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Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
by Aarthi Padmanabhan 08 Oct '15

08 Oct '15

Hi Eugenio the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/ Should I reinstall freesurfer? thanks! ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.iglesias(a)bcbl.eu> Sent: Tuesday, September 29, 2015 10:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation This is really weird. Can you please confirm that the file /Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib exists? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- Sent: Tuesday, September 29, 2015 11:39:00 AM Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation Hi Eugenio, Thanks for the response. I just tried that and it still didn't work (same error message). Subject Stamp: freesurfer-Darwin-OSX-dev-20150826 Current Stamp: freesurfer-Darwin-OSX-dev-20150826 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lab wheel 638418 Sep 29 08:37 /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Sep 29 08:39:10 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 90075 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Sep 29 08:39:10 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 90112 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Thanks, Aarthi ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.iglesias(a)bcbl.eu> Sent: Monday, September 21, 2015 1:02 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation Hi Aarthi, first of all, sorry for the late reply; you caught me on vacation. Would you mind trying the following: please unset your DYLD_LIBRARY_PATH environment variable, and the run the hippocampal subfield module. You can do that as follows: In bash: unset DYLD_LIBRARY_PATH In (t)csh: unsetenv DYLD_LIBRARY_PATH Let us know if this helps Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Aarthi Padmanabhan" <aarthi(a)stanford.edu> To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Saturday, September 19, 2015 9:32:55 AM Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation Hi, I had posted this earlier and am still having issues. Thank you, I tried running the Hippocampal Segmentation using the Dev version, I get the following error (running on a mac os x Yosemite): I just downloaded the dev version a couple of days ago. Recon-all -all runs fine, but it's unable to run the hippocampals segmentation component. recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1 Subject Stamp: freesurfer-Darwin-OSX-dev-20150826 Current Stamp: freesurfer-Darwin-OSX-dev-20150826 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lab wheel 605436 Sep 11 11:56 /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Fri Sep 11 11:57:14 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 6182 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Fri Sep 11 11:57:15 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 6219 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #------------------------------------------ Started at Fri Sep 11 11:57:12 PDT 2015 Ended at Fri Sep 11 11:57:15 PDT 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s 15-03-07.1_3T2 finished without error at Fri Sep 11 11:57:15 PDT 2015 done Thank you, Aarthi _______________________________________________ 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?
by Matthieu Vanhoutte 08 Oct '15

08 Oct '15

Hello Martin, Could you please find any time to answer me ? Many thanks ! Best regards, Matthieu Le 30 sept. 2015 13:57, "Matthieu Vanhoutte" <matthieuvanhoutte(a)gmail.com> a écrit : > Hi Martin, > > Thank you for helping ! > > 1) What should I use for the parameter estimation: "mass univariate" or Novel > mass-univariate tools (spatiotemporal models)" ? > > 2) I have one group of subjects with different timepoints (non equally > spaced and different numbers of timepoints), and would like to see the > significant change of FA according to time. Will LME study allow me to get > this change and how to define contrast to assess it ? Are the results of > this longitudinal study directionals, i.e. is it possible to establish an > increase or decrease of FA in significant regions according to time ? > > 3) Should the covariates (age, gender...) be demeaned or centered ? > > 4) Has the accurate time variable to be in years absolutely or could it > be also in days ? > > > Best regards, > > Matthieu > > > 2015-09-29 17:11 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: > >> Hi Matthieu, >> >> use lme_mass_fit_vw and the y is a simple vector. I would mask the image >> before doing this and only pass the brain voxels (to increase speed and >> reduce comparisons). >> >> Best, Martin >> >> >> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote: >> >> Hi Martin, >> >> I understand for the multiple comparisons problem. But if I consider a >> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for >> estimation), how could I consider a correction for multiple comparisons in >> this univariate case ? >> >> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass >> univariate case ? If yes, how do I have to format my 3D FA volume as input >> of the LME toolbox ? >> >> Best regards, >> >> Matthieu >> >> ------------------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> >> 2015-09-29 16:34 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: >> >>> Hi Matthieu, >>> >>> yes, multiple comparisons are a problem for any mass univariate >>> approach. You can use the FDR2 correction (in the lme matlab tools) which >>> is less conservative than standard FDR. You can also work in specific ROI's >>> and average there, to reduce the number of comparisons. >>> >>> Best, Martin >>> >>> >>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote: >>> >>> Hi Martin, >>> >>> Thank you for your answer. >>> >>> However, I would like to consider FA maps as a mass-univariate problem >>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my >>> voxels aren't independant, are they ? So, how to correct for multiple >>> comparisons then ? >>> >>> Best regards, >>> >>> Matthieu >>> >>> 2015-09-29 15:04 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Matthieu, >>>> >>>> if all your images are perfectly registered, you can do LME on a >>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other >>>> ROI measure. >>>> >>>> Best, Martin >>>> >>>> >>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote: >>>> >>>> Dear experts, >>>> >>>> I would like to know if it is possible to make a longitudinal study >>>> with LME toolbox from volume FA maps registered in a common space ? >>>> >>>> I don't have T1 images so the recon-all process couldn't be processed. >>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels >>>> format, could it be in good way for LME ? >>>> >>>> Thanks for helping ! >>>> >>>> Best regards, >>>> >>>> Matthieu >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> -- >>>> Martin Reuter, PhD >>>> Assistant Professor of Radiology, Harvard Medical School >>>> Assistant Professor of Neurology, Harvard Medical School >>>> A.A.Martinos Center for Biomedical Imaging >>>> Massachusetts General Hospital >>>> Research Affiliate, CSAIL, MIT >>>> Phone: +1-617-724-5652 >>>> Web : http://reuter.mit.edu >>>> >>>> >>>> _______________________________________________ >>>> 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> Martin Reuter, PhD >>> Assistant Professor of Radiology, Harvard Medical School >>> Assistant Professor of Neurology, Harvard Medical School >>> A.A.Martinos Center for Biomedical Imaging >>> Massachusetts General Hospital >>> Research Affiliate, CSAIL, MIT >>> Phone: +1-617-724-5652 >>> Web : http://reuter.mit.edu >>> >>> >>> _______________________________________________ >>> 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone: +1-617-724-5652 >> Web : http://reuter.mit.edu >> >> >> _______________________________________________ >> 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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longitudinal stream: adding a time point
by Adam, Ruth 08 Oct '15

08 Oct '15

Dear all, We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points) and instead register the third time point to the pre-existing template. What is the best way to do so? Is there a way to force recon-all to use a specific template? Many thanks! Best, ruthi

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Freesurfer v 6.0???
by Ajay Kurani 08 Oct '15

08 Oct '15

Hello Freesurfer experts, I wanted to see if the nightly dev builds of freesurfer are v6.0 with the new hippocampal subfields or if that download is in another section? If so can you send me the proper download location? Also is CUDA support still at 5.0 with this version or is there any updates to the cuda support? Thanks for your help. Sincerely, Ajay

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create label files
by Lim, Lena 08 Oct '15

08 Oct '15

Dear Experts, How do I extract the cortical thickness of a region of interest (which showed a group difference in the Qdec between-group analysis) for all the subjects so as to correlate with other measures in SPSS? There is no .label file in the Qdec folder; which file shall I use or do I have to draw the ROI manually? Many thanks, Lena

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Coordinate Question
by Ishan Patel 08 Oct '15

08 Oct '15

Hello, When I create a label file, it looks something like this: #!ascii label , from subject ECoG7_Output vox2ras=TkReg coords=white 111 1062 -19.007 -81.861 3.862 0.0000000000 3917 -29.743 -75.417 2.343 0.0000000000 6599 -37.731 -70.574 6.918 0.0000000000 9428 -44.497 -65.013 8.765 0.0000000000 Is there any way I can convert from the above coordinate system to Talariach normalized? Thanks!

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wm.mgz ventricle white matter problem
by Anastasia Klimovich-Smith 08 Oct '15

08 Oct '15

Dear freesurfer experts, I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0). Sometimes the ventricles are not fully filled and the white matter is localized within the remaining gaps. After manually filling the gaps in the wm.mgz (following the wiki - Fixing Common Geometric Inaccuracies in White Matter Surfaces) and rerunning (-autorecon2-wm) I still have the wm surface following the ventricle holes, even though I can see they are filled on wm.mgz. I used freesurfer v.5.1.0 before and didn't have these issues. How would you recommend fixing this? Thanks a lot, Ana

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Cortical Parcellation Atlas Question
by Yun Wang 08 Oct '15

08 Oct '15

Hi All, I am currently doing resting state fMRI functional connectivity across the cortical. Is it appropriate that I use Freesurfer cortical Parcellation altas such as Desikan-Killany Atlas to extract time series? Thanks! Yun

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tilted head
by Thục Trinh 08 Oct '15

08 Oct '15

Hi Freesurfer Experts, We are on the process of troubleshooting on all of our subjects and come across with the problem that we have not faced before. Here it is: We have several subjects that their heads were not in a perfectly straight line captured by using MRI. Does that affect to the segmentation of a recon, and more importantly somehow carry out some statistical values for further analysis (volume, cortical thickness)? As you can see, Axial view shows the head being tilted to the right. Sagital_lh and Sagital_rh images show how the white matter and gray matter segmentation are being bounded on the same slice 130 but in different hemisphere. Do we need to do something about it? If yes, how are we going to fix it? We are greatly appreciated to your patience and hopefully to get your response as soon as possible. Trinh

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VirtualBox Block
by Maya De Belder 08 Oct '15

08 Oct '15

Hi, I’m stuck with the following problem: I can’t start up the VirtualBox for Freesurfer5.3 because of a memory problem. I put 12GB of patient data on the disk en ran two subjects successfully through Freesurfer. However, I closed the VirtualBox and don’t seem to be able to restart it. My question is: - Is there a way to get around this? Is there a possibility to increase de memory size? - How much data is constructed by Freesurferprocesses when you run an MPRAGE through the processes? - Assume I don’t mind re-running those two subjects and will completely re-install the Virtualbox: is there a possibility to increase the disk size? - The data I have for 1 single patient will always be +- 500 MB, my study contains over 100 subjects. Is there a way to run the analysis in Virtualbox that way, or is an alternative suggested? Thanks in advance for the feedback, Maya De Belder PhD Student Ghent University Department of Experimental Psychology Henri Dunantlaan 2 B-9000 Ghent, Belgium +32 9 264 64 03

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