Re: [Freesurfer] Longitudinal pipeline with multiple scans at one time point

External Email - Use Caution Ah, that makes sense, thanks! We hadn’t really considered feeding them all in at the cross-sectional step, since to this point for these types of analyses we have been doing all averaging after freesurfer (on the individual extracted measures).

Re: [Freesurfer] Longitudinal pipeline with multiple scans at one time point

You are right that using all the scans will bias toward tp2. I think I would just run the cross for each time point using all the data you have. This will not bias the base because an average of the images within each time point will be used to make the base. If possible, you will want to make

[Freesurfer] Longitudinal pipeline with multiple scans at one time point

External Email - Use Caution I have a dataset consisting of individuals scanned at two time points 7 years apart. At the first time point, a single MPRAGE scan was collected for each individual; at the second, the same MPRAGE scan was collected, as well as an additional set of

Re: [Freesurfer] Longitudinal Pipeline

External Email - Use Caution Here is the tutorial page for longitudinal pipeline -

Re: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)

July 12, 2023 10:25 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2) External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipe

Re: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)

:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Jackson Lee Sent: Wednesday, July 12, 2023 10:25 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2) External Email - Use Caution Hi there,

Re: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)

, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Jackson Lee Sent: Wednesday, July 12, 2023 10:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2) External Email - Use Caution Hi there, I am hoping to process

[Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)

External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipeline available in FreeSurfer:

Re: [Freesurfer] Longitudinal Pipeline Issue

:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Pipeline Issue External Email - Use Caution Hello Freesurfer Team I'm attempting to create the base for the longitudinal scan process, as described in the Longitudinal Tutorial (MailScanner has detected a possible

[Freesurfer] Longitudinal Pipeline Issue

External Email - Use Caution Hello Freesurfer Team I'm attempting to create the base for the longitudinal scan process, as described in the Longitudinal Tutorial

Re: [Freesurfer] Longitudinal pipeline {Disarmed}

External Email - Use Caution Hi Vittal, please see my response from Nov 30th on this list. Best, Kersten. Am 04.12.2020 um 08:16 schrieb vittal korann mailto:vittalkor...@gmail.com>>: External Email - Use Caution Dear FreeSurfer experts This is just a gentle

Re: [Freesurfer] Longitudinal pipeline {Disarmed}

External Email - Use Caution Dear FreeSurfer experts This is just a gentle reminder of my previous mail. Diers Kersten has replied to my query. He asked me to send a few details pertaining to my issue. I shared all the necessary details with you people and waiting for your

Re: [Freesurfer] Longitudinal pipeline {Disarmed}

External Email - Use Caution Hello VIttal, thanks for the info about the design. You wrote before that the Matlab variable X (i.e., the design matrix) has a dimension of 47x6. X is a translation of the study design into a numerical matrix, which is part of the statistical

Re: [Freesurfer] Longitudinal pipeline {Disarmed}

External Email - Use Caution No problem, thanks! So I shall send an email only to freesurfer or would it fine if I put you in cc? With regards Vittal On Mon, Nov 30, 2020 at 4:25 PM Diers, Kersten /DZNE wrote: > Hi Vittal, > > Sorry, I can only help on the public freesurfer

Re: [Freesurfer] Longitudinal pipeline question

By post processing and stats, do you mean mris_preproc, mri_surf2surf, and mri_glmfit? You can run v6 of those on data reconned with any version of FS On 7/28/2020 1:25 PM, Rachel Romeo wrote: External Email - Use Caution Hi, I am working with some longitudinal data that was

[Freesurfer] Longitudinal pipeline question

External Email - Use Caution Hi, I am working with some longitudinal data that was originally run through troubleshooting/recon-all in freesurfer 5.3. A lot of time went into the edits, so I definitely do not want to replicate these in freesurfer 6. Do I need to run the

[Freesurfer] Longitudinal pipeline in pediatric sample with TIV difference

External Email - Use Caution Hello Freesurfers experts, I have a pediatric sample and I wanted to use the longitudinal pipeline (the time acquisitions are 8 years apart and age range is from 6 years to 17). I saw that longitudinal pipeline assumes that TIV doesn't change, which

Re: [Freesurfer] Longitudinal Pipeline (fwd)

.jenkin...@ndcn.ox.ac.uk> > To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Longitudinal Pipeline > > Hi Aaron and Hi Bruce! > There is code to convert ANTs format to FSL,

Re: [Freesurfer] Longitudinal Pipeline (fwd)

FYI -- Forwarded message -- Date: Tue, 16 Jan 2018 19:59:38 + From: Mark Jenkinson <mark.jenkin...@ndcn.ox.ac.uk> To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitu

Re: [Freesurfer] Longitudinal Pipeline

Thank you very much. Your last email gave me a lot to work with. On Mon, Jan 15, 2018 at 9:18 AM, Bruce Fischl wrote: > Hi Aaron > > we compute the warp and save it in the mri/transforms/talairach.m3z, but > don't apply it (so don't require an extra resampling). I

Re: [Freesurfer] Longitudinal Pipeline

Hi Aaron we compute the warp and save it in the mri/transforms/talairach.m3z, but don't apply it (so don't require an extra resampling). I know we have some tools around to convert to ANTS format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!) cheers Bruce On Mon, 15 Jan

Re: [Freesurfer] Longitudinal Pipeline

Is the warp saved anywhere and where can I find it? Also is the warp compatible with FNIRT in any way. I am interested in combining warps together to reduce the number of re-sampling steps. Thank you so much in advanced On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl

Re: [Freesurfer] Longitudinal Pipeline

in the last stage there is a nonlinear atlas alignment that is specific to each timepoint. We are working on building a nonlinear base, but it is not distributed yet. cheers Bruce On Sun, 14 Jan 2018, Aaron Tanenbaum wrote: > > I am interested in knowing what type of alignment goes into

[Freesurfer] Longitudinal Pipeline

I am interested in knowing what type of alignment goes into the last stage of the longitudinal pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find the warp? ___ Freesurfer mailing list

Re: [Freesurfer] freesurfer longitudinal pipeline

Hi Paul, step 4 basically means that you should take results from the *.long.baseid directories and not look at the original cross sectional directories or the base output. The page on statistic describes different tools to do that. Yes, --s is replaced. All information on the subject ids

Re: [Freesurfer] freesurfer longitudinal pipeline

Thank you very much Martin for your response. I do understand the statistical analysis ascept, my question was more in line with the last step (i.e. step 4) of the work flow summary ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). You suggested we calculate the difference

Re: [Freesurfer] freesurfer longitudinal pipeline

Hi Paul, for the statistical analysis take a look at the available options here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics for asegstats2table you can use the --qdec-long flag with an appropriate text file containing the columns fsid and fsid-base . This will convince

[Freesurfer] freesurfer longitudinal pipeline

Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and

Re: [Freesurfer] Longitudinal Pipeline

Hi Theo, - not sure what test you mean. Have a second person correct the data and compare ? - you can run 1.5. and 3 T data in the longitudinal pipeline, however (similar to cross sectional processing) you will not know if the differences of the results are due to anatomical changes or due

[Freesurfer] Longitudinal Pipeline

Hi All, Is it standard practice to conduct test when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to analyse data acquired (1.5T - time point one) with time-point two (3T) in the longitudinal pipeline? Thanks Theo

[Freesurfer] Longitudinal Pipeline

Hi All, Is it standard practice to conduct reliability when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to analyse data acquired (1.5T - time point one) with time-point two (3T) in the longitudinal pipeline? Thanks Theo

Re: [Freesurfer] Longitudinal Pipeline

Yes, that is why it is experimental. However, global atrophy will affect the ventricles (they are growing) which is an effect in the opposite direction, so maybe it cancels out to some extend. Best, Martin > On 12 Apr 2017, at 23:55, Arman Eshaghi wrote: > > Thanks

Re: [Freesurfer] Longitudinal Pipeline

Thanks Martin. Should I be worried about affine transform masking out the global atrophy if I am using the whole brain (no skull stripping)? Arman On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter wrote: > Hi Arman, > > should be possible by passing the - - affine

Re: [Freesurfer] Longitudinal Pipeline

Hi Arman, should be possible by passing the - - affine flag. I think I also experimented around with a -base-affine flag to recon-all for that (instead of -base). It is experimental! Best, Martin > On 07 Apr 2017, at 13:34, Arman Eshaghi wrote: > > Hi, > > I

[Freesurfer] Longitudinal Pipeline

Hi, I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years. Thanks, Arman

Re: [Freesurfer] longitudinal pipeline surface error

Thank you so much! Mihaela On Tue, Apr 5, 2016 at 4:41 PM, Martin Reuter wrote: > Hi Mihaela, > > you can use our BrainPrint tool (after running FS) to see how closely the > brain shape matches: > > http://reuter.mit.edu/publications/pid/wachinger-brainprint15 >

Re: [Freesurfer] longitudinal pipeline surface error

Hi Mihaela, you can use our BrainPrint tool (after running FS) to see how closely the brain shape matches: http://reuter.mit.edu/publications/pid/wachinger-brainprint15 http://reuter.mit.edu/software/brainprint/ Best, Martin On 04/05/2016 12:49 PM, Mihaela Stefan wrote: Hi Martin, Just an

Re: [Freesurfer] longitudinal pipeline surface error

Hi Martin, Just an update on this. It turned out that there was just a DICOM mismatch for this subject but now that you mentioned it, I wonder what people do to make sure that the same person returns for follow-up in a longitudinal study. Even when there is one study coordinator for the entire

Re: [Freesurfer] longitudinal pipeline surface error

Wow! I haven't thought about that but it's possible since we had a few study coordinators along the way. So it could be the case that the study coordinator didn't know the subject who came at follow-up. Hopefully it will be just a DICOM mismatch. Will see how it goes.. :) On Thu, Mar 31, 2016 at

Re: [Freesurfer] longitudinal pipeline surface error

I have seen cases where annonymization messed up ID's and individual time points came from a different subject. That could mess things up quite bad. (Also if the person sends their sibling or friend, because they don't have time to come to the follow up themselves, has also happened - not to

Re: [Freesurfer] longitudinal pipeline surface error

Hi Martin, We ran this subject twice but we got the same error. The norm is not aligned. They almost look like two different brains. I double checked the exam numbers to make sure that these three exams belong to the same person. They indeed seem to belong to the same person but I will re-run

Re: [Freesurfer] longitudinal pipeline surface error

Hi Mihaela, does the cross sectional run of that time point, and the base look OK? Also check if this time point is aligned correctly to the base (e.g. open norm.mgz from the long and the base, they should be aligned). If all this is OK, then I would recommend to re-run this long run again,

Re: [Freesurfer] longitudinal pipeline

HI Song, are you talking about the longitudinal tractography? If you have longitudinal data, then yes, we recommend the use of longitudinal processing both for the structural and for the tractography. That's what they have been developed for. Best, Martin On Jan 26, 2015, at 5:50 PM, Inkyung

[Freesurfer] longitudinal pipeline

Hi Freesurfer Experts, Is the longitudinal pipeline still recommended for the DTI data analysis if structural changes occur at different time points (e.g., pre and post-treatment)? Or is it better to use the standard pipeline? Are other options available? Thanks so much! Song

Re: [Freesurfer] Longitudinal pipeline + LME question

smartphone, please excuse brevity. Original message From: Brianna Damadian bdama...@buffalo.edu Date:07/03/2014 1:57 AM (GMT+01:00) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal pipeline + LME question Hi Martin, Thanks

[Freesurfer] Longitudinal pipeline + LME question

Hello experts, We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely,

Re: [Freesurfer] Longitudinal pipeline + LME question

/02/2014 10:04 PM (GMT+01:00) To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal pipeline + LME question Hello experts, We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However

Re: [Freesurfer] Longitudinal pipeline + LME question

Sent via my smartphone, please excuse brevity. Original message From: Brianna Damadian Date:07/02/2014 10:04 PM (GMT+01:00) To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal pipeline + LME question Hello experts, We are setting out to look

[Freesurfer] Longitudinal Pipeline for Subjects with only 1 assessment

Dear FS Experts, I am running a longitudinal analyses, and I'd like to use the Linear Mixed Effect framework as even subjects with only 1 time-point can be included into the model. How do I create the base for a subject with only 1 TP? Is this the correct approach? recon-all -base *[basename]*

Re: [Freesurfer] Longitudinal Pipeline for Subjects with only 1 assessment

Hi Elijah, the recon-all command is correct. The error you are getting is something else. Does the ribbon file exist? I would re-run that base from scratch, could be an IO problem or disc space etc. Martin On 05/30/2014 08:56 AM, Elijah Mak wrote: Dear FS Experts, I am running a

Re: [Freesurfer] Longitudinal pipeline question

Hi Irene, both images should be smoothed the same. You only have two time points in each subject? Which FreeSurfer version are you using? And these images are from the *.long.base directories (or are they from the independent runs)? -Martin On Thu, 2011-11-03 at 15:20 +0100, Irene Altarelli

Re: [Freesurfer] Longitudinal pipeline question

Dear Martin, thanks for your quick reply. I am using version 5.1. I only have two timepoints per subject and I took the snapshots from the independent runs. What bothers me is that the difference is not present in the 001.mgz images, but seems to appear later in the workflow. Thanks again,