Freesurfer

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Re: [Freesurfer] Problems with recon for manually fixed
by Goeckner, Bryna 27 Jan '22

27 Jan '22

External Email - Use Caution We are using FS 7.2 Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program Date: Wed, 26 Jan 2022 16:43:44 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Problems with recon for manually fixed Talairach To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <8e0752c5-13fa-755e-c416-4253ce5043b3(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" what version of FS are you using? On 1/21/2022 2:21 PM, Goeckner, Bryna wrote: > > ????????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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The better 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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PETSurfer: Which is the right way to turn off PVC?
by Zhener Zhang 27 Jan '22

27 Jan '22

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

27 Jan '22

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

27 Jan '22

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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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