Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

(no subject)
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/1lsmxJ1l6wT0WmnW3q7zuS6JngCO6upWHYdXR6E3TNhC0oD… 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

1 0

mri_hippocampal-subfields error: MATLAB exited for no reason
by 林鈺庭 28 May '21

28 May '21

External Email - Use Caution Dear FreeSurfer Developers: We apply the hippocampal module with MATLAB R21014b runtime and FreeSurfer7.1.1, but it came up with the error: *MATLAB is exiting because of fatal error/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 10056 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML S029 /Applications/freesurfer/7.1.1/subjects 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0Darwin brain116deiMac.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64* We are not sure about why this happened, could you help us with this? The log file was attached for more information here. We really are grateful for your help! Best regards, Josephine 附件區域回覆轉寄 <https://secure-web.cisco.com/11rTrqymMYMcH_eeEPP7ge_uzRzUBowJD6taZTwGWfL6TP…> <https://secure-web.cisco.com/1bbb-usARQx9jFtVINlRA40dlq1rtBNU9ktSSnatA0Wxho…>

1 0

preproc-sess fmri image to self surface
by Mingyang Xia 27 May '21

27 May '21

External Email - Use Caution Dear freesurfer expert: My name is Mingyang. I want to preprocess fmri image and map the timepoints to its corresponding T1 surface. However, when I use preproc-sess command, it seems that the output image has the wrong dimensions. Could you give me some advice? Thank you Mingyang

2 2

Registration from FreeSurfer to HCP842 Space
by Milena Radoman 27 May '21

27 May '21

External Email - Use Caution Dear FreeSurfer Team, Hope you are doing well! I've run into an issue I hope you can help me with. After running recon-all on my subjects, I proceeded with the thalamic segmentation step. I'm specifically interested in extracting the mediodorsal (MD) thalamus for a subject (by first individually extracting mediodorsal lateral and mediodorsal medial nuclei and combining them using fslmaths). Before doing so, I've first converted my data from freesurfer to native space. Once I've obtained my nucleus of interest I then loaded it into DSI Studio, which I'm using to extract my tract of interest. Given the data in the DSI studio was in the native space, the MD nucleus aligned perfectly. The problem is that DSI studio tracking takes forever when I do the registration to the native space, so instead I've decided to run a registration of my DTI data to the HCP842 template (in order to make my results comparable to some of my colleagues and to help the tracking run faster). The problem is that now when I load my dorsomedial nucleus, it doesn't appear where it should and I would need to do a different registration (my understanding is freesurfer to ICBM152 since apparently that's what HCP842 template is related to). I've been able to use the script below, but the nucleus doesn't show up quite where it should (it's showing up more anterior to the thalamus). mri_label2vol --reg $FRESURFER_HOME/average/mni152.register.dat --seg ThalamicNuclei.v12.T1.FSvoxelSpace.mgz --temp icbm_avg_152_t1_tal_lin.nii --o ThalamicNuclei.v12.T1-anat.mgz Any advice? Thank you in advance for your help!! -- *Milena Radoman* PhD Candidate | PECTS Fellow Graduate Program in Neuroscience The University of Illinois at Chicago *DISCLAIMER: The information transmitted by this email is intended only for the person or entity to which it is addressed. This email may contain proprietary, business-confidential and/or privileged material. If you are not the intended recipient of this message, be aware that any use, review, retransmission, distribution, reproduction or any action taken in reliance upon this message is strictly prohibited. If you received this in error, please contact the sender and delete the material from all computers.* ᐧ

2 1

More lgi questions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 27 May '21

27 May '21

Hi all, I am trying to extract LGI measures as prescribed in https://secure-web.cisco.com/17RNO0jXsWejJpXwwC1TbKXfwLIWB9IY53g1Ab5f3XjIUV… So I follow this: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats but receive this error (I have also tried in root): 7.1.0 cwd cmdline mri_segstats --annot 10100_S2654UFQ/ lh aparc --i /mnt/V/Datasets/BSNIP2/Processing/temp/10100_S2654UFQ/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats sysname Linux hostname Alpha machine x86_64 user victor whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /mnt/V/Datasets/BSNIP2/Processing/temp/10100_S2654UFQ//label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 error: No such file or directory error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.10100_S2654UFQ/.lh.176.ctab): could not open for writing error: No such file or directory error: CTABreadASCII(/tmp/mri_segstats.tmp.10100_S2654UFQ/.lh.176.ctab): could not open file ERROR: reading /tmp/mri_segstats.tmp.10100_S2654UFQ/.lh.176.ctab Is this something that I can fix? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

CSF file
by Camargo, Aldo 27 May '21

27 May '21

External Email - Use Caution Hi Freesurfer experts: I used recon-all all to in my MPRAGE image and I would like to know which file is the corresponding to the CSF (cerebral spinal fluid). Also, which is the correct file to choose for the brain extracted image, because I see 2 files that can be: T1.mgz, brain.mgz , which one is the correct ? Also for GM the file is aparc+aseg.mgz the correct file ? Thanks a lot and have a nice day, Aldo

2 1

How to extract the GM and WM
by Camargo, Aldo 27 May '21

27 May '21

External Email - Use Caution Hi Freesurfer experts: I want to extract the White Matter and the Gray Matter from a T1 image. I have extracted the brain by using the command: recon-all with the option -autorecon1 Thanks a lot and have a nic day, Aldo

3 4

Problem with talairach check in Freesurfer 7
by Gabor Perlaki 27 May '21

27 May '21

External Email - Use Caution Dear all, I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected. the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm" gives the following message in the terminal: "Not reading in xfm fileinfo". Both T1 and brainmask is loaded, but the transformation seems to be not applied. the command "tkregisterfv --s bert --fstal --surf orig" works only without the flag --surf. the command "tkregister2 --s bert --fstal" gives the following messages: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" The green border is not shown, only the target and movable images are visible. Any idea how to fix this? Best, Gabor

2 3

mris_anatomical_stats() for ODI maps inflated to surface
by Jensen, Alexandria 27 May '21

27 May '21

External Email - Use Caution Hello fellow Freesurfer users, I am attempting to reproduce the analysis conducted by Parker et al. in their 2018 paper, “Cortical microstructure in young onset Alzheimer's disease using neurite orientation dispersion and density imaging” (https://secure-web.cisco.com/1UgnQVFBMbbUsDXUzai5AvAOzqeQ34tRV2D60a4CwFPoV9…) Cortical reconstruction of the T1 structural image was done in Freesurfer and NODDI processing using the NODDI toolbox in Matlab. The final steps I am attempting to complete include (1) projecting the ODI/NDI maps to an inflated surface to create surface maps (2. Materials and Methods, 2.5 Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values across both hemispheres for a selected number of ROIs from the Desikan parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. paper has provided the Freesurfer functions used in each of these final steps, but I am getting stuck on step (2) and am now worried that I have made an error in step (1). Below is the code I have written so far to project an ODI map onto an inflated surface: bbregister \ --s freesurfer \ --mov odi.nii \ --init-fsl \ --reg register.dat \ --dti tkregister2 \ --s freesurfer \ --mov odi.nii \ --reg register.dat \ --surf mri_vol2surf \ --src odi.nii \ --out odi_in_cortex.nativespace.mgh \ --srcreg register.dat \ --hemi lh \ --projfrac 0.5 When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. The issue I have is when I try to use mris_anatomical_stats(). I have tried different combinations of label and annotation files but am either getting errors or no errors but also no output. Any guidance would be much appreciated! I am new to Freesurfer and have been learning it as part of my graduate research assistantship. I am using Freesurfer version 7.1.1 on a macOS Catalina, version 10.15.7 operating system for reference. Cheers, Alexandria Jensen

3 9

mri_glm fit: gd2mtx method dods--C unrecoginzied
by Francisca Ferreira 27 May '21

27 May '21

External Email - Use Caution Dear Experts, I am new to FS. I'm trying to run mri_glm fit I've created FSGD with 2 classes -responders vs non-responders to a given intervention- and 3 variables to be regressed out-according age, gender, laterality. I've made my FSGD file is made in accordance with documented FS directions. I've created the contrast vector in accordance to Nregressors and it works out to be 1 -1 0 0 0 0 0 0 I add I'm using DODS to do this task. the constructed command I used is this mri_glmfit \--y lh_test.smoothed10FWHM.mgh \--fsgd newCH.fsgd dods\--C groupdiff.mtx \--surf fsaverage lh\--cortex \--glmdir lh.test.glmdir 1) The first problem encountered is INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done I have tried to demean my data adding the flag --demean, which I found in more than one forum, but i think this is an incorrect flag as it didnt work anyway. 2) I have constructed my contrast vector also in accordance with FS directions, in a text editor adding the extension .mtx I'm getting this error ERROR: gd2mtx method dods--C unrecoginzied. Legal values are dods, doss, and none. Help would be much appreciated. KR F. Ferreira

2 1

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