Freesurfer

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Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires?
by Daniel Westfall 08 Jul '20

08 Jul '20

External Email - Use Caution Hi Douglas, It looks like the previous processing used 'recon-all -all -norm2-b 20 -norm2-n 5 -no-isrunning', this was from 2012 so I referenced the recon-all.log for this info. According to the log the original data was 0.9 mm size and then confirmed to 1 mm size. My hypotheses are specific to thickness (whole brain and ROIs based on the Yeo 7-network parcellation). So, basically I am trying to determine if I should convert to the -hires pipeline to take advantage of the submillimeter pipeline to get a more accurate representation of the cortical thickness. Or if using the previously processed 5.3 1mm conformed scan is fine. The cost/benefit really just alludes to the amount of time it will take to QC ~600 scans if I re-run in 7.1. If there is a huge advantage of switching to the -hires pipeline for cortical thickness measures then that is something I can move forward with. Thank you ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, July 8, 2020 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 197, Issue 16 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Updating submillimeter data from 5.3 to 7.1 with -hires? (Douglas N. Greve) 2. Re: Freesurfer Hippocampal Subfield Misalignment (Jenna Katherine Blujus) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Jul 2020 11:15:56 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8f7a8545-49e3-4a51-575f-3caa60db80e0(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" How did you do the 5.3 analysis? in 1mm/conformed space? And what are you hoping to accomplish by running it in v7.1 with -hires? On 7/8/2020 10:46 AM, Daniel Westfall wrote: > > ????????External Email - Use Caution > > Hi Everyone, > > I have access to two large datasets (~600 scans) that were previously > collected, processed, QC'd, and manually edited where necessary in > Freesurfer 5.3 with recon-all. However, the data is 0.9 mm isotropic > collected in a 3T scanner. I am attempting to decide if the > cost/benefit is worth switching the pipeline to Freesurfer 7.1 with > the -hires flag? The processing time is not the issue, mainly redoing > QC and manual corrections is the concern. > > 1. To publish 0.9 isotropic is it necessary to use the -hires pipeline? > 2. Is it appropriate to apply corrections calculated in the > Freesurfer 5.3 standard pipeline to Freesurfer 7.1 -hires (and > double check). Or do the manual QCs need to be completed from the > ground up? > 3. With the other 2 questions in mind, is it better to just go ahead > and convert the data to Freesurfer 7.1 -hires? > > Thank you, > Daniel > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 08 Jul '20

08 Jul '20

Hi! I meant that if the hippocampus was oversegmented (e.g., over the amygdala), you’d still have to paint new labels in those regions (as amygdala, in our example). You could use the Matlab functions under $FREESURFER_HOME/matlab (in particular MRIread and MRIwrite) to programmatically move the edits from aseg.mgz to wmparc.mgz. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, July 8, 2020 at 11:37 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix the surrounding labels"? Thank you, Jenna Message: 3 Date: Tue, 7 Jul 2020 20:53:12 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <85489126-5DC1-4464-810B-01A7E825895A(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it?s only 1 subject in a bigger study, I?d probably call it a QC fail and leave it out. If it?s a single case you?re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeigle… Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Hippocampal Subfield Misalignment Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

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Updating submillimeter data from 5.3 to 7.1 with -hires?
by Daniel Westfall 08 Jul '20

08 Jul '20

External Email - Use Caution Hi Everyone, I have access to two large datasets (~600 scans) that were previously collected, processed, QC'd, and manually edited where necessary in Freesurfer 5.3 with recon-all. However, the data is 0.9 mm isotropic collected in a 3T scanner. I am attempting to decide if the cost/benefit is worth switching the pipeline to Freesurfer 7.1 with the -hires flag? The processing time is not the issue, mainly redoing QC and manual corrections is the concern. 1. To publish 0.9 isotropic is it necessary to use the -hires pipeline? 2. Is it appropriate to apply corrections calculated in the Freesurfer 5.3 standard pipeline to Freesurfer 7.1 -hires (and double check). Or do the manual QCs need to be completed from the ground up? 3. With the other 2 questions in mind, is it better to just go ahead and convert the data to Freesurfer 7.1 -hires? Thank you, Daniel

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Question about 3T images and brain atlas compatibility
by Hye Min Shin 08 Jul '20

08 Jul '20

External Email - Use Caution Hello, I wanted to extract brain morphometry data (cortical thickness, surface areas, volume, etc) using PALS-B12 atlas. I have some 3T MRI images that I have preprocessed using Freesurfer 3T flag. I am wondering if it would be ok to extract MRI data from 3T images on atlases such as PALS-B12. How do we know whether certain atlases are insensitive to field strength? Best, Julia Shin

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Mapping labels from left hemisphere to right hemisphere in fsaverage space
by Yash Patel 08 Jul '20

08 Jul '20

External Email - Use Caution Hi all, I have manually drawn roi onto fsaverage space on the left hemisphere. Is there a way to transfer these labels to the right? The end goal is to extract cortical measures from labels in both hemispheres and then will be averaged for further analysis. Not interested in asymmetry. Thank you for you advice, Yash Get Outlook for iOS<https://aka.ms/o0ukef>

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 08 Jul '20

08 Jul '20

Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it’s only 1 subject in a bigger study, I’d probably call it a QC fail and leave it out. If it’s a single case you’re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, July 7, 2020 at 16:24 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

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Atlas question
by Sara Lyn 08 Jul '20

08 Jul '20

External Email - Use Caution Hi FS developers I'm doing an ROI analysis with data data and was wondering if there exists a merged Freesurfer white matter parcellation and Johns Hopkins University white matter label atlas. If yes what is it called and where can I find it? I am trying to label the mean FA skeleton mao with this merged atlas and then deproject it to subjects native space. Thank you

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Occasionally aparc+aseg is in different orientation to input
by Ian 08 Jul '20

08 Jul '20

External Email - Use Caution Hi Freesurfers. I have a very strange problem - out of several thousand scans I've run recon-all on, some give the output in an orientation different to the input. The input here is: And the output is: I always run it in the same way... can you shine a light on what I may be missing? Ian

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bbregister using freesurfer v7
by Ellen Ji 08 Jul '20

08 Jul '20

External Email - Use Caution Dear experts, I am running bbregister and have a couple questions: 1) I am using freesurfer version 7. My understanding is that I do not need any --init argument anymore, and without it, by default it uses init-coreg. Could you confirm this? (I tested the below and it seemed fine) bbregister --s subject1 --mov $dtipath/subject1/data.nii.gz --dti --reg mri/register.dat 2) A colleague performed recon-all using freesurfer v6. Is it ok if I use bbregister on these subjects using freesurfer v7 or should I install v6? Many thanks for your input! Ellen Ji, PhD Postdoctoral researcher ***** Individual Differences in Psychosis (IDP) Lab Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch

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Problem with skull strip & general beginner questions
by Nils Böer 07 Jul '20

07 Jul '20

External Email - Use Caution Hello everyone, I hope you can help me with my little problem I encountered after manually editing the skull strip. Because my internet provider crashed I'm unable to upload the log file right now and writing this from my phone. For context: I'm analyzing data with freesurfer 6.0 because the data sets already went through the recon-all process some months ago with freesurfer 6.0. I just got the data sets and my first step was to manually edit bad skull strips using tkmedit. This worked fine but after I finished and saved the data set I wanted to run: recon-all -autorecon-pial -subjid P_01 This stopped with errors and at the bott of the log i found this note which probably led to the crash: MghRead(/usr/local/freesurfer/subjects/P_01/MRI/../MRI/asset.presurf.mgz, -1): could not open file I looked into the folder and can't even find this file. Did I miss a step I have to do before or can this be due to getting the data after running recon-all on a different PC? My pre-processing pipeline looks like this (keep in mind I already get the data after recon-all was completed): 1. Skull Strip (either manually or using gcut depending on data quality) 2. Checking surfaces visually and talairach transforms if needed 3. White matter intensity normalization. Do I need to change the order here or am I missing something completely? I'm new to freesurfer and have to get into it myself. The broad tutorials online help but it's hard to check what I have to do in which order and how. If you have other guides I can check this would be an incredible help. Thanks for the help and sorry for the long email, I really appreciate every tip. Best regards, Nils

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