Freesurfer

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30058 discussions

White matter hypointensities
by Maksimovskiy, Arkadiy 03 Feb '18

03 Feb '18

Dear Experts, I was wondering if anyone might know why the WM hypointensities total number in aseg does not match the sum of left and right white matter hypointensities. Thanks, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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talaraich transformation error
by Dijkshoorn, A.B.C. (Aicha) 03 Feb '18

03 Feb '18

Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my subjects I get the following error when I run the auto-recon1 command: \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun 4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64 recon-all -s N192_con_recon exited with ERRORS at Fri Feb 2 12:32:02 CET 2018 Is there any way I can work around this error? Kind regards, Aicha Dijkshoorn

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Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)
by Dorit Kliemann 02 Feb '18

02 Feb '18

ops. I guess that should have been obvious to me! Thanks! Dorit

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segmentHA_T2.sh
by Eva Hilland 02 Feb '18

02 Feb '18

Dear freesurfer experts, I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973… I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below Is this a matlab runtime problem? Many thanks in advance Eva -------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: Invalid MEX-file '/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.11) Expected in: /usr/lib/libstdc++.6.dylib in /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135) MATLAB:invalidMEXFile Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018

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Control Points Not Working
by Arsenije Subotic 02 Feb '18

02 Feb '18

Dear experts, I’m currently performing quality control for my data, and most of my issues so far have been that in many cases adding control points has not been able to extend the white surface. I’ve also noticed that most of the regions where I have needed to add CPs are in the parietal regions of the brain. Does anyone know how many control points are usually recommended to be added? I have so far had cases where I have had to add hundreds of CPs and I have still had mixed success. Thank you, Arsenije

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segmentHA_T2.sh
by Eva Hilland 02 Feb '18

02 Feb '18

Dear FS experts, I am now trying the dev version for centos6 to run the segmentHA_T2.sh script. I get the following error: /bin/.: Permission denied. I have tried to change persmissions in freesurfer/bin and still get the same error. Does anyone have experience with this? Best regards, Eva

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options for a poor T1
by Jason Tourville 01 Feb '18

01 Feb '18

We have a few scans from kids that look like the image shown in the attached pic. We see a falloff in signal intensity in the gray matter that results in lots of cortex being excluded from the pial surface (e.g., along the dorsal surface and lateral temporal areas in the image). Typically, we would toss out this data and try to require from the subject or drop the subject from our analyses. But because of the age and clinical diagnosis of this subject we'd like to try to salvage this scan. Can you offer any suggestions for how to improve the reconstruction? Is there a parameter that we can change that will allow the pial surface to fall farther from the white matter surface in terms of voxel intensity and distance? We would trade the need for more manual edits to get greater inclusion of cortex within the pial surface. Do you have any tools or suggestions for a better intensity normalization of the original T1? Thanks for any help that you can provide. Best, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Resolution difference in longitudinal analysis
by Zeynep Basgoze 01 Feb '18

01 Feb '18

Hi dear freesurfer gurus, I'm trying to do a longitudinal analysis, and whenever I run recon-all -base I face this error: "WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s." I have checked the archive before writing to you. I am using freesurfer 5.3.0, and apparently this version is a little sensitive towards this issue; however even if I tried to add ' --notallow-geo ' to the code as suggested, I keep getting this warning: "Volumes differ in resolution v1res 1.000025 1.000000 1.000000 v2res 1.000099 1.000000 1.000000 diff -0.000074 0.000000 0.000000" The sequence was identical across time points, both volume & surface based outputs from recon-all look fine. I am just worried that having these resolution differences would cause us to interpret the longitudinal analysis results incorrectly. Therefore I'd like to know how seriously this much of a resolution difference would affect our results. Thank you very much in advance. Best regards, Zeynep P.S. I also attach the whole log just in case (the error I mentioned is highlighted).

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Fwd: Differences between version 5.2.0 and 6.0.0
by Patrik Krumpolec 01 Feb '18

01 Feb '18

Hello! Thank You for the answer. So, If I understand this in good way - version 6.0 works with original data voxel size and the data are not conformed to voxel size 1x1x1 mm. Can I ask if also version 5.3 conform data that have different voxel size from 1x1x1 mm. Thank You very much! patrik krumpolec 2018-02-01 16:13 GMT+01:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Patrik > > we report both the number of voxels and the volume of each structure in > the stats files. Even for 1mm data we use partial volume estimation in the > newer versions so that these numbers will not be the same. In general we > find that the partial volume estimation helps accuracy, and that 6.0 is > usually more accurate than 5.2 > > cheers > Bruce > > > On Thu, 1 Feb 2018, Patrik Krumpolec wrote: > > > I want to ask about differences in brain segmentation with freesurfer > version 5.2.0 and 6.0.0.My > > dicom data have original size 0.375x0.375x0.75 mm and 600, 640, 224 > voxels. If I process the data > > vith the version 5.2.0, freesurfer conformed the data to 1 mm size and > 256 voxels for all > > directions. In the result brain structures has volume eguals to number > of voxels. > > But if i use version 6.0.0, there are data not conformed and in the > results the volume of structure > > is different form number of voxels. > > > > So, now I don't know what results is correct: from the version 5.2.0 or > 6.0.0 > > > > At first I think that version 6.0.0 is not good because my collegues > from another institution have > > results with the volume eguals to number of voxels (version 5.3) but > they have data with voxel size > > 1x1x1 mm. So, I think that it is natural that volume is eguals to number > of voxels. But my data have > > not 1x1x1 mm voxel size. > > > > Please, Could You help me! Thank You very much! > > > > patrik krumpolec > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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Re: [Freesurfer] Combining scans with different protocols
by Gudbrandsen, Maria 01 Feb '18

01 Feb '18

Dear FreeSurfer Team, Unsure whether this is the correct email for queries, apologies it not. I am wondering if it is possible to combine data set from two different protocols with different slice numbers. For example, (see attached screenshots): 1st - SAG ADNI GO ACC SPGR – 196 slices, 1.2 slice thickness, 1.2 slice gap and FoV: 270, Matrix: 256x256 2nd – ADNI MPRAGE – 166 slices - 1.2 slice thickness, 1.2 slice gap and FoV: 260, Matrix: 256x256 Many thanks, Maria

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