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Re: [Freesurfer] recon-all bad talairach
by Douglas N Greve 26 Mar '13

26 Mar '13

Hi Jon, it is not supposed to be horizontal. The anatomy in the target is just supposed to match that in the moveable. doug ps. please respond to the list. thanks! On 03/26/2013 02:35 PM, Jon Wieser wrote: > HI doug, > i viewed it with tkregister2. the transform looks poor, the ac-pc line is not horizontal. > i have attached a pic > Jon > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, March 26, 2013 11:28:01 AM > Subject: Re: [Freesurfer] recon-all bad talairach > > Hi Jon, the data are not reoriented or resliced into talairach space. It > is just the transform that is computed. To inspect whether this was done > right, use > > tkregister2 --s subject --fstal > > doug > > > On 03/26/2013 12:20 PM, Jon Wieser wrote: >> Hello >> I ran recon-all auto_recon1. and the resulting brainmask file, has a poor talairazation. the ac-pc line is not horizontal, it's tilted, and the interhemisphere fissure is tilted too. how do I fix this? >> I have attached a picture of the brain >> >> >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Xhemi stat questions
by Gabriel Gonzalez Escamilla 26 Mar '13

26 Mar '13

2 1

Admin please unsubscribe this email!
by Dalwani, Manish 26 Mar '13

26 Mar '13

Admin please unsubscribe this email address Thanks, Manish Dalwani

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qdec matrix error
by stdp82＠virgilio.it 26 Mar '13

26 Mar '13

Hi list, I'm performing qdec. This my file.dat 1 diagnosis discrete 2 1 Pathology 2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203 Number of subjects: 31Number of factors: 4 (1 discrete, 3 continuous)Number of classes: 2Number of regressors: 8 NPStest is scored from 0 to 8. Qdec produces this error: Creating output directory /Applications/freesurfer/subjects/subject_prova/qdec/UntitledLoading y from /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mghINFO: gd2mtx_method is dodsSaving design matrix to /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/Xg.datNormalized matrix condition is 1e+08Design matrix ------------------ 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.712 0.000; 1.000 0.000 0.000 0.000 2.671 0.000; 1.000 0.000 0.000 0.000 2.728 0.000; 1.000 0.000 0.000 0.000 2.646 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.750 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.784 0.000; 1.000 0.000 0.000 0.000 2.586 0.000; 1.000 0.000 0.000 0.000 2.641 0.000; 1.000 0.000 0.000 0.000 2.561 0.000; 1.000 0.000 0.000 0.000 2.545 0.000; 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.769 0.000; 1.000 0.000 0.000 0.000 2.740 0.000; 0.000 1.000 0.000 2.000 0.000 2.526; 0.000 1.000 0.000 2.000 0.000 2.761; 0.000 1.000 0.000 2.000 0.000 2.521; 0.000 1.000 0.000 0.000 0.000 2.592; 0.000 1.000 0.000 2.000 0.000 2.555; 0.000 1.000 0.000 2.000 0.000 2.671; 0.000 1.000 0.000 3.000 0.000 2.559; 0.000 1.000 0.000 3.000 0.000 2.469; 0.000 1.000 0.000 4.000 0.000 2.691; 0.000 1.000 0.000 2.000 0.000 2.522; 0.000 1.000 0.000 0.000 0.000 2.553; 0.000 1.000 0.000 2.000 0.000 2.702; 0.000 1.000 0.000 0.000 0.000 2.738; 0.000 1.000 0.000 0.000 0.000 2.789; 0.000 1.000 0.000 0.000 0.000 2.651;--------------------------------ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08--------------------------------Possible problem with experimental design:Check for duplicate entries and/or lack of range ofcontinuous variables within a class.If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat 2. The FSGD file (if using one) 3. And the design matrix aboveError in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat I don't understand what's happen? Thanks, Stefano

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R: Re: R: Re: R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 26 Mar '13

26 Mar '13

Thank you very much Eugenio, you are very kind! Stefano ----Messaggio originale---- Da: iglesias(a)nmr.mgh.harvard.edu Data: 26-mar-2013 17.00 A: <stdp82(a)virgilio.it> Cc: <zkaufman(a)nmr.mgh.harvard.edu>, "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: hippo subfield I would say intracranial volume from the aseg.stat table Cheers, /Eugenio On Tue, 2013-03-26 at 16:49 +0100, stdp82(a)virgilio.it wrote: > Thank you very much Eugenio. > > > I have a last question: Who is the best way to normalize > the HippocampalSubfieldSegmentation volume results? > > > Stefano > > ----Messaggio originale---- > Da: iglesias(a)nmr.mgh.harvard.edu > Data: 26-mar-2013 14.37 > A: <stdp82(a)virgilio.it> > Cc: <zkaufman(a)nmr.mgh.harvard.edu>, > "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield > > Ciao, Stefano > > to compute subfield volumes, you need to use the script > kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are > here: > > http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation > > In the wiki page you'll also find instructions to visualize the > output. > > Cheers, > > /Eugenio > > > On Tue, March 26, 2013 4:40 am, stdp82(a)virgilio.it wrote: > > Hi Zeke and other users, > > I have finished the Hippocampal Subfields parcellation. New > files .mgz are > > located in $SUBJECTS_DIR/mri. > > Now, I do not understand as I can calculate for each region the > thickness > > and volume. > > Can you help me, please? > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > Da: zkaufman(a)nmr.mgh.harvard.edu > > Data: 23-mar-2013 20.13 > > A: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: hippo subfield > > > > It's not enough to simply put the zip file in the > > /Applications/freesurfer/bin directory,,, you must extract its > contents to > > that directory. > > > > Just extract the zip file (anywhere on your machine will do). Then > copy > > and paste the extracted files to /Application/freesurfer/bin > > > > -Zeke > > > > On Mar 22, 2013, at 7:00 PM, <stdp82(a)virgilio.it> wrote: > > > >> Hi Zeke, > >> > >> as you explain I have download the kvl.zip and put it in > >> /Application/freesurfer/bin. > >> > >> After rerunning I have: > >> > >> [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% > recon-all > >> -s Diff01 -hippo-subfields > >> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > >> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > >> INFO: SUBJECTS_DIR > is /Applications/freesurfer/subjects/subject_prova > >> Actual FREESURFER_HOME /Applications/freesurfer > >> -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 > >> /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > >> Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: > Sun > >> Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 > x86_64 > >> #-------------------------------------------- > >> #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 > >> \n mkdir -p > >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > >> \n kvlSegmentHippocampalSubfields.sh Diff01 left > >> /Applications/freesurfer/subjects/subject_prova > >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > >> \n > >> Doing left side > >> meshFileName: > >> /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > >> compressionLookupTableFileName: > >> /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > >> > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > >> subjectName: Diff01 > >> side: left > >> inputDirectory: /Applications/freesurfer/subjects/subject_prova > >> outputDirectory: > >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > >> directory > >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 > >> already exists > >> directory > >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left > >> already exists > >> cd > >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left > >> cp > -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz > >> . > >> cp -f > >> /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . > >> cp -f > >> /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm > >> . > >> cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > >> kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 > -0.0330 > >> 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > >> dyld: Library not loaded: libITKCommon.3.16.dylib > >> Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > >> Reason: image not found > >> /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: > line 18: > >> 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz > -0.9991 > >> -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > >> 0.9996 -3.1939 > >> failed to do kvlApplyTransform imageDump.mgz > >> -0.9991 -0.0328 0.0258 144.0010 > >> -0.0330 0.9994 -0.0086 2.6560 > >> 0.0255 0.0094 0.9996 -3.1939 > >> Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: > Sun > >> Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 > x86_64 > >> > >> recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET > 2013 > >> > >> For more details, see the log file > >> /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > >> To report a problem, see > >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> > >> ----Messaggio originale---- > >> Da: zkaufman(a)nmr.mgh.harvard.edu > >> Data: 22-mar-2013 20.53 > >> A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> > >> Ogg: Re: [Freesurfer] hippo subfield > >> > >> Stefano, > >> > >> In order to fix this issue please follow these instruction exactly: > >> > >> 1) Download the file "kvl.zip" from this link: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ > >> > >> 2) Overwrite the existing kvl files in /Application/freesurfer/bin > with > >> the files in kvl.zip > >> > >> I was able to replicate your issue and solve it using the steps > above. > >> If these steps do not solve the issue for you, please respond with > a the > >> exact error you receive. > >> > >> Hope this helps. > >> > >> -Zeke > >> > >> > >> > >> > >> > >> On 03/22/2013 12:00 PM, stdp82(a)virgilio.it wrote: > >> > I'm running: > >> > > >> > recon-all -s Diff02 -hippo-subfields > >> > > >> > with the following error. > >> > > >> > Thanks. > >> > > >> > > >> > Stefano > >> > > >> > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > >> > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > >> > INFO: SUBJECTS_DIR is > >> /Applications/freesurfer/subjects/subject_prova/Diff02 > >> > Actual FREESURFER_HOME /Applications/freesurfer > >> > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > >> > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: > Sun > >> > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 > x86_64 > >> > #-------------------------------------------- > >> > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 > >> > \n mkdir -p > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > >> > \n kvlSegmentHippocampalSubfields.sh Diff02 left > >> > /Applications/freesurfer/subjects/subject_prova/Diff02 > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > >> > \n > >> > Doing left side > >> > meshFileName: > >> /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > >> > compressionLookupTableFileName: > >> > > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > >> > > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > >> > subjectName: Diff02 > >> > side: left > >> > > inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 > >> > outputDirectory: > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > >> > directory > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > >> > already exists > >> > directory > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > >> > already exists > >> > cd > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > >> > cp -f > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz > >> . > >> > cp -f > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz > >> . > >> > cp -f > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > >> > . > >> > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > >> > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 > >> -0.0330 > >> > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > >> > dyld: Library not loaded: libITKCommon.3.16.dylib > >> > Referenced > from: /Applications/freesurfer/bin/kvlApplyTransform > >> > Reason: image not found > >> > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: > line > >> 18: > >> > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz > -0.9991 > >> > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 > 0.0094 > >> > 0.9996 -3.1939 > >> > *failed to do kvlApplyTransform imageDump.mgz > >> > -0.9991 -0.0328 0.0258 144.0010 > >> > -0.0330 0.9994 -0.0086 2.6560 > >> > 0.0255 0.0094 0.9996 -3.1939* > >> > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version > 12.3.0: Sun > >> > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 > x86_64* > >> > * > >> > * > >> > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 > CET > >> 2013* > >> > > >> > For more details, see the log file > >> > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > >> > To report a problem, see > >> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > > >> > > >> > _______________________________________________ > >> > 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. > >> > >> > >> > > > > _______________________________________________ > > 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 > > > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > iglesias(a)nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias(a)nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.

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recon-all bad talairach
by Jon Wieser 26 Mar '13

26 Mar '13

Hello I ran recon-all auto_recon1. and the resulting brainmask file, has a poor talairazation. the ac-pc line is not horizontal, it's tilted, and the interhemisphere fissure is tilted too. how do I fix this? I have attached a picture of the brain -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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preproc-sess -surface flag
by Y.V. Jiang 26 Mar '13

26 Mar '13

Hi, I wonder if you could help with a basic question for preproc-sess in Version 5.2.0. The flag "-surface subject hemi": what should be the entry to "subject?" The tutorial says fsaverage, but for first-level analysis, should it match subjectname? Or should it always be fsaverage? If it needs to match subjectname, then this command cannot be run in a batch (because different subjects have different input to that line), is that true? Thank you. -Yuhong

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Cortical thickness in average space
by Rafa X 26 Mar '13

26 Mar '13

Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each subject? We want to avoid to trasform each cluster to every subject. Thank you all in advance, Rafa & Gabi.

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R: Re: R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 26 Mar '13

26 Mar '13

Thank you very much Eugenio. I have a last question: Who is the best way to normalize the HippocampalSubfieldSegmentation volume results? Stefano ----Messaggio originale---- Da: iglesias(a)nmr.mgh.harvard.edu Data: 26-mar-2013 14.37 A: <stdp82(a)virgilio.it> Cc: <zkaufman(a)nmr.mgh.harvard.edu>, "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield Ciao, Stefano to compute subfield volumes, you need to use the script kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation In the wiki page you'll also find instructions to visualize the output. Cheers, /Eugenio On Tue, March 26, 2013 4:40 am, stdp82(a)virgilio.it wrote: > Hi Zeke and other users, > I have finished the Hippocampal Subfields parcellation. New files .mgz are > located in $SUBJECTS_DIR/mri. > Now, I do not understand as I can calculate for each region the thickness > and volume. > Can you help me, please? > > Stefano > > > > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 23-mar-2013 20.13 > A: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: hippo subfield > > It's not enough to simply put the zip file in the > /Applications/freesurfer/bin directory,,, you must extract its contents to > that directory. > > Just extract the zip file (anywhere on your machine will do). Then copy > and paste the extracted files to /Application/freesurfer/bin > > -Zeke > > On Mar 22, 2013, at 7:00 PM, <stdp82(a)virgilio.it> wrote: > >> Hi Zeke, >> >> as you explain I have download the kvl.zip and put it in >> /Application/freesurfer/bin. >> >> After rerunning I have: >> >> [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all >> -s Diff01 -hippo-subfields >> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 >> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 >> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova >> Actual FREESURFER_HOME /Applications/freesurfer >> -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 >> /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log >> Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun >> Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 >> #-------------------------------------------- >> #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 >> \n mkdir -p >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults >> \n kvlSegmentHippocampalSubfields.sh Diff01 left >> /Applications/freesurfer/subjects/subject_prova >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults >> \n >> Doing left side >> meshFileName: >> /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz >> compressionLookupTableFileName: >> /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt >> boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz >> subjectName: Diff01 >> side: left >> inputDirectory: /Applications/freesurfer/subjects/subject_prova >> outputDirectory: >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults >> directory >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 >> already exists >> directory >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left >> already exists >> cd >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left >> cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz >> . >> cp -f >> /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . >> cp -f >> /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm >> . >> cp /Applications/freesurfer/data/GEMS/imageDump.mgz . >> kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 >> 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 >> dyld: Library not loaded: libITKCommon.3.16.dylib >> Referenced from: /Applications/freesurfer/bin/kvlApplyTransform >> Reason: image not found >> /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: >> 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 >> -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 >> 0.9996 -3.1939 >> failed to do kvlApplyTransform imageDump.mgz >> -0.9991 -0.0328 0.0258 144.0010 >> -0.0330 0.9994 -0.0086 2.6560 >> 0.0255 0.0094 0.9996 -3.1939 >> Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun >> Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 >> >> recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 >> >> For more details, see the log file >> /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >> ----Messaggio originale---- >> Da: zkaufman(a)nmr.mgh.harvard.edu >> Data: 22-mar-2013 20.53 >> A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] hippo subfield >> >> Stefano, >> >> In order to fix this issue please follow these instruction exactly: >> >> 1) Download the file "kvl.zip" from this link: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ >> >> 2) Overwrite the existing kvl files in /Application/freesurfer/bin with >> the files in kvl.zip >> >> I was able to replicate your issue and solve it using the steps above. >> If these steps do not solve the issue for you, please respond with a the >> exact error you receive. >> >> Hope this helps. >> >> -Zeke >> >> >> >> >> >> On 03/22/2013 12:00 PM, stdp82(a)virgilio.it wrote: >> > I'm running: >> > >> > recon-all -s Diff02 -hippo-subfields >> > >> > with the following error. >> > >> > Thanks. >> > >> > >> > Stefano >> > >> > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 >> > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 >> > INFO: SUBJECTS_DIR is >> /Applications/freesurfer/subjects/subject_prova/Diff02 >> > Actual FREESURFER_HOME /Applications/freesurfer >> > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log >> > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun >> > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 >> > #-------------------------------------------- >> > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 >> > \n mkdir -p >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults >> > \n kvlSegmentHippocampalSubfields.sh Diff02 left >> > /Applications/freesurfer/subjects/subject_prova/Diff02 >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults >> > \n >> > Doing left side >> > meshFileName: >> /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz >> > compressionLookupTableFileName: >> > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt >> > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz >> > subjectName: Diff02 >> > side: left >> > inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 >> > outputDirectory: >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults >> > directory >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 >> > already exists >> > directory >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left >> > already exists >> > cd >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left >> > cp -f >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz >> . >> > cp -f >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz >> . >> > cp -f >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm >> > . >> > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . >> > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 >> -0.0330 >> > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 >> > dyld: Library not loaded: libITKCommon.3.16.dylib >> > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform >> > Reason: image not found >> > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line >> 18: >> > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 >> > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 >> > 0.9996 -3.1939 >> > *failed to do kvlApplyTransform imageDump.mgz >> > -0.9991 -0.0328 0.0258 144.0010 >> > -0.0330 0.9994 -0.0086 2.6560 >> > 0.0255 0.0094 0.9996 -3.1939* >> > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun >> > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* >> > * >> > * >> > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET >> 2013* >> > >> > For more details, see the log file >> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log >> > To report a problem, see >> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> > >> > _______________________________________________ >> > 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. >> >> >> > > _______________________________________________ > 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 ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias(a)nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 26 Mar '13

26 Mar '13

Hi Zeke and other users, I have finished the Hippocampal Subfields parcellation. New files .mgz are located in $SUBJECTS_DIR/mri. Now, I do not understand as I can calculate for each region the thickness and volume. Can you help me, please? Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, <stdp82(a)virgilio.it> wrote: > Hi Zeke, > > as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. > > After rerunning I have: > > [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > #-------------------------------------------- > #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 > \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n > Doing left side > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > subjectName: Diff01 > side: left > inputDirectory: /Applications/freesurfer/subjects/subject_prova > outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists > directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists > cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > dyld: Library not loaded: libITKCommon.3.16.dylib > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > Reason: image not found > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 > > For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 22-mar-2013 20.53 > A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] hippo subfield > > Stefano, > > In order to fix this issue please follow these instruction exactly: > > 1) Download the file "kvl.zip" from this link: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ > > 2) Overwrite the existing kvl files in /Application/freesurfer/bin with > the files in kvl.zip > > I was able to replicate your issue and solve it using the steps above. > If these steps do not solve the issue for you, please respond with a the > exact error you receive. > > Hope this helps. > > -Zeke > > > > > > On 03/22/2013 12:00 PM, stdp82(a)virgilio.it wrote: > > I'm running: > > > > recon-all -s Diff02 -hippo-subfields > > > > with the following error. > > > > Thanks. > > > > > > Stefano > > > > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 > > Actual FREESURFER_HOME /Applications/freesurfer > > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > #-------------------------------------------- > > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 > > \n mkdir -p > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > \n kvlSegmentHippocampalSubfields.sh Diff02 left > > /Applications/freesurfer/subjects/subject_prova/Diff02 > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > \n > > Doing left side > > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > > compressionLookupTableFileName: > > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > > subjectName: Diff02 > > side: left > > inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 > > outputDirectory: > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > directory > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > > already exists > > directory > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > already exists > > cd > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz . > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz . > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > > . > > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 > > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > > dyld: Library not loaded: libITKCommon.3.16.dylib > > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > > Reason: image not found > > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: > > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 > > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > > 0.9996 -3.1939 > > *failed to do kvlApplyTransform imageDump.mgz > > -0.9991 -0.0328 0.0258 144.0010 > > -0.0330 0.9994 -0.0086 2.6560 > > 0.0255 0.0094 0.9996 -3.1939* > > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* > > * > > * > > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013* > > > > For more details, see the log file > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > _______________________________________________ > > 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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