > >>> > area’s average (only > > significant vertex)? > > >>> > > > >>> > 3. Can I get whole > vertex > > value or significant > > >>> vertex value? > > >>> > Because, I want to > > >>> > > > >>> > compare two groups > correlation > > using SPSS. In > > >>> addition, I want to > > >>> > compare > > >>> > > > >>> > thickness, volume and > surface > > area correlation > > >>> within the one > > >>> > group using SPSS. > > >>> > > > >>> > 4. I currently use the > default > > cluster > > >>> size(significant area > > >>> > threshold is 0mm^2). So, > I > > >>> > > > >>> > want to control > cluster size > > larger than > > default > > >>> cluster size. How > > >>> > can I control the > > >>> > > > >>> > cluster size? > > >>> > > > >>> > 5. In FreeSurfer > manual, GLM > > and Qdec have a > > same > > >>> results. But > > >>> > when I use the > > >>> > > > >>> > both(GLM, Qdec) group > analysis > > program results > > are > > >>> not same. What > > >>> > is differences > > >>> > > > >>> > between two analysis > program? > > How can I get > > same > > >>> result while GLM > > >>> > and Qdec? > > >>> > > > >>> > 6. How can I get > surface area > > and volume using > > >>> GLM(group analysis > > >>> > program)? > > >>> > > > >>> > > > >>> > thanks for your help > > >>> > > > >>> > > > >>> > 2015-07-27 14:28 > GMT+09:00 > > A-reum Min > > >>> <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com>> > > >>> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>: > > >>> > > > >>> > Hello bruce > > >>> > > > >>> > I solve this > > problem(12.png) > > >>> > > > >>> > Thank you > > >>> > > > >>> > 2015-07-27 13:03 > GMT+09:00 > > dgw > > >>> <dgwakeman(a)gmail.com > > <mailto:dgwakeman@gmail.com> > > <mailto:dgwakeman@gmail.com > > <mailto:dgwakeman@gmail.com>> > > >>> > > > <mailto:dgwakeman@gmail.com > > <mailto:dgwakeman@gmail.com> > > >>> <mailto:dgwakeman@gmail.com > > <mailto:dgwakeman@gmail.com>>>>: > > >>> > > > >>> > Hi A-reum, > > >>> > > > >>> > I think you may be > > able to get a faster > > >>> response if you > > >>> > include some > > >>> > details about your > > setup: I would start > > >>> with the following: > > >>> > > > >>> > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >>> > and run bugr. > > >>> > > > >>> > hth > > >>> > D > > >>> > > > >>> > On 7/26/15 5:17 PM, > > A-reum Min wrote: > > >>> > > Hi, Bruce > > >>> > > > > >>> > > When i use a Qdec, > > this > > message(12.png) > > >>> show up.. > > >>> > > How can i solve this > > problem? > > >>> > > > > >>> > > 2015-07-23 22:57 > > GMT+09:00 Bruce > > Fischl > > >>> > > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>>>>: > > >>> > > > > >>> > > 1. No, each > > subject has a > > different > > >>> #. You can map > > >>> > to fsaverage > > >>> > > (this is what > > -qcache does if you > > >>> specify it for > > >>> > recon-all), then > > >>> > > they will have > > the same #. > > >>> > > > > >>> > > 2. What result > > data do you mean? > > >>> > > > > >>> > > 3. Yes, although > > I'll leave the > > >>> details to Doug > > >>> > (since I don't > > >>> > > remember how his > > cluster code > > works). > > >>> > > > > >>> > > 4. The > > significance doesn't > > depend > > >>> on the cluster > > >>> > size unless you do > > >>> > > multiple comparison > > corrections (and > > >>> even then only > > >>> > if you do them a > > >>> > > certain way) > > >>> > > > > >>> > > cheers > > >>> > > Bruce > > >>> > > > > >>> > > > > >>> > > On Thu, 23 Jul > > 2015, A-reum Min > > wrote: > > >>> > > > > >>> > > HELLO developer > > >>> > > I have some > > question to you.. > > >>> > > > > >>> > > 1. Every > > patient is given to the > > >>> same number > > >>> > of vertex? > > >>> > > > > >>> > > 2. When i use a > > Qdec, How can I > > get the > > >>> > subject result data? > > >>> > > > > >>> > > 3. Could i get > > the significant > > vertex’s > > >>> > number, extent of the > > >>> > > significant area > > and gray matter > > volume? > > >>> > > > > >>> > > 4. Is it > > significant blue color > > >>> which how > > >>> > many connected > > >>> > > vertex? > > >>> > > > > >>> > > > > >>> > > 2015-05-29 2:03 > > GMT+09:00 A-reum Min > > >>> > <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>> > > >>> > > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > >>> > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>>: > > >>> > > hello developer~ > > >>> > > reconstruction is > > well done, so i'm > > >>> doing on > > >>> > 'qdec' step.. > > >>> > > Actually, i don't > > know how to treat > > the > > >>> Design > > >>> > menu exactly.. > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > Discrete(fixed > > factors) : diagnosis > > >>> > > continuous > > (covariate) : age , > > >>> > Left-Lateral-Ventricle > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > which one click > > before analyze? > > >>> > > > > >>> > > age range is > > 12years~24years/ > > >>> > > all subjects > > are adolescent. > > >>> > > and no > > outlier in age range.. > > >>> so.. age > > >>> > (continuous factor) > > does not > > >>> > > nasessart? > > >>> > > > > >>> > > > > >>> > > 2015-05-29 1:19 > > GMT+09:00 A-reum Min > > >>> > <naniyaah(a)gmail.com > > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>> > > >>> > > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > >>> <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>> > > >>> > > > <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com > > <mailto:naniyaah@gmail.com>>>>>: > > >>> > > hello developer~ > > >>> > > reconstruction is > > well done, so i'm > > >>> doing on > > >>> > 'qdec' step.. > > >>> > > Actually, i don't > > know how to treat > > the > > >>> Design > > >>> > menu exactly.. > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > Discrete(fixed > > factors) : diagnosis > > >>> > > continuous > > (covariate) : age , > > >>> > Left-Lateral-Ventricle > > >>> > > > > >>> > > > >>> > > > -------------------------------------------------------------------------- > > - > > >>> > > which one click > > before analyze? > > >>> > > > > >>> > > > > >>> > > > > >>> > > 2015-04-05 21:41 > > GMT+09:00 Bruce > > Fischl > > >>> > > > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>>>>: > > >>> > > I'm glad it worked > > out > > >>> > > Bruce > > >>> > > On Sun, 5 Apr > > 2015, A-reum Min > > wrote: > > >>> > > > > >>> > > Hello Bruce~ > > >>> > > You're > > right.. my PISA dicom > > file > > >>> > header > > >>> > > is too short > > >>> > > so, > > freesurfer didn't read > > it. > > >>> > > > > >>> > > Therefore I > > use another > > subjects > > >>> dicom > > >>> > > file and > > then freesurfer read > > it! > > >>> > > > > >>> > > thank you > > for u r adavice to > > me. > > >>> > > > > >>> > > I really > > appreciate u > > >>> > > > > >>> > > 2015-04-05 > > 7:08 GMT+09:00 > > Bruce > > >>> Fischl > > >>> > > > > <fischl(a)nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>> > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu> > > >>> > <mailto:fischl@nmr.mgh.harvard.edu > > <mailto:fischl@nmr.mgh.harvard.edu>> > > > > > > _______________________________________________ > > 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. > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

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Re: [Freesurfer] Sulcal depth units (Simon Vandekar)
by Simon Vandekar 22 Jan '16

22 Jan '16

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still unclear on what the units are. They are too small to be millimeters. Given other published measurements of sulcal depth I think they might be in centimeters, but can you confirm? Thanks again, Simon >Hi Simon > >I just took a look at the code and I believe that we make it 0 median >(not mean) and unit standard deviation. The curvatures can get quite large >in regions where the vertex spacing is small and the median is robust to >this. > >cheers >Bruce > > >On Sat, 24 Oct 2015, Simon Vandekar wrote: > >> Hi Bruce, >> >> I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. >> >> Thanks again, >> Simon >> >> >>> H I Simon >>> Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it >>> Bruce >>> >>>> On Oct 22, 2015, at 3:23 PM, Simon Vandekar <simonv(a)mail.med.upenn.edu> wrote: >>>> >>>> Hi Bruce, >>>> >>>> I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? >>>> >>>> >>>> sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) >>>>> mean(sulc$sulc) >>>> [1] -1.236923e-08 >>>> >>>>> var(sulc$sulc) >>>> [1] 0.3276958 >>>> >>>>> quantile(sulc$sulc) >>>> 0% 25% 50% 75% 100% >>>> -1.72503 -0.42128 -0.03963 0.40072 1.80980 >>>> >>>> >>>> Thanks again, >>>> Simon >>>> >>>> >>>> >>>> >>>> >>>> Hi Simon >>>> >>>> they are originally mm, but I believe we z-score normalize them so that >>>> the sulc file is 0 mean and unit variance. >>>> >>>> cheers >>>> Bruce >>>> On Wed, 21 Oct 2015, Simon >>>> Vandekar wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> >>>>> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. >>>>> Are the units for sulcal depth in mm or are they in arbitrary units? >>>>> >>>>> Thanks in advance, >>>>> Simon

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some questions about optseq
by charujing123 15 Jan '16

15 Jan '16

Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123

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Use of PVC PET images (V6) : between versions compatibility and intensity normalisation
by Matthieu Vanhoutte 15 Jan '16

15 Jan '16

Dear FS experts, 1) First Is it possible to use the partial volume correction provided in the v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ? 2) Does this method supply an intensity normalisation for PET images ? Best regards, Matthieu

3 19

Trac-all -path Segmentation error
by Katherine Damme 13 Jan '16

13 Jan '16

Hello Everyone! It looks as though my prep and bedp stages completed properly, but the prep stage ends in a segmentation errror. See attached and let me know your thoughts. I would prefer not to have to redo all steps if possible! Thank you!

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Freesurfer December 2015