Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Re: [Freesurfer] Help
by Douglas N. Greve 14 Dec '21

14 Dec '21

There is an automatic topology fixer in the stream. While sometimes it fixes an topo error properly, it does not always do so, so you will need to see whether it has fixed is or not. It is the white surface that is in error, which is created from the wm.mgz (or filled.mgz), so you will need to fix one of those volumes. On 12/14/2021 5:26 AM, Nilab Nasrullah wrote: > > External Email - Use Caution > > I am using freesurfer 7.1.This particular subject's segmentation > didn't include the cerebral cortex of the occipital lobe (see image > 1). Although I can see there are defects in that specific place, there > are also defects in other places (see atttached images). I have > followed the instructions on how to correct topological errors but > that doesn't seem to help much since it is the grey matter that is not > included in the segmentation. > > Can you provide me with some instructions on how to fix these defects? > > Thanks, > Nilab > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* 11 December 2021 00:24 > *To:* Nilab Nasrullah <nilab.nasrullah(a)stud.ki.se>; > freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Help > The data look pretty noisy in those images. My guess is that the WM is > not getting segmented properly in that temporal area or there is an > incorrectly fixed topology error. Try looking at the wm.mgz (or the > filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz > to see where the defects are. > > On 11/29/2021 9:41 AM, Nilab Nasrullah wrote: >> >> External Email - Use Caution >> >> Sure. See attached. >> >> //Nilab >> ------------------------------------------------------------------------ >> *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Sent:* 29 November 2021 15:40 >> *To:* Nilab Nasrullah <nilab.nasrullah(a)stud.ki.se> >> <mailto:nilab.nasrullah@stud.ki.se>; freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] Help >> Can you send them in plain, unzipped format? >> >> On 11/29/2021 4:07 AM, Nilab Nasrullah wrote: >>> >>> External Email - Use Caution >>> >>> I am attaching a few screenshots of the segmented brain as >>> zip-files. Hopefully, you can see the results. If not, let me know >>> so I can send it to you in a different format. >>> >>> Thanks, >>> Nilab >>> ------------------------------------------------------------------------ >>> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas >>> N. Greve <dgreve(a)MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> >>> *Sent:* 29 November 2021 04:01 >>> *To:* freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <freesurfer(a)nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* Re: [Freesurfer] Help >>> Can you send some pictures? >>> >>> On 11/23/2021 4:02 AM, Nilab Nasrullah wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi, >>>> >>>> I am editing subjects for a research project. After reconstruction, >>>> some parts of the brain are not included in the segmentation. >>>> Often, some parts of the temporal lobe and the cortex of the >>>> occipital lobe are not included. In some cases, the cortex of the >>>> frontal lobe is also affected. >>>> >>>> I have tried using controls points, but the results don't change. I >>>> have also reconstructed them again, running autorecon1 and >>>> autorecon2&3 separately. I have lowered the watershed parameters, >>>> used the gcut command and edited manually after autorecon1 but in >>>> the end, the results don't vary significantly compared to running >>>> recon-all -all. >>>> >>>> What can I do to include the missing parts? >>>> >>>> Thanks, >>>> Nilab >>>> >>>> >>>> >>>> /När du skickar e-post till Karolinska Institutet (KI) innebär >>>> detta att KI kommer att behandla dina personuppgifter. /Här finns >>>> information om hur KI behandlar personuppgifter >>>> 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>>>> >>>> >>>> /Sending email to Karolinska Institutet (KI) will result in KI >>>> processing your personal data./ You can read more about KI’s >>>> processing of personal data here >>>> 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1 0

Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 14 Dec '21

14 Dec '21

External Email - Use Caution Dear Douglas, Thank you for the answer! That's exactly what I wanted to know. About ROI analysis with GLM, how do I specify the results of the hippocampal subfields and nuclei of the amygdala in the GLM command? Thank you so much again! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 1

New tool for subcortical limbic segmentation (ScLimbic)
by Douglas N. Greve 14 Dec '21

14 Dec '21

I just wanted to alert you to a new tool in FreeSurfer to perform subcortical limbic segmentation. The documentation and download are here https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic The paper is here https://pubmed.ncbi.nlm.nih.gov/34571161/ It segments septal nuclei,basal forebrain, fornix, nucleus accumbens, hypothalamus (divided into mamillary bodies and the rest of hypothalamus); see attached pic. You might also be interested in a related tool from Benjamin Billot for segmenting the hypothalamus into subunits. You can find docs here https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits doug

1 0

Re: [Freesurfer] Questions about GLM
by Laura Willers de Souza 13 Dec '21

13 Dec '21

External Email - Use Caution Dear Douglas, Thank you for the answer! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

1 0

Definition of Premotor Area
by Tsolaki, Evangelia C. 13 Dec '21

13 Dec '21

External Email - Use Caution Hello Freesurfer Team, I am interested in using premotor, precentral gyrus and postcentral gyrus in my analysis. For the definition of the precentral gyrus and postcentral gyrus I use the following lines: fslmaths aparc+aseg.nii.gz -thr 1024 -uthr 1024 PreCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2024 -uthr 2024 PreCG_R.nii.gz fslmaths aparc+aseg.nii.gz -thr 1022 -uthr 1022 PostCG_L.nii.gz fslmaths aparc+aseg.nii.gz -thr 2022 -uthr 2022 PostCG_R.nii.gz To define the premotor area I use the labels rh.BA6_exvivo.label and lh.BA6_exvivo.label according to the script below: bbregister --s SubID_FreeSurfer --mov nodif.nii.gz --reg lowb2orig.dat --dti --init-fsl mri_label2vol --label SubID_FreeSurfer /label/rh.BA6_exvivo.label --reg lowb2orig.dat --fillthresh .3 --hemi rh --subject SubID_FreeSurfer --o BA6_R.nii.gz --temp nodif.nii.gz --proj frac 0 1 .1 When I check the location of the resulted BA6 and precentral gyrus masks, there is an overlap. Could you please advise if there is any other way to define premotor area? Thank you in advance, Evie ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

3 3

Freesurfer v7.x and bias correction -3T option not working
by Notestine, Christine 12 Dec '21

12 Dec '21

External Email - Use Caution We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks: * In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly. * However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction: * In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not. We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. * When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. * Below are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs: mri_nu_correct.mni.log: ... /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 ... AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz Using shrink factor: 4 ... -- Christine Fennema-Notestine, Ph.D.

2 6

Questions about contrasts
by Laura Willers de Souza 12 Dec '21

12 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ pathology (CU/CI) + CSF cortisol + pathology*CSF cortisol >From the GLM DODS analysis I want to know if: * the regression coefficient is significant only for the difference between groups, * or only for cortisol, * or for both, * or if the coefficient of the intercept between group and cortisol is significant. Is my FSGD file (attached) correct? What would the contrasts look like? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 1

Error: recon-all exited with ERRORS: failing without generating all surf files: How to modify wm.mgz to make it work?
by Sumit Sharma 12 Dec '21

12 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to generate the segmentation files by running the "the recon-all" command. The command is failing and I am getting the below error. ERROR: recon-all -s out_24 exited with ERRORS at Thu I searched and open the wm.mgz and other files using the below command following the tutorials: https://secure-web.cisco.com/1GbbXPOsSqlnYztwVk4vidqb-NyHGtLcthCKOl6FN_kuZ2… https://secure-web.cisco.com/1Da47ZnOFHuJQ-ZILQdgpeHcwfKHsJb7cuOQe4WoXHMu9w… Command: freeview -v out_24/mri/brainmask.mgz \ out_24/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f out_24/surf/lh.white:edgecolor=yellow \ out_24/surf/lh.pial:edgecolor=red \ out_24/surf/rh.white:edgecolor=yellow \ out_24/surf/rh.pial:edgecolor=red \ out_24/surf/lh.orig.nofix:visible=0 However, there are no surface files which are mentioned in the above command. The surface folder contains only the below files: lh.defect_borders lh.defect_labels lh.orig.nofix lh.qsphere.nofix rh.defect_borders rh.defect_labels rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.orig.premesh lh.smoothwm.nofix rh.defect_chull rh.inflated.nofix rh.qsphere.nofix Please suggest on how should I modify the wm.mgz file in such case: Below are my doubts: What I understood so far that wm.mgz contains information of white and non-white matter (whether gray matter or CSF), however I could see yellow color pixels of intensity 255 near the corpus callosum cavity which is non-white matter region, however when I modify the voxels in freeview using recon-edit option, I need to give 255 pixel value to the white matter region, I am a little bit confused on how to edit wm.mgz, whether to edit voxels in the white matter region with 255 value and erase in the non white region or do the opposite, Please guide. What is the best way to modify the wm.mgz if the surfaces are not generated? Please advise. 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2) Platform: ubuntu 3) recon-all.log: (PFA). Thanks and Regards Sumit Sharma ------------------------------------------------------------------------------------------------------------------------------ Sumit Sharma

3 2

Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 12 Dec '21

12 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if the analysis of hippocampal subfields and nuclei of the amygdala can only be done through ROI-based analysis or is there any way to perform GLM analysis with these data in freesurfer? 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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error in mri_sclimbic_seg
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 12 Dec '21

12 Dec '21

External Email - Use Caution I receive this error when I try to run mri_sclimbic_seg in dev 2021 12 06 How can I fix this? mri_sclimbic_seg --s 10105_S1200QUM/ --conform /usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s 10105_S1200QUM/ --conform Excluding seg [853] Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/dev7/models/sclimbic.ctab Loaded population stats /usr/local/freesurfer/dev7/models/sclimbic.volstats.csv Segmentation fault Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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