Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Over estimation of pial surface
by Charles Malpas 25 Mar '13

25 Mar '13

Dear Freesurfer experts, I am having a strange problem with a single brain. Freesurfer is over estimating the pial surface by a great deal. Two things are weird: (a) it occurs to the same brain scanned 6 months apart, and (b) it doesn't occur is 5.1 (I am using 5.2 now). I have attached some screen shots. Any help would be greatly appreciated! Kind regards, - Charles -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas(a)student.unimelb.edu.au Skype: charles.malpas

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R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 24 Mar '13

24 Mar '13

Hi Zeke, process finished without error in 2h. Thanks, 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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Re: [Freesurfer] Brodmann area thickness, surface area and volume
by _andreia_＠sapo.pt 24 Mar '13

24 Mar '13

Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: > Sounds like centos4 is probably the safest bet for you, although you > should ask the list this question. > > Sorry, I don't know what values you want to get in a table. > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: > >> Ah ok! Anyway, I'm thinking of working with 5.2, should I download >> the version for centOS 4 then? >> >> After running the new BAxxx.thresh.label files how can I get the >> values in a table? >> >> >> >> >> Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >> >>> It doesn't matter. You just need to use those .label files from >>> the fsaverage directory in the 5.2 distritbution. You don't need >>> to run any of the executables from the 5.2 distribution. >>> >>> On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>> >>>> I'm using Centos5, which file should I download? The one for >>>> CentOS 6 or > 4? >>>> > > Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>> > > You'll need to go to the section of recon-all.log under the >>>> heading "BA > > labels". You'll need to rerun the commands in >>>> that section, but instead > > of using the BAxxx.label files, us >>>> the BAxxx.thresh.label files, which > > you'll find in the >>>> fsaverage subject dir in the 5.2 distribution. >>>> > > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>>> > > > > Hello Anastasia, >>>> > > > How should I proceed to get the different BAs measures >>>> output with > > > > FS > 5.0? >>>> > > > Thank you very much! >>>> > > > Andreia >>>> > > > > Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>> > > > > The thresholded labels are in the 5.2 version of >>>> fsaverage > > > > > under: >>>> > > > $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label >>>> > > > > > On Sat, 23 Mar 2013, Bruce Fischl wrote: >>>> > > > > > > Anastasia? >>>> > > > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>>> > > > > > > Ok, that was my guess... I am running against a >>>> deadline, > > > > > > > any > > > > > news on >>>> > > > > > automatically computing the correct threshold script? >>>> Will I > > > > > > be > > > > able to >>>> > > > > > use it in 5.0? >>>> > > > > > > > Thanks you! >>>> > > > > > > > Andreia >>>> > > > > > > > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> > > > > > > > > yes. Surface area will be the affected much >>>> more than > > > > > > > > > > > > > > > > thickness (and > > >>>> > > volume of > > > > > > > > > course scales with area) >>>> > > > > > > > On Fri, 22 Mar 2013, _andreia_(a)sapo.pt wrote: >>>> > > > > > > > > Hi Bruce, >>>> > > > > > > > > > Thank you for the quick response! >>>> > > > > > > > > > In the meanwhile, does that also apply to >>>> cortical > > > > > > > > > > > > > > > > > > thickness > > >>>> > > > > and > > > > > > > > > > > > volume? >>>> > > > > > > > > > Thank you! >>>> > > > > > > > > > Andreia >>>> > > > > > > > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> > > > > > > > > > > Hi Andreia >>>> > > > > > > > > > > > the issue is that the BA labels contain >>>> every > > > > > > > > > > > > point > > > > > > > > > > >>>> that > > > > > > > > > > > > > > > > > > > > has any > > > >>>> non-zero >>>> > > > > > > > > probability (no matter how small!) of being >>>> in that > > > > > > > > > label. > > > > > > > So > > > > >>>> > the > > > > > > > > > > > > total >>>> > > > > > > > > label area is almost certainly always bigger >>>> than the > > > > > > > > > > > > > > > > actual > > > > > >>>> BA. > > > > > > > > > > > > Anastasia >>>> > > > > > > > > has some scripts for automatically computing >>>> the > > > > > > > > > correct > > > > > > > > > > > > >>>> threshold, > > > > > > > > > > > > and I >>>> > > > > > > > > believe she and Nick integrated them into 5.2 >>>> so that > > > > > > > > > the > > > > > > > stats > > > > >>>> > are >>>> > > > > > > > > computed both thresholded and unthresholded, >>>> > > > > > > > > > hopefully > > > > > > > they can > > > > >>>> > > > > > > > > > > > > > comment. >>>> > > > > > > > > Bruce >>>> > > > > > > > > > > > > > > > > > On Fri, 22 Mar 2013, > > > >>>> > > > > > > > > > > > > > > > _andreia_(a)sapo.pt >>>> > > > > > > > > wrote: >>>> > > > > > > > > > > > > Hi all, >>>> > > > > > > > > > > > > > I'm using FS 5.0 and some time ago >>>> I was > > > > > > > > > > > > > > told by > > > > > > > > > > >>>> > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> Bruce that I had > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > > > to >>>> > > > > > > > > > threshold the BA in order to have an >>>> approximate > > > > > > > > > > area > > > > > > > > when >>>> > > > > > > > > > > > > > > > > > > > > overlaying >>>> > > > > > > > > > in the inflated surface. To get surface >>>> area values > > > > > > > > > > I > > > > > > > > also > > >>>> > > > > need to > > > > > > > > > > > > > > use >>>> > > > > > > > > > the label_area and put a threshold >>>> > > > > > > > > > having the possibility to choose the >>>> surface that I > > > > > > > > > > > > > > > > > > want, > >>>> > > > > > either > > > > > > > > > > > > > > white >>>> > > > > > > > > > or pial. >>>> > > > > > > > > > > > > > But I can also get the BA stats in >>>> a table > > > > > > > > > > > > > > for > > > > > > > > > > > >>>> > all > > > > > > > > > > > > > > > > > > > > > > > > >>>> subjects and > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > areas >>>> > > > > > > > > > using either mris_anatomical_stats (on each >>>> label) > > > > > > > > > > or > > > > > > > > usinga > > > >>>> > > > > > > > > > > > > > > > > > script by >>>> > > > > > > > > > Jamaan to get the table (since I already >>>> have the > > > > > > > > > > > > > > > > > > ?.BA.stats > >>>> > > > > > > > > > > > > > > > > > > > files), >>>> > > > > > > > > > right? >>>> > > > > > > > > > > > > > My question is, which is the >>>> better/correct > > > > > > > > > > > > > > way > > > > > > > >>>> > > > > > to > > > > > > > > > > > > > > > > > > > > > > > >>>> > get the > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > thickness >>>> > > > > > > > > > and surface area values of the BA to export >>>> for > > > > > > > > > > > > > > > > > > statistical > > > >>>> > > > > > > > > > > > > > > > > > analysis >>>> > > > > > > > > > since there are the thresolds issue. >>>> > > > > > > > > > > > > > I want to study mainly cortical >>>> thickness > > > > > > > > > > > > > > and > > > > > > > > > > >>>> > > surface > > > > > > > > > > > > > > > > > > > > > > > >>>> > area but > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > also >>>> > > > > > > > > > look also at the volume (which is >>>> surface-based, > > > > > > > > > > thus >>>> > > > > > > > > > thickness*surface are will not be = volume >>>> since > > > > > > > > > > they > > > > > > > > are an > > >>>> > > > > > > > > > > > > > > > > > > average >>>> > > > > > > > > > from each label, right?). >>>> > > > > > > > > > > > > > I' not sure of which approach to >>>> follow > > > > > > > > > > > > > > now... > > > > > > > > > > >>>> > > Does > > > > > > > > > > > > > > > > > > > > > > > > >>>> it depend on > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > the >>>> > > > > > > > > > measure I'll be using? >>>> > > > > > > > > > > > > > Thank you! >>>> > > > > > > > > > > > > > Andreia >>>> > > > > > > > > > > > > > > > > > >>>> _______________________________________________ >>>> > > > > > > > > > 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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How to transform a ROI volume to dwi space?
by Ran Xu 24 Mar '13

24 Mar '13

Dear Freesurfer experts, I got the individual ROI volumes (not the surface) from aparc+aseg.nii.gz file, now I wanna use them as the seed regions in dwi space. I noticed that these ROIs are in the same space with "T1_brain", but this "T1_brain" is not the native T1. So could I register this T1_brain with the original T1, then applying transformation to these ROIs? Then, do registration between original T1 and dwi? All of registrations are linear or nonlinear? Thanks. Ran

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Merging PArcellation labels
by Anupa AV 24 Mar '13

24 Mar '13

Dear All, Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus.

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How to get an individual gray matter volume?
by Ran Xu 23 Mar '13

23 Mar '13

Dear Freesurfer experts, I used the Index from aseg.txt to get the left thalamus (Index 10), but the real volume I got is different from the size in aseg.txt. Its volume is 5007 in aseg.txt and I programmed a matlab code to find all values equaling to 10 in aparc+aseg.nii. However, the volume I got is 5237 from matlab code. Could you tell me how to extract the real ROI? I mean its volume number should be the same with the one in aseg.txt? Thanks.

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R: Re: hippo subfield
by stdp82＠virgilio.it 23 Mar '13

23 Mar '13

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-subfieldsSubject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfer-rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.logDarwin 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 \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff01side: leftinputDirectory: /Applications/freesurfer/subjects/subject_provaoutputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/leftcp -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 -3.1939dyld: 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 -3.1939failed 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 -3.1939Darwin 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.logTo 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.

2 1

Brodmann area thickness, surface area and volume
by _andreia_＠sapo.pt 23 Mar '13

23 Mar '13

Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial. But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right? My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue. I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?). I' not sure of which approach to follow now... Does it depend on the measure I'll be using? Thank you! Andreia

2 4

cortical recontruction error
by Claudia Dacquino 23 Mar '13

23 Mar '13

Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc <http://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc> -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia

2 1

Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology
by Bruce Fischl 23 Mar '13

23 Mar '13

p.s. I don't know why that option doesn't work - I didn't even realize it existed On Sat, 23 Mar 2013, falk.luese(a)gmx.net wrote: > Hi Bruce, > > well, there is an option called -correct_defect within > mris_fix_topology, which is meant to correct just one defect at a time. > However, after the defect is corrected one is getting a message like: > > ?TERMINATING AFTER CORRECTED DEFECT > > no such file or directory? > > I haven?t been able to figure out how to save this or if this is even > possible. Maybe I am missing the correct flag to do so. May it otherwise be > possible to remove certain defects from ?h.defect_labels or something > similar? > > The errors of the filled.mgz result in a faulty surface > reconstruction of ?h.orig.nofix and every following surface like ?h.white > and ?.pial in that area. Therefore I wanted to remove these in before and, > if possible, automatically. > > Best, > Falk > > Von: Bruce Fischl > Gesendet: ?22?. ?März? ?2013 ?19?:?14 > An: ""Falk Lüsebrink"" <falk.luese(a)gmx.net> > Cc: FreeSurfer > Betreff: Re: [Freesurfer] Two questions regarding mri_fill and > mris_fix_topology > > Hi Falk > > I don't think it's possible to fix just one defect, unless Florent > included some option that I am not aware of. > > I also wouldn't worry too much about the filled.mgz. Make sure that the > aseg.mgz and the ?h.white and ?h.pial are accurate > cheers > Bruce > On Fri, 22 Mar 2013, > "Falk Lüsebrink" wrote: > > > Dear FreeSurfers, > > > > I am processing some T1-weighted images of the human brain with an > isotropic resolution of .5 mm using version 5.1. > > > > After mri_fill my hemispheres are separated nicely and the cerebellum is > completely removed. However, looking at the filled.mgz, posterior and > > superior of the corpus callosum some residual of white matter can be found > in the longitudinal fissure. It does not remain if I look at the > > conformed data, altough these leftovers are found in the wm.mgz of both > datasets. As this does not happen using conformed data I assume that the > > cutting plane is not "broad" enough in case of higher resolution data or > something related. Is there some way to tweak this? > > > > Secondly, I currently skip the -fix stage of recon-all completely while > processing this data, but I would like to correct at least some of its > > defects. I already I have seen in the help of mris_fix_topology that it is > possible to fix just one defect and I extracted the defects and their > > number of vertices using the defect-seg script. Is it possible to save the > resulting surface, so I am able to correct the defects I want > > to consecutively? > > > > Best, > > Falk > > > > > >

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Freesurfer March 2013