Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Please remember to cite FreeSurfer in your OHBM abstract. Thanks!
by Douglas N. Greve 15 Dec '21

15 Dec '21

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Using several scanners as covariates in Qdec
by Nilab Nasrullah 15 Dec '21

15 Dec '21

External Email - Use Caution Hello, I am sending you this email again since it has not been posted and I haven't got a response from you. I am doing a cortical thickness analysis for a research project in Qdec. Since we have gathered the MRI-scans from different sites and used different scanners, I want to use 6 different scanners as covariates in the analysis. I have tried with making 6 columns and entered 1 for the subjects that used a specific scanner and entered zeros in all the other spaces. This has not worked but it works to to have three differetent scanners as covariates. Do you have a suggestion on what I can do? Thanks in advance, 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<https://secure-web.cisco.com/1xPxeRGBEaxLlTyN7VSDHFHB5fWEy5UrAK6QuJDXKufO37…>. 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<https://secure-web.cisco.com/1kBKH1iJP86S39drFgoihHyRdAU2RCkw19J7AILhGtsEyu…>.

1 0

Longitudinal BASE, missing data and potential time skew?
by Jacob Levenstein 15 Dec '21

15 Dec '21

External Email - Use Caution Dear Freesurfer friends, It seems that prior messages* on longitudinal recon with missing timepoints have suggested that it is okay for a subset of participants to include different numbers of timepoints into the longitudinal pipeline, so long as there is not a systematic bias (e.g., one group consistently contains more scans than another group, etc.). Assuming that is still true, I am working with an adolescent dataset from 11 year-olds scanned every 3 months for a year (4 scans total). For participants missing a scan at either timepoint 2 or timepoint 3, I was wondering if creating the BASE/subject-specific template from only three sessions might introduce a temporal bias toward either timepoint 1 (i.e., formed from timepoints 1, 2 & 4), or bias toward timepoint 4 (i.e., formed from timepoint 1, 3 & 4). With consideration to the developmental changes we anticipant measuring over the year, would you be concerned with the potential early vs late skew in the BASE for these missing data cases? If so, for the missing timepoint participants, I was wondering if I should then avoid generating their subject-specific templates in a way that imposes an even weighting across the three timepoints (i.e., .33 each), and instead adjust the weighting of each timepoint relative to time acquired over the year (e.g., temporal based average), such that timepoint 1 is weighted at .25 and timepoint 2 and 4 are weighted at .375. If this is not a sensible approach, could you please let me know what you think best? Thank you for your insight! Much appreciated, Jacob * https://secure-web.cisco.com/13XDoOLfZ54QTh8NENJtaYSGUInOnTixvVUeeTP66Z4AcO… * https://secure-web.cisco.com/1ivSG2acZebGirLVnyV8qW29ZHDaGha1z3dT3TsM9w986h…

2 1

mri_label2label: one-to-one for subjectNo --> ico
by Krieger, Donald N. 14 Dec '21

14 Dec '21

External Email - Use Caution Dear Bruce, Doug, and everyone, 1. I am projecting labels from a subject's labels onto the icosahedron and note that the mapping is not one-to-one. Because of this, I cannot tell which subject vertex maps to which icosahedron vertex which I need to able to do. What am I missing here? 2. Just double-checking something simple - The center of the icosahedron is as the origin, i.e. 0,0,0, yes? Thanks - Don

2 3

Re: [Freesurfer] Questions about contrasts
by Laura Willers de Souza 14 Dec '21

14 Dec '21

External Email - Use Caution Dear Douglas, Thank you so much for your answer! Sorry, but I don't think I explained myself correctly in the previous email. I want to analyze the difference in cortical thickness between two groups (CU and CI), adjusting for a covariate (cortisol CSF) and the interaction between them. So my model would be: cortical thickness ~ diagnosis + CSF cortisol + diagnosis*CSF cortisol Using the GLM DODS, the contrasts, according to the wiki example (https://secure-web.cisco.com/1PUyQNFnXt6UhBGwXfB_vPfCTd6uW7Jf3dH3GiO0aIPFHh…) would be: * To verify if only the diagnosis regression coefficient is significant (diagnosis changes cortical thickness regardless of cortisol): * 1 -1 0 0 * * To verify if the regression coefficient of the interaction between diagnosis and cortisol is significant (the two change cortical thickness dependently): * 0 0 1 -1 * * To verify if only the cortisol regression coefficient is significant (cortisol changes cortical thickness regardless of diagnosis): * 0 0 0.5 0.5 Are these contrasts corret to represent the model we designed? 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

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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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>>> >>> >>> /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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>>> >> >> The information in this e-mail is intended only for the person to >> whom it is addressed. If you believe this e-mail was sent to you in >> error and the e-mail contains patient information, please contact the >> Mass General Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> <https://secure-web.cisco.com/1y18A7n363y7yxVLPw5RZ2YD1g7fRvx2t7C0vsofFeZ7VH…> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the >> e-mail. >> >> Please note that this e-mail is not secure (encrypted). If you do >> not wish to continue communication over unencrypted e-mail, please >> notify the sender of this message immediately. Continuing to send or >> respond to e-mail after receiving this message means you understand >> and accept this risk and wish to continue to communicate over >> unencrypted e-mail. >> >> >> >> /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 >> <https://secure-web.cisco.com/1yQVwVpTbHd2YGzeOffvp90m78gs1EDW2_toNyCt9kKCAb…>. >> >> >> /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 >> <https://secure-web.cisco.com/1XSdkvJKiVag4V9l-ah2EhvATa6_pLuG_oS92Rbd2DaJcl…>. >> > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the Mass > General Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was > sent to you in error but does not contain patient information, please > contact the sender and properly dispose of the e-mail. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately. Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. > > > > /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 > <https://secure-web.cisco.com/1uYCbwFvSNCny8ogM5QvByWQ6yNVa8Gu49okGN28QybDYZ…>. > > > /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 > <https://secure-web.cisco.com/15OVMmX7_h8cFCgKH4QAJFgj460fd4bU01WSe5GCTfSH5S…>. >

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.

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