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mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch and Segmentation fault)
by Maria Kalemanov 30 Jul '19

30 Jul '19

Hello FreeSurfer developers, I have three issues with mris_curvature_stats: 1. I attempted to compute curvature on a *noisy sphere* surface (attached) using different -a parameter values, integers from 0 to 10, like this: mris_curvature_stats -a 5 -f surface -m -o noisy_sphere_r10_a5.stats -G --signedPrincipals --writeCurvatureFiles noisy_sphere noisy_sphere_r10 However, there is no slight difference between the curvatures in the output files. Also the runtimes do not vary. Am I calling the function wrong? Attached is also the ".stats" output in case it's of any use. 2. When running the same command as in 1. (without -a parameter) on a *noisy cylinder *surface (attached), I got the following standard output with errors: Outputting results using filestem [ noisy_cylinder_r10_h25.stats ] Toggling save flag on curvature files [ ok ] Toggling 'signedPrincipals' flag ON [ ok ] Toggling save flag on curvature files [ ok ] Setting surface [ noisy_cylinder/noisy_cylinder_r10_h25.surface ] Reading surface... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [#FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 94, faces = 4, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 106, faces = 4, packed = 2 No such file or directory ##################FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1344, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1346, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1347, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1348, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1350, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1351, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1352, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1354, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1356, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1389, faces = 4, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1393, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1394, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1395, faces = 4, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1398, faces = 3, packed = 2 No such file or directory #] [ ok ] FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1399, faces = 3, packed = 2 Determining KH curvatures... [FACES_Hcurvature_determineSign: During call 2, the passed faces do not share an edge 3. When running the same command as in 1. (without -a parameter) on a *smooth cylinder* surface (attached), I got the following standard output with an error: Saving surf/smooth_cylinder_r10_h25.surface as a surface Outputting results using filestem [ smooth_cylinder_r10_h25.stats ] Toggling save flag on curvature files [ ok ] Toggling 'signedPrincipals' flag ON [ ok ] Toggling save flag on curvature files [ ok ] Setting surface [ smooth_cylinder/smooth_cylinder_r10_h25.surface ] Reading surface... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [run_freesurfer_curvature.sh: line 10: 24318 Segmentation fault (core dumped) mris_curvature_stats -f surface -m -o ${BASE}.stats -G --signedPrincipals --writeCurvatureFiles $SUBJECT $BASE I've searched the list and no similar errors have been reported. Does anyone know why the errors happen? Can it be because the cylinder surfaces are open and have edges? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: SUSE Linux Enterprise Server 12 SLES 12 SP 1 3) uname -a: Linux hpcl5004 3.12.74-60.64.40-default #1 SMP Wed May 10 05:07:16 UTC 2017 (4eb35ec) x86_64 x86_64 x86_64 GNU/Linux Thanks and best regards Maria External Email - Use Caution

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segmentHA_T2.sh longitudinal version?
by Daniel Callow 30 Jul '19

30 Jul '19

External Email - Use Caution Hello, I have recently used segmentHA_T1_long.sh and was pleased with the segmentation results. However, I now have a longitudinal data set that has additional T2 high-resolution scans of the hippocampus as well as T1's. I know there is a segmentHA_T2.sh script to incorporate these types of scans. However, there doesn't seem to be a longitudinal version for this. Is this something that is being worked on? Or is there another reason that T2 should not be used with longitudinal analysis? Thank you for any advice you can provide, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 30 Jul '19

30 Jul '19

External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels: mri_aparc2aseg --s subject name --annot annotation name --o output name and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not?? Any help would be appreciated. Regards, Mahshid

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MNI target to surface
by Lauri Tuominen 30 Jul '19

30 Jul '19

External Email - Use Caution Dear Freesurfers, I am targeting the MNI152 coordinate -38,44,26 with TMS. I would like to use this target as an ROI/seed in surface based analyses. How would I: 1. Transfer the coordinate onto fsaverage surface? 2. Expand the coordinate into a 5mm radius sphere. Thank you so much! Lauri Tuominen

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FreeSurfer version
by FAST Study 29 Jul '19

29 Jul '19

External Email - Use Caution Hi! I am re-running all recon-all using version 6.0. I was running a full list of subjects when our server crashed - and I would like to begin where it stopped. How do I check which subjects have been run on the latest version (v. 6)? Thanks so!

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TRACULA for kids/children
by Daniel Callow 29 Jul '19

29 Jul '19

External Email - Use Caution Hello, Is it possible to run TRACULA on baby/children brain scans? If so how would one go about doing this? Could I just change set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz to a different baby/child atlas? If not how would I go about this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Multiple Comparison Correction, Paired T-Test
by FAST Study 29 Jul '19

29 Jul '19

External Email - Use Caution Dear Dr. Greve: Thank you for your help. I see the attached outputs from the paired t-test - please see attached image. I hope to correct for multiple comparisons, e.g., mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwp .05 --3spaces What is the --glmdir - or input? - in the command? Thanks!

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Recon-all files not saved
by Pratik Kashyap 29 Jul '19

29 Jul '19

External Email - Use Caution Hello experts, I'm running recon-all by wrapping it in a Nipype workflow. (cmdline: recon-all -all -i {data/T1_files(iterfield)} -openmp 64 -sd . -s seg ) The workflow(p1.py) executes smoothly without errors. But it doesn't save the final output files. There is no 'fsaverage' directory created either. 'Runtime_info.txt' shows no errors either, it shows that the files are being created successfully too. I decided to then run a pipeline(p2.py) with recon-all node as an input to the bbregister node. Looks like it fails after the recon-all node. I've attached the recon-all.log file as well, it exits the command after the mri_nu_correct step without further information. Please help, as all my future work is contingent on recon-all running smoothly. Thank, Pratik Kashyap Research Support Assistant @Nathan Kline Institute Graduate Teaching Assistant ECE @Purdue Purdue Neurotrauma Group Chief of Staff @Purdue Graduate Student Govt. ECE Senator @ECEGSA

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Error in Analyze: Couldn't open ... fwhm10.fsaverage.mgz
by Renew Andrade 29 Jul '19

29 Jul '19

External Email - Use Caution Dear FreeSurfer experts: I am processing in qdec 3 subjects with the GUI and I have this terminal output. Error in Analyze: Couldn't open /Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file. lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? Nuisance factors: Right-Hippocampus 1.000 0.000 0.000; I have executed recon-all -s IXI_20_Guys_T1 -s IXI_22_Guys_T1 -s IXI_25_Guys_T1 -qcache -target avgsubj20_22_25 -no-isrunning without any errors. Also make_average_subject make_average_subject --out avgsubj20_22_25 --subjects IXI_20_Guys_T1 IXI_22_Guys_T1 IXI_25_Guys_T1 without any errors. The problem is that I only have files like “...fwhm10.fsaverage.mgz" in one subject in this case IXI_25_Guys_T1 not in IXI_22_Guys_T1 or IXI_20_Guys_T1. I do not know if that is a mistake of processing or myself it seems by the output in qdec that I need files like “...fwhm10.fsaverage.mgz” in every subject subdirectory “surf”. Thanks for your help in advance!

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Cluster sizes discrepancy for mri_surfcluster vs mri_segstats
by Mark Wagshul 29 Jul '19

29 Jul '19

External Email - Use Caution Hi. I have a question about cluster size determination within Freesurfer. We are running linear mixed model on our Freesurfer generated volume data over the left and right cortex parcellations, and would like to look at cluster size at the p < 0.01 cluster-forming threshold level. 1) After running the models, we have created a .mgh image of the F-stats results, separately for the negative and positive results, saving them with fs_write_Y. 2) We then run these data through mri_surfcluster, which reports the maximum cluster size of 216 voxels. This was run with the command: a. mri_surfcluster --hemi lh --in F_lhstats.mgh --o F_lhstats _negCluster.mgh --subject fsaverage --thmin 6.8 --sign pos b. The "sign" is set to positive because this is running on F-numbers. 3) Next, we run mri_segstats on the output of the last command to get the location and sizes of the individual clusters, as follows: a. mri_segstats --seg F_lhstats _negCluster.mgh --annot lh.aparc.annot lh parc --slabel fsaverage lh --seg --sum F_lhstats_negCluster.txt The problem is that this is the output of that file (F_lhstats_negCluster.txt): # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg F_lhstats_negCluster.mgh --annot lh.aparc.annot lh parc --slabel fsaverage lh --seg --sum F_lhstats_negCluster.txt # sysname Linux # hostname loginnode2 # machine x86_64 # user mwagshul # anatomy_type volume # # SUBJECTS_DIR /home/mrrc-all/MRE_LAB/Holtzer/QdecAnalysis # subjectname fsaverage # SegVolFile F_lhstats_negCluster.mgh # SegVolFileTimeStamp 2019/07/18 11:21:52 # Annot fsaverage lh parc # Label fsaverage lh --seg # ExcludeSegId # Only reporting non-empty segmentations # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # NRows 8 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 0 161454 161454.0 Seg0000 2 6 524 524.0 Seg0006 3 7 897 897.0 Seg0007 4 8 413 413.0 Seg0008 5 9 311 311.0 Seg0009 6 10 165 165.0 Seg0010 7 11 61 61.0 Seg0011 8 12 17 17.0 Seg0012 This clearly is reporting clusters larger than the 216 voxels reported by mri_surfcluster. Hope someone can help us figure out the discrepancy here, thanks! (As an aside, what are we doing wrong with the mri_segstats command which is not printing out the actual anatomical locations for each cluster?). Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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