Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 discussions

PETSurfer: Which is the right way to turn off PVC?
by Zhener Zhang 27 Jan '22

27 Jan '22

External Email - Use Caution Hello, I have a question regarding the following PETSurfer command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output I have been trying to run the analysis without applying partial volume correction, but it seems like there are two ways to turn it off: One is to set the point-spread function to 0 by adding “—psf 0”, The other one is to get rid of “—psf” altogether and add “—no-tfe”. We tried both and they produced slightly different results. The second method “—no-tfe” produced lower uptake values for each ROI. Which one would you recommend to properly turn PVC off? Thanks in advance! Best regards, Zhener

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Re: [Freesurfer] Error in mri_glmfit
by Laura Willers de Souza 27 Jan '22

27 Jan '22

External Email - Use Caution Sorry for such a simple mistake and thank you so much for all the help! Best, Laura.

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Uncorrected significance map completely yellow
by Laura Willers de Souza 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I am performing an analysis of the relationship between cortical thickness and cortisol, following exactly what is on the wiki https://secure-web.cisco.com/1VtREEtXgXDhC0vSO4t4FWNu1rcpl4ibhN-xtsPTmXPjIy… However, the uncorrected significance map for the interaction contrast is turning completely yellow (image below). [cid:aa464798-57de-4e8a-8be6-fce6a4cd9c2a] After correcting for multiple comparisons, the result is a whole-brain cluster... I am sending the fsgd file, the matrix files (just for mri_glmfit, because I ended up deleting the analysis with mri_glmfit-sim to redo with some changes and see if it fixed the problem) and the commands. This is what appears on the command screen after running the command for freeview. But the same things appear for images that are loading correctly. libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast libGL error: failed to load driver: swrast ls found reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) What am I doing wrong? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 26 Jan '22

26 Jan '22

External Email - Use Caution Dear Douglas, Once again, thanks so much for the reply! About the mask, I just don't put anything or put "nomask"? With your suggestions, the command looks like this: mri_fdr --fdr .05 --pos --thfile $SUBJECTS_DIR/hipposubfields.lh.T1.v21.CU_CI.glmdir/sig.table.dat --i $SUBJECTS_DIR/hipposubfields.lh.T1.v21.CU_CI.glmdir/group.diff.CU_CI/sig.mgh nomask hipposubfields.lh.T1.v21.CU_CI.mgh --thfile $SUBJECTS_DIR/hipposubfields.rh.T1.v21.CU_CI.glmdir/sig.table.dat --i $SUBJECTS_DIR/hipposubfields.rh.T1.v21.CU_CI.glmdir/group.diff.CU_CI/sig.mgh nomask hipposubfields.rh.T1.v21.CU_CI.mgh Do you think this is correct? As it was before (without the input to --thfile) it was giving the following error: [cid:dc620acd-9f58-4011-af98-9e402ccec268] [cid:c62e8d3e-dc3d-4327-94b1-edd4f34f4150] I believe that with these fixes it should work fine, right? Thank you so much again! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: domingo, 02 de dezembro de 2022 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala Dear Douglas, Thanks so much for your answer. Could you check if the following commands to perform ROI analysis with GLM are correct? *1.* Create the table with the volumes of the hippocampal segmentation (1 command for each hemisphere - only replace lh with rh): asegstats2table --statsfile hipposubfields.lh.T1.v21.stats --fsgd CU_CI.fsgd\ --meas volume \ --all-segs \ --tablefile hipposubfields.lh.T1.v21.CU_CI.dat *2.* GLM Analysis – DODS (1 command for each hemisphere - only replace lh with rh): mri_glmfit \ --table hipposubfields.lh.T1.v21.CU_CI.dat \ --fsgd CU_CI.fsgddods \ --C group.diff.CU_CI.mtx \ --glmdir hipposubfields.lh.T1.v21.CU_CI.glmdir *3.* Correction for multiple comparisons – FDR: mri_fdr --fdr .05 --pos --thfile --i contrast/lh.sig.mgh lh.mask.mghhipposubfields.lh.T1.v21.CU_CI.mgh --no-log10p --i contrast/rh.sig.mgh rh.mask.mghhipposubfields.rh.T1.v21.CU_CI.mgh --no-log10p For this one, you don't need a mask. Also, don't use --no-log10p (the output of mri_glmfit is in log10p). --thfile needs an argument (eg, threshold.dat) Are these commands correct? Another question, in this type of analysis is image smoothing common? Like was done here https://secure-web.cisco.com/1SGYPC_eq9hJS6qUpwzydiUkja0rf_66vRxg4eWTYKPIeQ… <https://secure-web.cisco.com/1we0tWxEcmAWpL06CsQ9vqTCkjuPHErSGyrotLh2MGxv3l…> No, it would make no sense here because this is an ROI analysis Thank you so much again! Best regards, *Laura Willers de Souza *

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mri_info orientation string ???
by Xiaojiang Yang 26 Jan '22

26 Jan '22

External Email - Use Caution Dear Freesurfer Developers, I have scrutinized the Freesurfer source code from github, found that this might be a bug in Freesurfer. Basically, the string "Orientation : ???" comes from the function MRIdircosToOrientationString defined in mri.cpp, which depends on the MRI structure's member ras_good_flag. However, when reading a dicom file using the function DICOMRead2 defined in DICOMRead.cpp, the member ras_good_flag seems to be never been assigned a "ras good flag" value 1. That's why I got the orientation string value of "???". Would anyone correct or confirm my finding? Thank you! John Xiaojiang Yang <https://secure-web.cisco.com/1z35I78V94iRbbYPmh53mt00toQQUpCtob0Flq38T-DIF4…> Mon, 10 Jan 2022 09:23:09 -0800 <https://secure-web.cisco.com/1xlKT8odwFmJHyltnD83Zsoh2rGvmR8Hww2q4lAdH_dB7q…> External Email - Use Caution Dear Freesurfer Experts, I have a question regarding the orientation string gotten from mri_info. When I apply mri_info command to a DIOM series I generated programmatically, I get the "???" result, and hence primary slice direction is also unknown: ...... Orientation : ??? Primary Slice Direction: unknown ...... I already had the " Image Position Patient" and "Image Orientation Patient" written in the DICOM header. Don't know what other important info is missing. Could you tell me what key information is used in DICOM header to determine this orientation when using mri_info? Thanks! John

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Supercomputer
by REEM ABU BAKR BAHATHIQ 26 Jan '22

26 Jan '22

External Email - Use Caution Hi dear freesurfer list. I want to run recon-all command on 400 NIFTI images using laptop connected to my universty supercomputer How can I do that?? Any help And what about the organization of data structure I'm new to neuroimaging, as well as Linux systems. Thank you in advance

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recon-all error: mpr2mni305 failed
by Hickling, Alice 26 Jan '22

26 Jan '22

External Email - Use Caution Hi FreeSurfer Developers, I'm trying to run recon-all on a high resolution (0.65mm iso) MP2RAGE however I am receiving the following error. talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log These are the options that I am using. recon-all -all -s Freesurfer -i denoised_MP2RAGE.nii -T2 mean_denoised_MP2RAGE_T2W.nii -T2pial -multistrip -hires Please let me know if you can help. * FreeSurfer version: 7.2.0 (freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b) * Platform: CentOS Linux release 7.9.2009 (Core), Rocks release 7.0 (Manzanita) * Uname -a: Linux compute-0-14.local 3.10.0-957.27.2.el7.x86_64 #1 SMP Mon Jul 29 17:46:05 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux * Recon-all.log: see attached * Talairach_avi.log: see attached Best wishes, Alice

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questions of tracula group analysis, freeview and pair analysis
by Zeng, Qi 26 Jan '22

26 Jan '22

External Email - Use Caution Hi, I got a couple of questions regarding group analysis of tracula with a longitudinal pipeline, freeview output heatmap key, and pair analysis's fsgd & correction analysis. 1). I followed FsTutorial/TraculaStatistics - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1AjTV10_qUpg01X4rpJJaZQufhlsihHV7tqqL_DCJ36KH6…> to conduct a GLM group analysis for tracula results. But for the first step, should I conduct a long_mris_slopes to get the rate of change just as surface-based analysis for a longitudinal pipeline? 2). I tried freeview my sig.mgh results both for positive and negative for my surface group analysis, is there a heatmap key I can put into the image or available to export? 3). I created the FSDG file for pair analysis as follows to indicate both the same and difference within the pair subject to hope to regress out the effect of age at baseline and time_diff between subjects, is that the correct way of formatting? and also how to create the subject name here if my previous FSDG is sub01_ses-1.long.sub01_base and sub01_ses-2.long.sub01_base for the subject name. > GroupDescriptorFile 1 > Class Main > Variables Age_bl Time_diff > Input sub01pair Main 30 7.1 > Input sub02pair Main 40 2.2 > Input sub03pair Main 50 3.7 > Input sub04pair Main 60 0.7 4). Even not indicated in the pair analysis page, a cluster correction "mri_glmfit-sim" is also necessary for the last step, right? Thank you so much! Best, Qi

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Problems with recon for manually fixed Talairach
by Goeckner, Bryna 26 Jan '22

26 Jan '22

External Email - Use Caution Hi, I am trying to decide how to proceed after manually updating a talairach since various ways I’ve tried the recon process give me different results. Our group used Freesurfer 7.2 for processing data with the T2 and 3T flags as follows: recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all After visual inspection, I made adjustments to the talairach using tkregister2 and then used the code below to rerun the recon: recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all When this was done, the talairach.xfm file was restored to the talairach from the original recon, while the talairach.xfm~ was still the fixed version. At no point in this entire process did the talairach (fixed or original) generate an error. To avoid the overwriting of the talairach.xfm file, I tried using (separately) the -notalairach and -notal-check flags. For both, the talairach.xfm file stayed as the fixed talairach, but I got different aseg and aparc results. I’d like to know more about how these to flags differ and if you have a recommendation on which process is best. The plan is to eventually use this data in TRACULA. Thanks for your help, Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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manual segmentation
by 刘卫 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, Hello, I would like to ask if there are other correction methods besides multiple comparison correction when surface based group analysis. Can I use the 6.0 version of free to analyze the results of the 7.2 version preprocessing?

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Freesurfer January 2022