Re: [Freesurfer] Longitudinal stream bug ?

messed things up, maybe. Have a nice day! Lauri From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lauri Tuominen Sent: November-03-22 2:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal stream bug ? CAUTION: External Mail. Do

[Freesurfer] Longitudinal stream bug ?

External Email - Use Caution Hi FreeSurfer Developers, I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS, freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5. I use the following command: long_mris_slopes --qdec ../tables/long.all.table.dat \

Re: [Freesurfer] Longitudinal Stream Error

Best, Andrew *From:* Greve, Douglas N.,Ph.D. *Sent:* Wednesday, February 16, 2022 10:37 AM *To:* Willett, Andrew Sunday ; Freesurfer support list *Subject:* Re: [Freesurfer] Longitudinal Stream Error Does that file exist? ps. Please remember to post to the list. Thanks!

Re: [Freesurfer] Longitudinal Stream Error

? Best, Andrew From: Greve, Douglas N.,Ph.D. Sent: Wednesday, February 16, 2022 10:37 AM To: Willett, Andrew Sunday ; Freesurfer support list Subject: Re: [Freesurfer] Longitudinal Stream Error Does that file exist? ps. Please remember to post to the list. Thanks! On

Re: [Freesurfer] Longitudinal Stream Error

Does that file exist? ps. Please remember to post to the list. Thanks! On 2/15/2022 5:06 PM, Willett, Andrew Sunday wrote: Dr. Greve, I hope this email finds you well. Thank you for your response to my listed question on Freesurfer’s mailing list on Sunday! I wanted to reach out to followup

Re: [Freesurfer] Longitudinal Stream Error

h the community's conventions. I am encountering errors when processing Freesurfer longitudinal stream (Freesurfer v6.0). Cross-sectional streams proceeded and completed without error, but base template creation and all following longitudinal steps failed. *I created a txt script for the bas

[Freesurfer] Longitudinal Stream Error

This is my first time seeking support here so I apologize if I am not familiar with the community's conventions. I am encountering errors when processing Freesurfer longitudinal stream (Freesurfer v6.0). Cross-sectional streams proceeded and completed without error, but base template cre

Re: [Freesurfer] Freesurfer longitudinal stream error

Try running it without the -parallel flag. If you want to use multiple cores, then add -threads N (N= number of cores) On 7/6/2021 4:29 AM, Susanne Gellißen wrote:     External Email - Use Caution Dear FreeSurfer Developers, I am processing MRI data using the freesurfer processing stream w

Re: [Freesurfer] Longitudinal Stream Problem

w to avoid doing this in the future? Thanks, Laura *From: *"Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Tuesday, June 23, 2020 at 10:18 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] Longitudinal Stream Problem If you run t

Re: [Freesurfer] Longitudinal Stream Problem

suggestions for how this happened and how to avoid doing this in the future? Thanks, Laura From: "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, June 23, 2020 at 10:18 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Longitudinal St

Re: [Freesurfer] Longitudinal Stream Problem

<mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to di

Re: [Freesurfer] Longitudinal Stream Problem

quot;freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Longitudinal Stream Problem It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When

Re: [Freesurfer] Longitudinal Stream Problem

mgh.harvard.edu" Subject: Re: [Freesurfer] Longitudinal Stream Problem OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into. On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E]

Re: [Freesurfer] Longitudinal Stream Problem

y, June 19, 2020 at 6:10 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] Longitudinal Stream Problem OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig

Re: [Freesurfer] Longitudinal Stream Problem

*Freesurfer support list *Date: *Thursday, June 18, 2020 at 9:12 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] Longitudinal Stream Problem I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

Re: [Freesurfer] Longitudinal Stream Problem

. danielianbase.tar.gz. Thanks, Laura From: "Douglas N. Greve" Reply-To: Freesurfer support list Date: Thursday, June 18, 2020 at 9:12 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Longitudinal Stream Problem I have not seen that file appear. Can you re-upload it? O

Re: [Freesurfer] Longitudinal Stream Problem

! Laura *From: *"Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Tuesday, June 16, 2020 at 10:10 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] Longitudinal Stream Problem I have your data, but it does not have the base image. Can you upload

Re: [Freesurfer] Longitudinal Stream Problem

0:10 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Longitudinal Stream Problem I have your data, but it does not have the base image. Can you upload that as well? On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote: External Email - Use Caution Hi Douglas

Re: [Freesurfer] Longitudinal Stream Problem

.  Upper cortical and frontal regions are unaffected. Thanks for your help! Laura *From: *"Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] Longitudinal Str

Re: [Freesurfer] Longitudinal Stream Problem

er support list Date: Friday, June 12, 2020 at 10:35 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Longitudinal Stream Problem Hard to tell from just that view. Was there a lot of brain change with that time point? Or was there an MRI artifact? If no to both, then you

Re: [Freesurfer] Longitudinal Stream Problem

Hard to tell from just that view. Was there a lot of brain change with that time point? Or was there an MRI artifact? If no to both, then you can upload all the cross, the base, and that one long. Follow instructions below (you can make one tarball for all subjects) From the linux command line

Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

AM To: Freesurfer support list Cc: Douglas Merkitch Subject: Re: [Freesurfer] Longitudinal stream finalsurfs misalignment? Hi Doug, probably something went wrong during the editing. E.g maybe you edited files in the cross sectional or base directories and copied/saved these to the longitudinals or vice-

Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

Hi Doug, probably something went wrong during the editing. E.g maybe you edited files in the cross sectional or base directories and copied/saved these to the longitudinals or vice-verca. There should be no mis-alignments. I would recommend this: 1. run one such subjects without edits through

[Freesurfer] Longitudinal stream finalsurfs misalignment?

External Email - Use Caution Hey all, I have a group of subjects with 2 time points that I've run thru the longitudinal processing stream. All goes OK until I run the recon-all -long and the resulting .long. subject dirs have the finalsurfs misaligned (i.e. one subject has the

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, no, sorry. Maybe you can find a local biostatistician who knows. A slope estimate with less time points is more uncertain than one with more time points (obviously). Also a slope estimate with time points on a line is more certain than one with time points values all over the place

Re: [Freesurfer] Longitudinal Stream - LONG step

> From: freesurfer-boun...@nmr.mgh.harvard.edu mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. vard.edu> > Sent: Thursday, December 6, 2018 3:46:27 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Longitudinal Stream - LONG step >   > Does the orig.mgz file look

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, I come back on my previous question concerning survival bias in LME. Do you have an advice ? Best, Matthieu > Le 19 oct. 2018 à 16:30, Matthieu Vanhoutte a > écrit : > > Hi Martin, > > Do you mean that high attrition (less time points

Re: [Freesurfer] Longitudinal Stream - LONG step

PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream - LONG step Does the orig.mgz file look ok? On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote: > > > Hello FreeSurfer Developers, > > I'm attempting to run the longitudinal stream, but in

Re: [Freesurfer] Longitudinal Stream - LONG step

Does the orig.mgz file look ok? On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote: > > > Hello FreeSurfer Developers, > > I'm attempting to run the longitudinal stream, but in the [LONG] step > of one time-point of on of my subjects, I have the following error: > > MRInormInit(): > INF

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, Do you mean that high attrition (less time points with time) would induce more variance on the slope estimates but this effect would be compensated by LME modeling ? Would there be proportion of early drop outs to respect in order to compen

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, in LME it is OK if subjects have differently many time points in general. You need to ask a statistician about your specific setup, but I think it might be OK (basically less time points, means more variance on the slope estimates, but that should be considered in LME). But I am not

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, Thanks for your answer. I actually compare neurospychological scores at baseline between drop-out subjects and subjects with full time-points. If I ever find that drop-out subjects are more severely affected than the subjects with full time

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, 1) survival analysis is typically used if you want to detect if the time to an event is longer in one group vs the other (e.g. one group gets placebo the other drug and we want to know if recurrence is later in the drug group). Not sure this is what you need. The nice thing is, it ca

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, It's been a long time since this discussion but I return on this from now... The problem is that I followed longitudinal images of two groups where I had mainly missing time points at the end. Than you suggested: *If you have mainly missing

Re: [Freesurfer] Longitudinal stream for cross-sectional analysis?

Hi K, I would recommend to use the data from the longitudinal directories also for the cross sectional analysis. That data will be less noisy than from independent processing (which is what you also find). Since the longitudinal stream goes through many different processing steps than the re

[Freesurfer] Longitudinal stream for cross-sectional analysis?

Good morning Martin et al., We are analyzing cortex and subcortical volumes for 2 groups with (mostly) 2 scans per participant. We want to report longitudinal findings as well as cross-sectional group differences at each of the 2 time points. For the time point 1 and time point 2 analyses, does it

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

Hi Matthieu, sorry for the late reply. Yes you should be able to do that (as long as it is consistent for all subjects). Test it for one subject and then run the rest. Best, Martin > On 30 Jan 2017, at 16:51, Matthieu Vanhoutte > wrote: > > Dear experts, > > Does anybody could answer my la

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

Dear Antonin, Thanks for the advices. Best, Matthieu > Le 30 janv. 2017 à 17:45, Antonin Skoch a écrit : > > Dear Matthieu, > > your issue is discussed here: > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html > > and indirectly also here: > http://www.mail-archive.

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

Dear Matthieu, your issue is discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html and indirectly also here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg5.html I think that with V6.0 you maybe could get slightly better results (some bugs

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

Dear experts, Does anybody could answer my last request ? Best, Matthieu 2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte : > Dear FS's experts, > > I have run all my cross with v5.3 and hesitate to run all longitudinal > process with v6. Does that make sense and will improve the process or would >

[Freesurfer] Longitudinal stream with v6 but cross with v5.3

Dear FS's experts, I have run all my cross with v5.3 and hesitate to run all longitudinal process with v6. Does that make sense and will improve the process or would it be risky to do this ? Many thanks for your lights ! Best regards, Matthieu ___ Free

Re: [Freesurfer] longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?

Hi Antonin, I see. The problem with the intersection would be that it could be zero in spite of several edits that move around. Still would be better than nothing. Feel free to test that (e.g. you can load that in matlab, intersect and then apply to the wm from base to see if it helps). Let me

Re: [Freesurfer] longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?

Dear Martin, thanks for the feedback. We had to edit cross due to the fact that 1. our dataset is involved also in cross-sectional studies 2. we are continuously acquiring timepoints but want to do some analyses with data we already have Therefore only editing the base was not an option for us.

Re: [Freesurfer] longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?

Hi Antonin, in most cases it should be sufficient to only edit wm.mgz in the base, instead of editing all time points. This is a big time saving especially if you have many time points. I don’t think merging edits from cross will work well, as there could be atrophy and lots of non-linear def

[Freesurfer] longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?

Dear experts, I am currently starting longitudinal analysis of data I previously corrected in cross-sectional stream (FreeSurfer v5.3). The analysis comprises quite large number of subjects - approx 150 subjects, each scanned twice. All subjects are already inspected and errors corrected in cros

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, 1. yes, LME needs to be done first so that values can be sampled from the fitted model for the SA. 2. yes, I was talking about gradient non-linearities etc that could be in the image from the acquisition. We currently don’t use non-linear registration across time points (only rigi

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Dear FS's experts, Could you answer me about questions from below inline precedent mail ? Best regards, Matthieu 2016-11-22 21:31 GMT+01:00 Matthieu Vanhoutte : > Hi Martin, > > Please see inline below: > > Le 22 nov. 2016 à 17:04, Martin Reuter a > écrit : > > Hi Matthieu, > (also inline) >

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Martin, Please see inline below: > Le 22 nov. 2016 à 17:04, Martin Reuter a écrit : > > Hi Matthieu, > (also inline) > >> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte >> mailto:matthieuvanhou...@gmail.com>> wrote: >> >> Hi Martin, >> >> Thanks for replying. Please see inline below:

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, (also inline) > On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte > wrote: > > Hi Martin, > > Thanks for replying. Please see inline below: > >> Le 21 nov. 2016 à 20:26, Martin Reuter > > a écrit : >> >> Hi Matthieu, >> >> a few quick answer

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Martin, Thanks for replying. Please see inline below: > Le 21 nov. 2016 à 20:26, Martin Reuter a écrit : > > Hi Matthieu, > > a few quick answers. Maybe Jorge knows more. > Generally number of subjects / time points etc. cannot be specified > generally. All depends on how noisy your data

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, a few quick answers. Maybe Jorge knows more. Generally number of subjects / time points etc. cannot be specified generally. All depends on how noisy your data is and how large the effect is that you expect to detect. You can do a power analysis in order to figure out how many sub

[Freesurfer] Longitudinal stream : LME and limits of model

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would mis

[Freesurfer] Longitudinal Stream on HCP Data

Aww thank you for clarifying Michael. I definitely misread Matthew's post. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] Longitudinal Stream on HCP Data

ist Date: Tuesday, November 8, 2016 at 9:15 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Longitudinal Stream on HCP Data Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into the FreeSurfer processing stream. Matthew Glas

Re: [Freesurfer] Longitudinal Stream on HCP Data

Hi Tim for a long time we have had a post-processing routine that uses T2 or FLAIR images for post-hoc surface deformation. This existed long before the HCP, although I did tweak it for the Wash U HCP acquisition to make it perform better. The upcoming v6 has the overall best performance with t

Re: [Freesurfer] Longitudinal Stream on HCP Data

November 8, 2016 at 9:15 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Longitudinal Stream on HCP Data Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP d

[Freesurfer] Longitudinal Stream on HCP Data

Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into the FreeSurfer processing stream. Matthew Glasser mentioned in a post on the HCP mailing list about a month back that this is being actively worked on by FreeSurfer: http://www.mail-archive.co

[Freesurfer] Longitudinal Stream: Recon-all and Base template

Hello All, I am planning to run the longitudinal stream on my data set and I have a few questions: 1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individua

Re: [Freesurfer] Longitudinal stream - Single time-point subjects

Hi Joann, to assert that single time point results are comparable to results from subjects with more than 1 time point, the single time point needs to be send through a fake/artificial longitudinal stream. It will thus undergo the same processing steps (including interpolation to the template)

[Freesurfer] Longitudinal stream - Single time-point subjects

Dear All, When I was inspecting the longitudinal data for single time-point subjects, it differed quite a bit from the cross section. Can someone please explain why this is/could be so? How is the template generated for a single time-point subject? I'm using FS 5.3. I did my edits at the cross se

Re: [Freesurfer] propagating edits across in the FreeSurfer longitudinal stream

Hi Jessica, if you only have little changes across longitudinal time points, CP edits can be transferred from the base (instead of the cross runs) into specific longitudinal runs by specifying the -uselongbasectrlvol when running the -long. See https://surfer.nmr.mgh.harvard.edu/fswiki/Longit

[Freesurfer] propagating edits across in the FreeSurfer longitudinal stream

Dear FS Community, I am currently using FreeSurfer 5.3 to conduct a longitudinal analysis of atrophy in Semantic Dementia. Because of the profound temporal pole atrophy in these patients, I have been making a lot of manual edits (mostly control points and wm edits) to the baseline scan, and the

Re: [Freesurfer] longitudinal stream: adding a time point

lumes marked on the old 2 > time-points base to a new 3 time-points base? > Have a nice week. > > Best, > ruthi > > Message: 3 > Date: Thu, 8 Oct 2015 20:18:47 +0200 > From: Martin Reuter <mailto:mreu...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesu

Re: [Freesurfer] longitudinal stream: adding a time point

Hi Ruthi, it is possible to add time points retrospectively without re-creating the base. However this will likely induce a processing bias, as the 3rd time point is treated differently from the first two. How big that is going to be nobody knows (it depends on your data and on the number of ti

[Freesurfer] longitudinal stream: adding a time point

Dear all, We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points)

[Freesurfer] Longitudinal stream

Dear Freesurfer experts, I would like to perform a longitudinal analysis with freesurfer 5.1 and I have some questions regarding the whole processing stream. I have BL and 1Y follow-up from all patients (110), and moreover I have 2Y follow-up from only some patients (more or less 50). Do you re

Re: [Freesurfer] longitudinal stream percentage change

By the way, smoothing can remove the thickening (if there is only a little and mainly thinning ). Best, Martin On 08/05/2013 02:18 PM, Martin Reuter wrote: > Hi Bastian, > > actually (see other mail today) it computes percent thickening per year > as it is the slope of the linear fit into the me

Re: [Freesurfer] longitudinal stream percentage change

Hi Bastian, actually (see other mail today) it computes percent thickening per year as it is the slope of the linear fit into the measurements (thickness with respect to age or time). If the slope is negative, there is thinning. The results (within subject and on fsaverage) have signs so they a

[Freesurfer] longitudinal stream percentage change

Dear freesurfer-experts, I have successfully done a longitudinal analysis on cortical thickness changes over 2 timepoints (0 and 1 year). My question is: If I look at the -individual- overlays of perc. change (i.e. pc1fit), only positive values are shown. whereas at the -fsaverage- view, positve

Re: [Freesurfer] longitudinal stream - template

Hi Yolanda, if you want to simulate a study where one obtains 2 time points (6 months apart) or 2 time points (12 months apart) and then compare the results, you would need to run these two independently through free surfers longitudinal stream (one time including 0 and 6 month, the other time

Re: [Freesurfer] longitudinal stream - template

Hi Martin, Thank you for your answer, but my idea was to compare the atrophy rates when using scans at 6 months (0 - 6 months) and scans at 12 months (0 - 12 months). If my templates are built with more time points, the results will be biased, right? Regards, Yolanda 2013/3/18 Martin Reuter : >

Re: [Freesurfer] longitudinal stream - template

Hi Yolanda, actually it is advantageous if the template is build from more time points. You don't need to process the images again, just do your statistical analysis with the time points you are interested in. But: why restrict the statistics to a subset of the data? If you are interested in y

[Freesurfer] longitudinal stream - template

Dear FreeSurfer experts, I have run a longitudinal study considering multiple time points (7 scans/subject on average) with FS 5.1. However, I am interested in the percent changes between two time points only (between 0 and 6 months and between 0 and 1 year). Should I run the longitudinal stream f

Re: [Freesurfer] Longitudinal stream with special options

Dear Martin Thanks a lot for your comment Cheers Jürgen On [DATE], "Martin Reuter" <[ADDRESS]> wrote: > Hi Jürgen, I have never tested these flags in the long stream. It should not > hurt to pass them in the base and in the long. In the long, the talairach from > the base is used anyway, so t

Re: [Freesurfer] Longitudinal stream with special options

Hi Jürgen, I have never tested these flags in the long stream. It should not hurt to pass them in the base and in the long. In the long, the talairach from the base is used anyway, so the -use-mritotal should have no effect there, but the -nuintens... should. Best, Martin On Sat, 2013-01-05 at 0

[Freesurfer] Longitudinal stream with special options

Dear FS experts I run the cross sectional step (step 1) for a longitudinal analysis with the following options: recon-all -s $s -all -talairach -use-mritotal -nuintensitycor-3T I would like to know whether I have also use these options in the creation of the base template (step 2) and in the lon

Re: [Freesurfer] Longitudinal Stream...

Hi Gonzalo, On Fri, 2010-03-05 at 16:47 -0300, Gonzalo Rojas Costa wrote: > Hi: > > I processed a Longitudinal Stream between two MRIs of same patient taken in > different dates... I used the following commands: > > i) recon-all -all -s , recon-all -all -s > ii) recon-all -base -tp -tp -al

[Freesurfer] Longitudinal Stream...

Hi: I processed a Longitudinal Stream between two MRIs of same patient taken in different dates... I used the following commands: i) recon-all -all -s , recon-all -all -s ii) recon-all -base -tp -tp -all iii) recon-all -long -all Which information was stored in the .long. folder ?...

Re: [Freesurfer] longitudinal stream command line arguments

either can be used. -tp is just short for -base-tp On Fri, 2009-06-19 at 10:27 -0500, Dabbs (Kevin) wrote: > > > The command line arguments for creating the base subject in Freesurfer > Ver. 4.4 longitudinal stream do not agree between the Wiki and recon- > all --help. > > On the Wiki support

Re: [Freesurfer] longitudinal stream command line arguments

I looked at the revision history of the wiki and it shows a change to "-tp" so I believe that is the correct one to use. However, I was able to run both versions without error. When Nick returns, he can confirm but I think you should be fine using -tp. Allison -- On Fri, 19 Jun 2009, Dabbs (

[Freesurfer] longitudinal stream command line arguments

The command line arguments for creating the base subject in Freesurfer Ver. 4.4 longitudinal stream do not agree between the Wiki and recon-all --help. On the Wiki support page, 2. create the base template and process it cross sectionally: recon-all -base -tp -tp ... -all >From recon-all

[Freesurfer] longitudinal stream

Hi All, We have recently tracked down a bias in the longitudinal processing stream. We believe we have a fix for the problem, but it will take us a bit of time to get it working and well-tested. We'll keep you posted as to when we will have a new version. Feel free to email me if you have any