[Freesurfer] longitudinal analysis – Is correcting the Base enough?

External Email - Use Caution Dear FreeSurfer Team, I am working with a longitudinal design (before and after treatment), and based on the website's recommendation (

[Freesurfer] Longitudinal analysis: error "no data found in mri/orig"

External Email - Use Caution Hello FreeSurfer developers, I have created the "subjects" folder, and I included a large sample of participants inside the folder. I have performed transversal analysis (CROSS), all successfully. I am now performing a longitudinal analysis with the

Re: [Freesurfer] Longitudinal Analysis for functional connectivity data?

gt; > Best, > > Tracy > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Tuesday, November 5, 2019 3:22 PM > *To:* freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] Longitudinal Analysis for functional connectivity data?

of Greve, Douglas N.,Ph.D. Sent: Tuesday, November 5, 2019 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Analysis for functional connectivity data? You can use the longitudinal anatomical analysis to inform the functional analysis across time

Re: [Freesurfer] Longitudinal Analysis for functional connectivity data?

You can use the longitudinal anatomical analysis to inform the functional analysis across time, but there is not a longitudinal functional analysis per se. On 11/5/2019 2:15 PM, Barbour, Tracy,M.D. wrote: Hello Freesurfer experts! I see that there is a longitudinal processing pipeline for

[Freesurfer] Longitudinal Analysis for functional connectivity data?

Hello Freesurfer experts! I see that there is a longitudinal processing pipeline for volume/cortical thickness. I was wondering if the same pipleline could be used for resting state functional connectivity based analysis? Best, Tracy ___ Freesurfer

Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions

Hi Kody, scanner effects across vendor could be larger than disease effects. You can attempt an analysis but you will have a tough time to publish it given these differences and no real way to control for scanner effects. Maybe scan 5-10 people on all these scanners and show that scanner

Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions

External Email - Use Caution Hi Kody - In my view, its best not to do group comparisons using data from scanners of different field strengths. Even between scanners of same magnetic field strength (e,g., 3T Siemens and 3T GE), there are large variations that need to be covaried

Re: [Freesurfer] FreeSurfer Longitudinal analysis

yes, it will be much more sensitive/specific. Note that you have to run the cross-sectional first in any case though cheers Bruce On Mon, 11 Jun 2018, Глеб Макшаков wrote: External Email - Use Caution Dear all, I’ve just started using FreeSurfer and I need your advice. I

[Freesurfer] FreeSurfer Longitudinal analysis

External Email - Use Caution Dear all, I’ve just started using FreeSurfer and I need your advice. I have two series of images made 1 year apart from each other. Is it correct to use a Longitudinal Stream to process those images instead of simple cross-sectional counting and

[Freesurfer] Longitudinal analysis of multiple scanner acquisitions

External Email - Use Caution Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Lea, sorry for the late reply, just in case this is still of interest: 1. It is possible to process all cross data with 5.3 and then base and long with 6.0. As long as you do the same for all subjects it should be fine, just don't mix across subjects. Also depending on the size if only

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Martin, thank you so much for your detailed answer. I will see how we can implement these modifications. Just two quick follow up questions: 1) I have half of the data already processed with the CROSS step using FS 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Could be all that is needed is to add this: mycluster ='sbatch --mail-type=FAIL --mail-user= -N 1 --ntasks-per-node=10 --partition=work --export=ALL -o /%(username)s/logs/job.%J.out- e /%(username)/logs/job.%J.err "%(command)s"' and comment the lines # if queue is not None ... # pbcmd =

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

hi lea, in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer and then submit each subject's longitudinal pipeline as a separate slurm job. cheers, satra On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter wrote:

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Hi Lea, I wrote that script to simplify processing on our cluster which uses qsub PBS for submission. I have never used SLURM so far. There is two functions that you (or someone who knows this stuff) would need to modify: def submit and def wait_jobs The submit procedure basically

[Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Dear FS experts, I am trying to do a longitudinal analysis of around 250 adolescents with up to 4 data points each. Given the complexity I would like to use the long_submit_jobs script which is described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts Unfourtunately it does

Re: [Freesurfer] Longitudinal analysis using data with only two timepoints and LME

Hi Christoph, 1) I would use only intercept as random effect. I like to keep the model simple and - as you say - there is only a max of 2 time points. If you like you can do a model comparison (see wiki page) to compare the two models. 2) I would use the exact time in years (as float with

[Freesurfer] Longitudinal analysis using data with only two timepoints and LME

Dear FreeSurfer community, I have a few questions regarding the usage of the LME matlab tools for longitudinal data analyses, and how to set up the model. We have patients and control data that we want to compare with respect to cortical changes over time (two time points: baseline and

[Freesurfer] longitudinal analysis or cross-sectional anslysis of the subfield of hippocampus

Dear all, I have 2 groups (patients and controls), and I want to analysis the subfields of the hippocampus. Some of the subjects have 2 scans (before treatment and post treatment) and some subjects only have one scan(before treatment). aim 1: I want to compare the subfied volume of the

Re: [Freesurfer] Longitudinal analysis of rates or percent changes

Hi Katarina, if your run it regularly, and then run it including the —generic-time, and get the same result twice, we can conclude that the —generic-time has not effect. You should be fine. Best, Martin > On 14 Feb 2017, at 19:38, Katarina Trojacanec >

Re: [Freesurfer] Longitudinal analysis of rates or percent changes

Hi Martin, Thanks for your reply. I removed the time column from the qdec table (below is some sample content of the new qdec table): fsid fsid-base age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 81.3 y AD M x x x x sc

Re: [Freesurfer] Freesurfer longitudinal analysis accuracy

Hello Gabor, a few quick comments: i) Although we typically aim for maximizing both, accuracy and reproducibility are different things. In a longitudinal study you are often particularly interested in the reproducibility of the findings, in the sense of their repeatability across different

Re: [Freesurfer] Freesurfer longitudinal analysis accuracy

I've found the article "Within-subject template estimation for unbiased longitudinal image analysis" by Reuter et al. It only examines a limited number of structures for the reproducibility of longitudinal Freesurfer. Are there any other paper that examines the cerebellum as well? Any suggestion

[Freesurfer] Freesurfer longitudinal analysis accuracy

Dear all, We've run longitudinal Freesurfer on 30 healthy subjects. We have two subgroups (n=15) and we found a significant longitudinal change in the left and right cerebellar cortex in one of our subgroups. However, this change is very small: mean=0.67% range: -1.61-2.3% for the right

Re: [Freesurfer] Longitudinal analysis

Hi Jaiashre, when switching scanners within a longitudinal study you will see effects that are caused by the scanner (or a scanner / age, scanner /disease, scanner / motion interaction). If the majority of your subjects is scanned on the same scanner for most time points, then you may be able

[Freesurfer] Longitudinal analysis

Hi FreeSurfer Team, We are doing a longitudinal analysis with three time points which are six months apart. The subjects at any time point were scanned on either one of the two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our analysis. Most of the subjects show decrease

Re: [Freesurfer] Longitudinal analysis: creat cluster ROI and extract baseline and followup values

Is the mc-zabs annot based on thickness differences? If so, you can run mri_segstats on the stack from each time point, eg, mri_segstats ---annot fsaverage lh /path/to/mc-zabs.the13sig.ocn.annot --i timepoint1.lh.stack.mgh --avgwf timepoint1.lh.stack.dat --excludeid 0 this will create the .dat

Re: [Freesurfer] Longitudinal analysis: creat cluster ROI and extract baseline and followup values

Dear Martin and Douglas, I created the cluster ROIs (mc-zabs.the13sig.ocn.annot) for the two groups. What is the detailed command line to calculate the baseline and followup cortical thicknesses from the *.long.* directories? Thanks, Yawu On Thu, May 12, 2016 at 9:07 PM, Martin Reuter

Re: [Freesurfer] Longitudinal analysis: creat cluster ROI and extract baseline and followup values

If you used mri_glmfit, then you can use mri_glmfit-sim to create significant clusters. It will create an annotation of the significant clusters, and you can pass that to mri_segstats along with the stack of thickness images to extract the mean thickness in each cluster. On 05/12/2016 04:23

[Freesurfer] Longitudinal analysis: creat cluster ROI and extract baseline and followup values

Hi Freesurfers, I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create

Re: [Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

Dear FS Experts, I have followed the steps for doing a Repeated Measures ANOVA 2x2 in Freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova also following the previous post: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026287.html .

Re: [Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2 {Disarmed}

Thank you very much for your prompt response. However, I am doing the same analysis (with Repeated Measures ANOVA 2x2) in different MRI acquisitions, so I would like to do the same analysis in freesurfer. Could you please help me? Thank you, Best regards, Maria. 2016-02-18 23:22 GMT+01:00

Re: [Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

It will be much easier if you subtract time point 1 from 2 then do a two-group t-test. See https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis On 02/18/2016 05:37 AM, María Díez Cirarda wrote: > Dear FS experts, > > I am trying to do a longitudinal analysis with a Repeated Measures > ANOVA

[Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

Dear FS experts, I am trying to do a longitudinal analysis with a Repeated Measures ANOVA 2x2, with two groups (experimental and control group) and two times (pre and post treatment). First, I have followed the Longitudinal Processing Tutorial: 1) I have 2 acquisitions per subject so, I created

Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}

?     Bests, John    Sent: Saturday, January 30, 2016 at 5:51 AM From: "Martin Reuter" <mreu...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed} Hi Joh

Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}

gt; To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate > Hi John, > > you should check if the number of time points per subject is relatively > random across your two patient groups.

Re: [Freesurfer] Longitudinal analysis--mass univariate

To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate Hi John,   you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s

Re: [Freesurfer] Longitudinal analysis--mass univariate

Hi John, you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3. You can compare the atrophy across these two groups easily with LME. Or you can also test

[Freesurfer] Longitudinal analysis--mass univariate

Hi Dr Martin, I have two groups of patients and one group of controls. The patients scanned multiple times but the number of time points is different between the subjects. The controls have only one time point.   I aim to : 1. I wanted to study the changes in cortical thickness over time in

Re: [Freesurfer] Longitudinal analysis with single timepoint scans

Hi Bronwyn, with FS 5.3 you can run the single-tp images through a 'fake' longitudinal stream. After processing crossectionally simply run the base with only the single time point, and then run the long with that base. This will make the results comparable as the images will go through same

Re: [Freesurfer] Longitudinal analysis with single timepoint scans

Thanks very much Martin. That's perfect. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au

[Freesurfer] Longitudinal analysis with single timepoint scans

Hi Freesurfer Mailing List, We are running a longitudinal analysis (in R) using 2 time points with scans that have been through the Freesurfer longitudinal pipeline. We were also hoping to incorporate individuals with only a single scan into our analysis. Does it make sense to use long images

Re: [Freesurfer] Longitudinal analysis with QDEC

Hi Pawel, your directory naming looks a little weird. What is the subjects directory ? Are all your subjects (all cross, base and long of all subjects) in CT_10? What is BLD013_ is that the name of the base (=subject template)? Did you run the long_mris_slopes command (follow instructions

[Freesurfer] Longitudinal analysis with QDEC

Hello Dear FreeSurfer Developers, Thank You once again for helping me a couple of months ago. Today I came across a new obstacle, as I have been trying to analyse longitudinal material. I have performed all preparation steps and I started performing statistical analysis in Qdec when receiving

Re: [Freesurfer] longitudinal analysis

Hi Martin, Now clear. Thanks. Yawu On Mon, Jul 6, 2015 at 8:50 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Yawu, no, that would be the simple average. Temporal average is the linear fit (within each subject) evaluated at the mid time. So if you had 10 time points at the same

Re: [Freesurfer] longitudinal analysis

Hi Yawu, no, that would be the simple average. Temporal average is the linear fit (within each subject) evaluated at the mid time. So if you had 10 time points at the same day and 1 a year later, it would look like a .5 years time point. This is used to compute symmetrized percent change,

[Freesurfer] longitudinal analysis

Dear Freesurfer experts In the command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR, Do-avg will compute the temporal average. I do not quite understand

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's super! Thanks

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

O'Hanlon [erikohan...@rcsi.ie] Sent: 20 November 2014 13:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Martin, I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

/BugReporting Any ideas very much appreciated. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Eugenio, Yes, it seems to have happened on a few cases, I've only started running it with the subfields and the jobs are running on a cluster so many have not run to end yet but al that have, exit with the error. I've attached

[Freesurfer] Longitudinal analysis and hippocampal subfields

Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] *Sent:* 18 November 2014 17:04 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option

Re: [Freesurfer] longitudinal analysis and linear mixed effects models

Hi Emma, yes, LME is Matlab, but the wiki page describe the use step-by-step. LME makes sense in your case because some subjects have less time points than others. The alternative (if only a very small minority of subjects differs from the rest) would be the 2-stage approach, where you

Re: [Freesurfer] longitudinal analysis and linear mixed effects models

: Martin Reuter mreu...@nmr.mgh.harvard.edu Para: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 24 de septiembre de 2014 8:55 Asunto: Re: [Freesurfer] longitudinal analysis and linear mixed effects models Hi Emma, yes, LME is Matlab, but the wiki page describe

[Freesurfer] longitudinal analysis and linear mixed effects models

Hi FS, I want to conduct a within-subjects longitudinal analysis, I thought I would be able to run a LME model in QDEC but this doesn't seem to be the case at all, is this correct? It seems I have to do everything using Matlab (big sigh).

Re: [Freesurfer] Longitudinal Analysis Questions

Hi Panos Yes, except you would not pass the -all flag as you don't want to rerun everything: recon-all -base base_subject_name -tp tmp1 -tp tmp2 ... -tp tmpN -autorecon2-cp -autorecon3 Best, Martin On 04/01/2014 01:41 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Martin, Thanks for your

Re: [Freesurfer] Longitudinal Analysis Questions

Hi Martin, That sounds great. Thanks for your time! Panos Hi Panos Yes, except you would not pass the -all flag as you don't want to rerun everything: recon-all -base base_subject_name -tp tmp1 -tp tmp2 ... -tp tmpN -autorecon2-cp -autorecon3 Best, Martin On 04/01/2014 01:41 PM,

Re: [Freesurfer] Longitudinal Analysis Questions

Hi Panos, 1. you need to edit the base. That is actually more important than editing the individual (cross) time points from the first stage, especially when the edits are supposed to improve the surface. The reason is that the surface is taken from the base to initialize all time points in

Re: [Freesurfer] Longitudinal Analysis Questions

Hi Martin, Thanks for your reply! Yes, that definitely makes sense. I had an additional probably elementary question: I tried to reconstruct the base after I added some control points to it, using the command recon-all -autorecon2-cp -autorecon3 -subjid base_subject_name but the following error

[Freesurfer] Longitudinal Analysis Questions

Hi FS community, I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise: 1) Is the base template created from the recon-all -base

Re: [Freesurfer] Longitudinal analysis - the effect of FS release?

Hi Sasa, no time frame for 6.0 release as far as I know. since you only processed the first time point, I'd recommend to re-process everything with 5.3. Never process one time point with one version and the other with a different version! Theoretically you could run the second time point with

[Freesurfer] Longitudinal analysis - the effect of FS release?

Hi, we have a longitudinal data set and have processed all of the baseline data using FS v5.1.0. We are now about to start preprocessing follow-up brains. Can you please give your opinion on whether we had better stick with v5.1.0 for the follow-up data as well or whether it would be safe to

Re: [Freesurfer] Longitudinal analysis within one group

Dear Doug and Martin, Thanks a lot. I just have one group including 20 subjects. The scans have been done in a range of 0.9 to 1.5 years difference (tp2-tp1). Is ooh if I use the instructions from Paired Analysis : https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis ? Regards, Best regards,

Re: [Freesurfer] Longitudinal analysis within one group

mreu...@nmr.mgh.harvard.edu Cc: Douglas Greve gr...@nmr.mgh.harvard.edu,free surfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis within one group Dear Doug and Martin,  Thanks a lot. I just have one group including 20 subjects. The scans have been done

[Freesurfer] Longitudinal analysis within one group

Hi, Would you please advise if it is possible to do longitudinal statistical analysis within a group with two time points in Qdec. And if it is not possible in Qdec how I suppose to do it? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list

Re: [Freesurfer] Longitudinal analysis within one group

you can't do it in qdec, use the command line stream, ie, mris_preproc, mri_surf2surf to smoooth, mri_glmfit, and mri_glmfit-sim doug On 01/30/2014 09:18 AM, amirhossein manzouri wrote: Hi, Would you please advise if it is possible to do longitudinal statistical analysis within a group with

Re: [Freesurfer] Longitudinal analysis within one group

Hi, with one group you want to check if atrophy is significantly different from zero? That is probably the case for any group (e.g. aging), so it won't tell you anything really. Also, if you don't find atrophy in a region it doesn't mean it's not there (only your group size is too small to

Re: [Freesurfer] Longitudinal analysis of one timepoint

From: Sarah Whittle Sent: Friday, 22 March 2013 6:50 AM To: Martin Reuter Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Longitudinal analysis of one timepoint Ok, thank you. From: Martin Reuter [mreu

Re: [Freesurfer] Longitudinal analysis of one timepoint

] Longitudinal analysis of one timepoint Ok, thank you. From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Friday, 22 March 2013 12:36 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one

Re: [Freesurfer] Longitudinal analysis of one timepoint

point? Thanks, Sarah From: Sarah Whittle Sent: Friday, 22 March 2013 6:50 AM To: Martin Reuter Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Longitudinal analysis of one timepoint Ok, thank you

Re: [Freesurfer] Longitudinal analysis of one timepoint

: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process

Re: [Freesurfer] Longitudinal analysis of one timepoint

: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sarah, you deal with the time during post-processing (statistical analysis). Yes, you have differently many rows for each

Re: [Freesurfer] Longitudinal analysis of one timepoint

Ok, thank you. From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Friday, 22 March 2013 12:36 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sarah, you

Re: [Freesurfer] longitudinal analysis

Hello Martin, Thank you for your swift reply. I failed to make myself clear, and will try describing my study again. First, an important point: the study is not longitudinal per se, but I am interested in applying the methods of longitudinal analysis. I only have one time point, all the scans

Re: [Freesurfer] longitudinal analysis

Hi Joy-Loi, yes, you can do that using the free surfer tools (e.g. check if 'atrophy', i.e. change across the two methods, is different from zero, meaning if there is a bias). Any of the statistical methods described here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics can do

Re: [Freesurfer] longitudinal analysis

Hi Joy-Loi, so you have 2 time points? the first with a single scan, the second with two within-session scans that you want to average? I don't understand exactly what you are trying to do. To test differences in reliability you'd have to scan a bunch of subjects twice in a session and then

Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32

Re: [Freesurfer] Longitudinal analysis of one timepoint

Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time

Re: [Freesurfer] Longitudinal analysis of one timepoint

From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1

Re: [Freesurfer] Longitudinal analysis of one timepoint

  De: Sarah Whittle swhit...@unimelb.edu.au Para: Martin Reuter mreu...@nmr.mgh.harvard.edu; Nick Schmansky ni...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 6 de marzo de 2013 17:17 Asunto: Re: [Freesurfer] Longitudinal analysis of one

Re: [Freesurfer] Longitudinal analysis of one timepoint

To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points

Re: [Freesurfer] Longitudinal analysis of one timepoint

Thanks very much! From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sarah, you

Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream.

[Freesurfer] longitudinal analysis

Hi guys, I am currently running a longitudinal analysis on a set of scan. It is currently running and so far it has taken 5 days. It seems to be taking a large amount of time on a process called labelling slice. I have run the same analysis on other subjects which took about 6 hours to

Re: [Freesurfer] longitudinal analysis

Hi Paul what is the actual binary being run? Bruce On Fri, 18 Jan 2013, paul horton wrote: Hi guys,   I am currently running a longitudinal analysis on a set of scan.  It is currently running and so far it has taken 5 days. It seems to be taking a large amount of time on a process called

Re: [Freesurfer] Longitudinal analysis - contrast

] Longitudinal analysis - contrast Ok ! The good part - you were right - something changed - the error :) Now its: /??? Undefined function or method 'matlabpool' for input arguments ... Error in lme_mass_fit at 123 Error in == lme_mass_fit_vw at 73 / I will try

Re: [Freesurfer] Longitudinal analysis - contrast

Bernal-Rusiel jbernal0...@yahoo.es *Enviado:* Jueves 6 de diciembre de 2012 16:45 *Asunto:* Re: Re: [Freesurfer] Longitudinal analysis - contrast Hello Martin, Thanks for your confirmation. I downloaded the last version of FreeSurfer: the dev5-20120624, from the ..fswiki/LMEModels

Re: [Freesurfer] Longitudinal analysis - contrast

12:52 Asunto: Re: [Freesurfer] Longitudinal analysis - contrast Hi Jorge, Sorry, but I am not following :( What is ni ? if ni is number of repeated measures for each subject (as sortData help says) - then, for each subject we did only 2 repeated measures, so ni should be ni = [2]; if ni

Re: [Freesurfer] Longitudinal analysis - contrast

__ De: Alex Hanganu al.hang...@yahoo.ca Para: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal-Russiel jbernal0...@yahoo.es Enviado: Miércoles 5 de diciembre de 2012 18:20 Asunto: Re: [Freesurfer] Longitudinal analysis - contrast

Re: [Freesurfer] Longitudinal analysis - contrast

Bernal-Rusiel jbernal0...@yahoo.es Enviado: Miércoles 5 de diciembre de 2012 18:20 Asunto: Re: [Freesurfer] Longitudinal analysis - contrast Can you please help with this ? Thanks in advance ! best, Alex

Re: [Freesurfer] Longitudinal analysis - contrast

...@yahoo.ca Para: Martin Reuter mreu...@nmr.mgh.harvard.edu CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal-Rusiel jbernal0...@yahoo.es Enviado: Jueves 6 de diciembre de 2012 16:45 Asunto: Re: Re: [Freesurfer] Longitudinal analysis - contrast Hello Martin, Thanks for your

Re: [Freesurfer] Longitudinal analysis - contrast

*Asunto:* Re: [Freesurfer] Longitudinal analysis - contrast Hello Martin, thanks for the quick reply ! as I understood, from the LongitudinalTutorial, after long_mris_slopes the results can be seen for each subject, and in order to see the group results, all

Re: [Freesurfer] Longitudinal analysis - contrast

Yeah, wrote that wiki page yesterday after all the emails on the list. Glad it helps. Best, Martin On Wed, 2012-12-05 at 13:49 -0500, Alex Hanganu wrote: Hello Martin, Thanks for pointing out about qdec, I missed that part. We performed this analysis on qdec. Thanks for explaning the

Re: [Freesurfer] Longitudinal analysis - contrast

-Jorge De: Alex Hanganu al.hang...@yahoo.ca Para: jorge luis jbernal0...@yahoo.es CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 5 de diciembre de 2012 13:50 Asunto: Re: [Freesurfer] Longitudinal analysis - contrast Hi Jorge, thanks

Re: [Freesurfer] Longitudinal analysis - contrast

Hi Jorge, On the page presenting the ../fswiki/LinearMixedEffectsModels, I think there is a misunderstanding - You show the command: mris_preproc --qdec but --qdec is not recognized, and in the help menu of mris_preproc I don't see this flag. So I guess you meant the --fsgd flag. so,

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