Re: [Freesurfer] Longitudinal Processing Stream Version

Subject: [Freesurfer] Longitudinal Processing Stream Version External Email - Use Caution Hello, I have a question about longitudinal stream processing. On the wiki page (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http

[Freesurfer] Longitudinal Processing Stream Version

External Email - Use Caution Hello, I have a question about longitudinal stream processing. On the wiki page (

Re: [Freesurfer] Longitudinal processing of single time point data

: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Hemond, Christopher Sent: Wednesday, March 29, 2023 2:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal processing of single time point data External Email - Use Caution Dear Freesurfer experts, I am processing

[Freesurfer] Longitudinal processing of single time point data

External Email - Use Caution Dear Freesurfer experts, I am processing longitudinal data from subjects participating in a pre-post analysis; a few subjects do not have follow-up data. I'd like to still include these subjects and plan on using mixed effects analysis methods given

Re: [Freesurfer] Longitudinal processing

External Email - Use Caution Many thanks. Best regards On Thu, Jun 24, 2021, 10:07 Douglas N. Greve wrote: > If you are going to compare the volume across subject, then it does need > to be corrected with eTIV > > On 6/15/2021 8:06 AM, AJ wrote: > > External Email - Use

Re: [Freesurfer] Longitudinal processing

If you are going to compare the volume across subject, then it does need to be corrected with eTIV On 6/15/2021 8:06 AM, AJ wrote: External Email - Use Caution Hi, After running longitudinal processing and creating base and long runs, When looking at volumes of various structures

[Freesurfer] Longitudinal processing

External Email - Use Caution Hi, After running longitudinal processing and creating base and long runs, When looking at volumes of various structures over time of the same subject, are the volumes not need to be corrected by eTIV since head size does not vary overtime? Many

[Freesurfer] Longitudinal processing: QA

External Email - Use Caution Hello FreeSurfer developers, I am trying to apply longitudinal processing on T1w MRI data for two timepoints (~8 months between the two TP) in adolescents in order to perform vertex-based analyses. I am following the online tutorial here for the

[Freesurfer] Longitudinal processing with freesurfer 7.1.0

External Email - Use Caution Dear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error: longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri

Re: [Freesurfer] [FREESURFER] longitudinal processing base_tmps does not exist error

Hi Seonjoo, your base command is missing the "-all" so no processing is done in the base, which is why the file is missing later.. Best, Martin On Wed, 2019-08-07 at 17:27 +, Lee, Seonjoo wrote: > External Email - Use Caution > Dear Freesurfer, > Could you help me to

[Freesurfer] [FREESURFER] longitudinal processing base_tmps does not exist error

External Email - Use Caution Dear Freesurfer, Could you help me to resolve this error? I looked up the previous postings, but the recommendation (copying files in the same folder etc.) did not help. Thank you. $ recon-all -base template -tp 002_S_0295_S32678 -tp

Re: [Freesurfer] Longitudinal processing

Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Martin Reuter Gesendet: Montag, 13. Mai 2019 12:56 An: Freesurfer support list Betreff: Re: [Freesurfer] Longitudinal processing Hi Falk, yes, the output of long_mris_slopes and long_stats_slopes is in percent (100 * rate

Re: [Freesurfer] Longitudinal processing

Hi Falk, yes, the output of long_mris_slopes and long_stats_slopes is in percent (100 * rate / value_of_fit_at_mid_time). Also running 1mm data is different (as you know :-) from .8 so maybe you would analyze both separately, e.g. creating one base on 1mm time points and another on the .8mm ?

[Freesurfer] Longitudinal processing

External Email - Use Caution Dear all, I'm a beginner in using the longitudinal processing pipeline (as well as statistical analysis) and it would be great to get some insights or hints to analyze my data. I have a dataset consisting of 11 subjects each acquired at 7 different

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

nt with his typo. :D > > > > Best, > > Falk > > > > Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Juergen Haenggi > Gesendet: Freitag, 25. Januar 2019 10:35 > An: Freesurfer Mailinglist >

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

...@nmr.mgh.harvard.edu Im Auftrag von Juergen Haenggi Gesendet: Freitag, 25. Januar 2019 10:35 An: Freesurfer Mailinglist Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS   External Email - Use Caution Dear Falk

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

t; im Auftrag von "falk.luesebr...@med.ovgu.de [falk.luesebr...@med.ovgu.de] Gesendet: Freitag, 25. Januar 2019 10:41 An: Freesurfer Mailinglist Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Ca

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

falk.luesebr...@med.ovgu.de Gesendet: Freitag, 25. Januar 2019 10:42 An: Freesurfer Mailinglist Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Caution Dear Juergen, Thanks for your quick reply! Actually

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

' #sys.exit(1) At least Martin is consistent with his typo. :D Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Juergen Haenggi Gesendet: Freitag, 25. Januar 2019 10:35 An: Freesurfer Mailinglist Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear Falk I have no idea, but recognised that the error refers to --qedc and not to --qdec. maybe there is a spelling error somewhere that is related to your problem. HTH Cheers Jürgen

[Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear all, Has anyone run the longitudinal pipeline successfully using the WSL? I'm running it with Ubuntu 18.04.1 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I'm trying to process my first longitudinal data set following the

Re: [Freesurfer] Longitudinal processing - LAS and RAS orientation baseline vs follow-up

Hi Elena, FreeSurfer put inputs in RAS coordinates (during the conform step at the very beginning), so it will take care of this. But only if the correct information is available from the input image header. If that header was corrupted earlier, it is impossilbe to know what coordinates the

Re: [Freesurfer] Longitudinal processing and paralllel flag

Hi Erik, usually we parallelize the number of subjects, rather than the individual pipelines. That gives us the best performance. Best, Martin On Thu, 2018-12-06 at 11:07 +, Erik O'Hanlon wrote: > External Email - Use Caution > Hi FS experts, > > I'm running a

[Freesurfer] Longitudinal processing - LAS and RAS orientation baseline vs follow-up

External Email - Use Caution Dear FreeSurfer Experts, I have some baseline and follow-up MRI scans that I would like to process through the longitudinal stream. Some of the baseline images were originally in Analyze format (LAS orientation) and were converted into nifti

[Freesurfer] Longitudinal processing and paralllel flag

External Email - Use Caution Hi FS experts, I'm running a longitudinal process with three time points per subject and was wondering if you can advise on the typical time to process? Can the -parallel flag be added to the base and long steps? I'm running this on a cluster that

Re: [Freesurfer] Longitudinal Processing question

Hi Ryan, FreeSurfers Longitudinal pipeline assumes head size is relatively fixed. The problem with growing heads is that the surfaces from the subject-template will not fit well to later (or earlier) time points and that the algorithm can potentially not recover. If surfaces look OK it means

[Freesurfer] Longitudinal Processing - Retaining Manual Edits

External Email - Use Caution Dear FreeSurfer Developers, We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the

[Freesurfer] Longitudinal Processing question

External Email - Use Caution Hello FreeSurfer experts, I have a few questions on the longitudinal processing stream. I am interested in studying longitudinal morphometry changes in a pediatric population. The age range of this population is between 4-20 years with age deltas

Re: [Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log

Hi Kaley, if you scroll down the log file you should find something like new invocation of recon-all with the correct time stamp and v6 text. The old log is kept and the new one is appended. I am also not sure it is OK to re-run the base with 6.0. It could be that this looks OK in single

Re: [Freesurfer] Longitudinal processing: cannot find input volume error

Hi Arsenije, I have never seen this. You could try: - convert the norm.mgz to norm.nii.gz and back (keep a backup of the old one) and see if that changes anything - you can also re-run this case from scratch to see if maybe anything else is wrong . Could have been an IO issue. Best, Martin

[Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log

External Email - Use Caution Hello FreeSurfer experts, I previously emailed regarding processing longitudinal data in v6.0 using bases with manual edits that had been completed in v5.3. I went ahead and ran recon-all -all on the base of a subject (originally generated in v5.3)

[Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0

External Email - Use Caution Hello FreeSurfer experts, We have a large dataset (n=140) that is being processed through the longitudinal pipeline. We have already generated the cross-sectionals and conducted manual edits to the bases in v5.3.0. What is the latest stage (cross,

[Freesurfer] Longitudinal processing: cannot find input volume error

External Email - Use Caution Dear Freesurfer experts, I’m having problems with one of my participants when I am trying to create the base template for my longitudinal analysis. I get an error saying that the input volume (norm.mgz) for my followup time-point cannot be opened,

Re: [Freesurfer] Longitudinal processing with different FS versions

Thanks to both of you. On Mon, Apr 16, 2018 at 12:18 PM, Martin Reuter wrote: > Hi Susanna, > > yes, as you feared, you should rerun the first time point so that all time > points are run by the same version. Edits should be preserved (although > maybe more or

Re: [Freesurfer] Longitudinal processing with different FS versions

Hi Susanna, yes, as you feared, you should rerun the first time point so that all time points are run by the same version. Edits should be preserved (although maybe more or probably less edits would be necessary). And it is really a bad idea to compare across groups where the groups where

Re: [Freesurfer] Longitudinal processing with different FS versions

Susanna carino!! On Fri, Apr 13, 2018 at 10:21 AM, Susanna Carmona Cañabate < susannacarm...@gmail.com> wrote: > Dear Freesurfers, > > We are running a longitudinal study with 4 time points. The first two time >

[Freesurfer] Longitudinal processing with different FS versions

Dear Freesurfers, We are running a longitudinal study with 4 time points. The first two time points were processed and edited with the 5.3 version of Freesurfer and the other two time points with FS6. I assume we have to re-run the first two time points with the new versión, but is there a way to

Re: [Freesurfer] Longitudinal processing -qcache ERROR

Hi Lisa, not sure where the problem comes from. But generally one would not do the qcache on the base. Qcache maps results to fsaverage and nobody should ever look at the base results except for debugging purposes. The base is the within-subject template and it is used to initialize the

[Freesurfer] Longitudinal processing -qcache ERROR

Hi everyone, During my PhD, I'm using some longitudinal data and at the setp called "BASE" but when i want to make a qcache processing with the last version of FreeSurfer (i.e. 6.0)(command used : "*recon-all -base template_1-02 -qcache*") it doesn't work. I have a error message : "Error : cannot

[Freesurfer] longitudinal processing - OS re-installation

Dear FreeSurfers, I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study and now I have problems with my machine. It started to work very slowly and it's losing the Internet connection frequently without apparent reason. I believe there's a bug that affects its performance

Re: [Freesurfer] longitudinal processing - OS re-installation

that should be fine Bruce On Wed, 8 Apr 2015, Mihaela Stefan wrote: Dear FreeSurfers, I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study and now I have problems with my machine. It started to work very slowly and it's losing the Internet connection frequently without

Re: [Freesurfer] longitudinal processing - OS re-installation

Thanks! Mihaela On Wed, Apr 8, 2015 at 12:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: that should be fine Bruce On Wed, 8 Apr 2015, Mihaela Stefan wrote: Dear FreeSurfers, I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study and now I have problems with

Re: [Freesurfer] longitudinal processing, template and flags

Thanks Martin for your reply, I am agree with you on point 1. What would you say in the case that we are interested in rates of decline from baseline to 12 months, but besides 6 months follow-up we also have 24 months?. Here I see more conceptual problems. In an hypothetical context of severe

Re: [Freesurfer] longitudinal processing, template and flags

motion artifacts). Best Martin Sent via my smartphone, please excuse brevity. Original message From: Daniel Ferreira dani...@ull.es Date:01/31/2014 3:41 AM (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu,mreu...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal

Re: [Freesurfer] longitudinal processing, template and flags

Hi Daniel, 1. yes. But why not include 6 month in your study if you have those scans??? You will get much more reliable slope estimates with 3 time points compared to 2, so including that time point will not only help for the image processing part, but also in your statistics (you gain

[Freesurfer] longitudinal processing, template and flags

Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing

Re: [Freesurfer] Longitudinal Processing Pipeline

Hi David, in newer versions (not sure exactly when I added this) you can pass -addtp to the -long run. That will add the time point to the study without re-running the base. However this will probably introduce a processing bias as this time point will be treated differently from the other

[Freesurfer] Longitudinal Processing Pipeline

Question regarding longitudinal processing pipeline. Is there a way to force the -long procedure to use an individual base template for a time point not used to create the base in the first place? David F. Tate, Ph.D. ___ Freesurfer mailing list

[Freesurfer] Longitudinal processing - Surface area

Dear all, I am interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical patients. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering

[Freesurfer] longitudinal processing versioning

Hi guys, We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet. I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3. I see two possible

Re: [Freesurfer] Longitudinal processing

Hi Jon, I am also confused about this whole discussion. It seems from what you said earlier that at some point you have been able to run freesurfer on your images. You did not use the -i flag back then, but somehow managed to get from the original dicom (via nifti, via some mri_convert

Re: [Freesurfer] longitudinal processing versioning

Hi Michael, I think you should be fine with option 1. Just make sure that all cross are run with the same version (5.1). It is a little more complicated to keep track of things, but there should be no bias. That way you don't have to worry about edits. If you only have very few edits, I

[Freesurfer] Longitudinal processing

As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s subjID for the second and third steps of the workflow. jon ___ Freesurfer mailing list

Re: [Freesurfer] Longitudinal processing

In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running? On Mon, 8 Jul 2013, Jonathan Holt wrote: As I'm having trouble importing nifti files

Re: [Freesurfer] Longitudinal processing

Allison I'm running the followingrecon-all -all -s subjID -i path/to/niftiattatched is the error recon logI've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've

Re: [Freesurfer] Longitudinal processing

I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison On Mon, 8 Jul 2013, Jonathan Holt wrote: Allison I'm running the following recon-all -all -s subjID -i

Re: [Freesurfer] Longitudinal Processing Error

Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whats...@umich.edu wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: No, it's not nifti, that should work. Can you send me your log file and the command you issued.

Re: [Freesurfer] Longitudinal Processing Error

and the command nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt whats...@umich.edu wrote: Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whats...@umich.edu wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31

[Freesurfer] Longitudinal Processing Error

Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0. threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates

Re: [Freesurfer] Longitudinal Processing Error

Hi Jon have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote: Log file indicates manual talairach alignment may be necessary.  ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.

Re: [Freesurfer] Longitudinal Processing Error

I have tried to inspect the tal xfms that were created in the brief time this string was running recon-all -all -s tpNid -i path_to_tpN_dcm while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty. upon further

Re: [Freesurfer] Longitudinal Processing Error

Martin, I did find that info and tried to follow the instructions, but you'll see based on my last message the talairach files didn't seem to contain anything? On Mon, Jul 1, 2013 at 2:29 PM, Jonathan Holt whats...@umich.edu wrote: I have tried to inspect the tal xfms that were created in

Re: [Freesurfer] Longitudinal Processing Error

Hi Jon, are you passing your images? tpNid is a placeholder for the id of your subject+time point, for example it could be jon_01 the path_to_tpN_dcm needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using).

Re: [Freesurfer] Longitudinal Processing Error

Hi Jon, this is not really a longitudinal problem. You can look at this tutorial on how to check/fix bad talairach: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview Best, Martin On 07/01/2013 01:03 PM, Bruce Fischl wrote: Hi Jon have you visually inspected the

Re: [Freesurfer] Longitudinal Processing Error

Martin, definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue? jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote: Hi Jon, are you passing your images? tpNid is a placeholder for

Re: [Freesurfer] Longitudinal Processing Error

No, it's not nifti, that should work. Can you send me your log file and the command you issued. Thanks, Martin On 07/01/2013 03:13 PM, Jonathan Holt wrote: Martin, definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's

Re: [Freesurfer] Longitudinal processing

Hi Linn, do you mean the brain mask in the cross sectional runs gets worse after you run the longitudinal steps (base and long)? That is not really possible, as these steps don't touch the cross data (only read from it). If you mean that the brain mask in the long looks worse than in the cross

Re: [Freesurfer] longitudinal processing

Hi Linn, did you ever solve this? you need to specify a name for the base and the tp1id and tp2id are placeholders for the id's of the corresponding 2 cross sectional time points. Don't typ;e the '...' So for example: recon-all -base linn-base -tp linn1 -tp linn2 -all linn1 and linn2

Re: [Freesurfer] Longitudinal processing error

Hi Sabin, what was the recon-all command you used for this? Thanks, Martin On 02/05/2013 09:51 AM, Sabin Khadka wrote: Hi all, I am running longitudinal processing and it keeps on crashing with no error message whatsoever in middle of one or the other processing steps. I am not sure if

Re: [Freesurfer] longitudinal processing of one timepoint

Hi Luigi, 1 is the right way of calling it. 2 will have a negative effect in the sense that it takes the same image twice and then creates the mid-space at the same location, so 2 could be biased. 1 is creating an artifical mid-space and makes sure the image gets mapped there. Best, Martin

[Freesurfer] longitudinal processing of one timepoint

Dear FreeSurfer experts, I know that it is possible to submit data with only one timepoint into the longitudinal stream with FreeSurfer 5.2. My question is, what is the exact command? is it: 1) recon-all -base templateid -tp tp1id -all or 2) recon-all -base templateid -tp tp1id -tp tp1id -allI

[Freesurfer] longitudinal processing with -FLAIRpial

Dear Freesurfer Ninjas, I have been playing around with the new beta version, and am very interested in the -FLAIRpial option. I have been using this successfully on cross-sectional runs, but would like to extend it to cross sectional runs. I have played around with trying to get this to work,

Re: [Freesurfer] longitudinal processing with -FLAIRpial

Hi Charles, the FLAIRpial is a recent addition and has only been added to the cross sectional stream so far. I can take a look at porting this to the longitudinal stream but probably not for 5.2. Best, Martin On Feb 7, 2013, at 7:23 AM, Charles Malpas c.mal...@student.unimelb.edu.au wrote:

[Freesurfer] longitudinal processing

Dear Freesurfer experts, I just tried creating the -base for longitudinal processing on two time points using recon-all -base templateID -tp tp1id -tp tp2id ... -all After doing this, I received no error messages and a third folder named after the template name I had given it it was present

[Freesurfer] longitudinal processing

Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the normal recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a

[Freesurfer] longitudinal processing

Sorry, another question about longitudinal processing; just realized that my institution has been using version 5.0, so all the cross sectional processing has been done with this version, is it ok to go ahead and do base and long with version 5.1 once I have managed to get this installed?

Re: [Freesurfer] longitudinal processing

Hi Catherine, yes, the first step is independent (cross sectional) processing of all time points (normal recon-all). We usually do not recommend to mix versions. But the 5.1 longitudinal stream has been designed in a way that it can take the cross sectional data from 5.0. So it is possible.

Re: [Freesurfer] longitudinal processing

Hi Catherine, with edits I think it is best to re-use the 5.0 cross data for the longitudinal processing. Also conceptually there is a difference between longitudinal processing and longitudinal statistical analysis. The image processing will reduce variability of your measures and even if you

[Freesurfer] Longitudinal processing

Hello, I am using the longitudinal processing stream to analyze a data set. I have two questions: 1: We are expecting there to be significant changes in the volume of certain structures and gray matter between time point 1 and 2. We wanted to make sure the longitudinal stream is still

Re: [Freesurfer] Longitudinal processing

Hi Allison, with very large changes across time, the longitudinal stream can fail or may need more manual intervention (edits). We have run it successfully on Huntington's Disease patients with large changes and many time points. The only way to find out if it works on your data is to run it. I

[Freesurfer] Longitudinal processing 3 time point error

Hello, I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors. Please see the output below: Resolution: 0 S( 256 256 256 ) T( 256 256 256 )

Re: [Freesurfer] Longitudinal processing 3 time point error

Hi Jamie, Three time points should not be a memory problem. You can try to run this on linux. Or you can get a new binary for the mac from our development version with several improvements and fixes including a memory leak that might have caused this. Let me know (you may want to rerun all your

Re: [Freesurfer] Longitudinal processing 3 time point error

Hi Martin, Thanks for the suggestion! I'm afraid that I'm limited to the Mac - how can I get the new binary? Thanks, Jamie -- Jamie Kawadler PhD student Imaging Biophysics Unit UCL Institute of Child Health 30 Guilford Street London WC1N 1EH 02079052192

[Freesurfer] longitudinal processing error

Hello, I am running longitudinal stream processing on mprage scans of some subjects who have been scanned multiple times using the same sequence with 32 NOVA channels on GE scanner. For most subjects the base run exited without error, however for few error was reported in the runs. The error

[Freesurfer] longitudinal processing (base-tps error)

HI all, I ran longitudinal processing with reco-all -base templateID -tp MRI_T1 -tp MRI_T2 -all but in base-tps file of template ID I found the subject ID of MRI_T1 twice instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able to do for MRI_T1 but could not do the same for

Re: [Freesurfer] longitudinal processing (base-tps error)

Hi Sabin, If the base-tps file contains a time point twice, that indicates that it has been created by passing the same time point twice, probably a typo. You need to remove the base and tp1.long and run again with the correct parameters. Best Martin On Apr 11, 2012, at 9:31, Sabin Khadka

[Freesurfer] longitudinal processing for lgi comparison

Hi all, Is there a longitudinal processing stream to compare local gyrification index (lgi) across two time points. -Sabin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] longitudinal processing for lgi comparison

No, should be very similar across time, or not? But the surfaces will be more reliable after longitudinal processing, can't you just run the lgi analysis on the tp?.long.base directories? Best, Martin On Wed, 2012-04-11 at 15:49 -0400, Sabin Khadka wrote: Hi all, Is there a longitudinal

Re: [Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Hi Mark, I talked to Allison and you should be able to rerun 5.1 on top of 5.0 but do NOT use the -clean flag (as it will delete your edits). Just make sure you make a backup copy of your data before doing this. Another thing: manual edits to the brainmask are treated differently from most

[Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Dear Everyone, First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream. I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years

Re: [Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Hi Mark, So the first thing is you absolutely need to re-run you 1st year data with 5.1 The reason is that you will introduce potential bias by running the different time points with different software (consistently). As a side note: The same is basically true when they do software updates on

[Freesurfer] longitudinal processing edema from lesion causing skewed registration

Hi, I am doing longitudinal processing of multiple subjects (each with 3 sessions) post stroke. However, some of the lesions are so extensive in the first session that they cause edema and push the brain midline. This greatly affects the pial surface on the lesioned hemishpere after

[Freesurfer] longitudinal processing of volumetry of same patient different dates...

Hi: How can I do a comparisson between the volumetry of the same patient but with MRI of different dates (longitudinal study) ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Longitudinal processing

Dear Martin and Douglas, I had the same question as Sandra and searching the mailing list I found your answers. However, it is not still clear for me which data I need to use for the mris_calc (reply from Martin) or mris_preproc (reply from Douglas), i.e. (tp1 tp2) or (tp1.long.template_id

Re: [Freesurfer] Longitudinal processing

Hi always use the data from tp.long.base , they are less variable and more accurate than the cross sectional results. (that is why you tun the long stream at all). Best Martin On 27.10.2010, at 09:13, sima chalavi sima.chal...@gmail.com wrote: Dear Martin and Douglas, I had the same

[Freesurfer] longitudinal processing

Hi, I am planing to process a longitudinal dataset with 3 timepoints. Is it worthy to begin already the cross-sectional processing with version 5.0 and then wait version 5.1 to continue from the template part. Or would you advice me to wait the release of version 5.1 for the entire

Re: [Freesurfer] longitudinal processing

Hi Marie, wait for 5.1. Martin has made some significant improvements. cheers Bruce On Mon, 18 Oct 2010, Marie Schaer wrote: Hi, I am planing to process a longitudinal dataset with 3 timepoints. Is it worthy to begin already the cross-sectional processing with version 5.0 and then wait

Re: [Freesurfer] longitudinal processing

Hi Bruce, What's the ETA for 5.1? thanks - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Mon, Oct 18,

Re: [Freesurfer] longitudinal processing

I'll leave that for Martin Bruce On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote: Hi Bruce, What's the ETA for 5.1? thanks - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter

Re: [Freesurfer] longitudinal processing

So if I understand correctly, you would not recommend getting a jump start on cross-sectional processing and editing under 5.0, rerunning everything under 5.1 once it comes out, then run (for the first time) longitudinal under 5.1? Are there going to be some incompatibilities with 5.1, where

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