Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

PVC to calculate myelin maps
by Marina Fernández 31 May '21

31 May '21

External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*. Can I use the PVC functions of PetSurfer for this purpose? And in case I can: Should I apply PVC only on T1? Or also in T2? Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)? Any other advice for calculating myelin maps would be welcome. Thank you in advance, Marina *Link: https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsO…

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Choosing projfrac/projdist and checking mri_vol2surf output
by M Pope 31 May '21

31 May '21

External Email - Use Caution Hi all, I have a question regarding checking the output of mri_vol2surf. I am converting a manually segmented volume ROI into a surface label in order to gain information such as cortical thickness. What is the best practice for quality control and checking the surface rendering of the ROI? Are there any protocols or suggestions? As slight changes in projfrac change the output by a large degree, it's difficult to assess what is the closest to the original volume ROI. The suggestions also vary (others say projfrac 0.5, others to use projfrac-max or projdist). The main output statistic I'm interested in cortical thickness of the region (if this influences the options). How do you choose and establish what is the best option? Thanks Marianna

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tkregister2 problem on its GUI
by 张威 31 May '21

31 May '21

External Email - Use Caution Hello Freesurfer developers, I am attempting to manually register a cerebral blood flow images to a T1 weighted images via the command tkregister2; I have successfully done the recon-all and bbregister followed the guide and got the report that "recon-all finished without error". I also got no problem to run the tkregister2 and the GUI display. In terse words, the problem is that GUI is clickable on several bottons but cannot make any changes within the bar of GUI. These are details: I cannot make any changes (coronal, sagittal, horizontal, brain slice, and translate brain) through the bar of the GUI, while I can click the botton (target, moveable, and COMPARE). I can try to close the GUI; a new window comes up and asks me if I want to save the changes, but all the botton (save, don't save, close and cancel) do not clickable. This new window can be closed but tkregister2 is still now working. I have done the similar work on Mac last year and I did not meet such a problem. I have searched the list and no similar errors have been reported. Does anyone have any thoughts on how to make it work? Also, I have attached the recon-all.log and register_perfusion.log (bbregister) in case it's of any use. 1) Freesurfer version: freesurfer-Linux-Centos6-x86-64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 18.04.5 LTS Thank you for your kind help, I hope you have a great day! Best, Wei

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Re: [Freesurfer] Questions about geting a license file
by fsbuild 31 May '21

31 May '21

External Email - Use Caution Hello Nana, Your browser should display a “CAPTCHA” box at the bottom of the freesurfer license page just above the button where you click “I AGREE”. If you do not see the CAPTCHA box in your browser then it is probably blocking some javascript that would allow it to be displayed.  Make sure you have javascript enabled in your browser.  You could try a different browser that does not block javascript (or cookies). You should check the “I’m not a robot” box and pick out the images it asks you for.  Then it should display a green checkmark.  Then click on the “I AGREE” button below. - R.On May 31, 2021, at 10:19, fengnana <fengnana_y(a)163.com> wrote:<微信图片_20210531221632.png>

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Re: [Freesurfer] about the root password of virtual box ubuntu 710 clone
by fsbuild 31 May '21

31 May '21

External Email - Use Caution Hello Wu, Sending the info to your posted email. - R.. On May 31, 2021, at 03:49, HuiNing Wu <huining.wu.psy(a)gmail.com> wrote:        External Email - Use Caution        Dear all,I'm using freesurfer virtual box ubuntu 710 clone.However, I didn't find the root password to enter sudo mode...Would you please let me know what it is or where it is?With best regards,Wu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Questions about geting a license file
by fengnana 31 May '21

31 May '21

External Email - Use Caution Dear Sir: I met registration error when I provided all the personal information to register the copy of FreeSurfer and obtain the license.txt key file, is there any way for me to get the license file? The error figure is attached and thank you for your kindness! Yours sincerely Nana Feng

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myelin maps
by Marina Fernández 31 May '21

31 May '21

External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I would like to perform a correction of partial volume effects to create the maps (Shafee, Buckner & Fischl, 2015)*, instead of creating the maps using HCP Pipelines. Can I use the PVC functions of PetSurfer for this purpose? And in case I can: Should I apply PVC only on T1? Or also in T2? Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)? Thank you in advance, Marina * Link: https://secure-web.cisco.com/1uklY3paR4n5Apdl5Hfz0cV9XIEUybKcHiz2RGaJAVrIhn…

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about the root password of virtual box ubuntu 710 clone
by HuiNing Wu 31 May '21

31 May '21

External Email - Use Caution Dear all, I'm using freesurfer virtual box ubuntu 710 clone. However, I didn't find the root password to enter sudo mode... Would you please let me know what it is or where it is? With best regards, Wu

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Group comparison with MD
by Antti Cajanus 29 May '21

29 May '21

External Email - Use Caution Dear Freesurfer experts, I’m trying to do a group comparison of cortical mean diffusivity. The study subjects form 2 groups (demented vs. non-demented). I’ve run recon-all and dt_recon on all of my study subjects. My goal is to create a surface, that has the mean diffusivity values sampled from the midpoint of the cortical thickness (50% the distance between WM and pia). I’m puzzled about three things; 1) Can I use the adc.nii created by dt_recon to represent the mean diffusivity or should I use something else? 2) Can I obtain the MD values from the midpoint of cortical thickness using mri_vol2surf command, using the optional ”–projfrac 0.5” flag? i.e. mri_vol2surf –src adc.nii.gz --out adc-to-midthick.mgz --hemi lh --projfrac 0.5 --srcreg register.dat 3) I want to smooth the the data with FWHM 15mm. Should I apply the smoothing in the mri_vol2surf (as registering the adc.nii to cortical ribbon) or in the mri_surf2surf phase (as registering the adc-to-midthick.mgz to fsaverage)? Thank you already in advance! Best, Antti Cajanus

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Hippocampal Subfield error
by Daniel Davidson Callow 28 May '21

28 May '21

External Email - Use Caution Hello, I am running into errors when running segmentHA_T2.sh ${subj} /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1 Approximately 10% of my subjects are being processed but for some reason, the majority fail to execute. Here is an output from the error log. ------------------------------ USER dcallow HOST compute-4-32.bswift.umd.edu <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV…> PROCESSID 4033 PROCESSOR x86_64 OS Linux Linux compute-4-32.bswift.umd.edu <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV…> 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT 2021 ------------------------------------------ Setting up environment variables --- INFO: error loading libraries in default configuration, trying with MCR libraries only LD_LIBRARY_PATH is .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering norm.mgz to additional volume makeIsotropic WARNING: not different enough, won't reslice! No more processes. ERROR: could not open /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh for reading ERROR: loading /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh as MGH Warning: File '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh' not found. [^H> In myMRIread at 64 In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H Attempt to reference field of non-structure array. Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211) MATLAB:nonStrucReference @#@FSTIME 2021:05:27:21:39:51 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61 P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 31.22 29.74 28.95 Linux compute-4-32.bswift.umd.edu <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV…> 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021 I am also getting a matlab_crash_dump file ------------------------------------------------------------------------ Segmentation violation detected at Thu May 27 21:51:52 2021 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : None Default Encoding : US-ASCII GNU C Library : 2.12 stable MATLAB Architecture: glnxa64 MATLAB Root : /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64 Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : No active display Fault Count: 1 Abnormal termination: Segmentation violation Stack Trace (from fault): [ 0] 0x00007f2b30f06213 /lib64/libpthread.so.0+00033299 pthread_join+00000035 [ 1] 0x00007f2a9f4d847d /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 2] 0x00007f2a9f4d8cac /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 3] 0x00007f2a9f5cae63 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 4] 0x00007f2a9f5af896 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 5] 0x00007f2a9f5a6b8d /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 6] 0x00007f2a9f5a6fd0 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 7] 0x00007f2a9f5aad00 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 8] 0x00007f2a9f5a5c3c /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 9] 0x00007f2a9f44fb03 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 10] 0x00007f2a9f42b9cc /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 11] 0x00007f2a9f42b132 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 12] 0x00007f2b21dcfc0a /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538 mexRunMexFile+00000090 [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644 [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308 [ 15] 0x00007f2b232ff329 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 16] 0x00007f2b2260fb70 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 18] 0x00007f2b225c2022 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 20] 0x00007f2b225c36ff /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 21] 0x00007f2b225c4334 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 22] 0x00007f2b2263952e /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 23] 0x00007f2b232ff329 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 24] 0x00007f2b2260fb70 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 26] 0x00007f2b225c2022 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 28] 0x00007f2b225c36ff /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 29] 0x00007f2b225c4334 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 30] 0x00007f2b2263952e /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 31] 0x00007f2b232ff329 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 32] 0x00007f2b225ecbf0 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 33] 0x00007f2b225ec449 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… inCallFcnWithTrap+00000086 [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… This error was detected while a MEX-file was running. If the MEX-file is not an official MathWorks function, please examine its source code for errors. Please consult the External Interfaces Guide for information on debugging MEX-files. If this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1B8en4WQVOmBM-TonUpSzamw674QdqjI_ltVT2KdTcbPbuP… A technical support engineer might contact you with further information. Any insight or help you can provide is greatly appreciated. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

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Freesurfer May 2021