Re: [Freesurfer] Error with recon-all long

Hi Bronwyn, I would guess that there has been a problem with the way you run the base. Take one case, copy the cross sectionals into a new directory and re-run the base from scratch. If your two time points are named like: TPID_001 and TPID_002 then the base command should be: recon-all

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 freesurfer

Hi, healthy controls usually show 0.5% atrophy per year or less. You have very young subjects, and the expectation there would be near to 0 change. Due to acquisition noise, hydration effects, head motion etc, you will of course always find individual cases with volume / thickness increase

Re: [Freesurfer] Longitudinal spatiotemporal LME vs. V-LME

Hi Ann-Kathrin, for age you should use age at baseline (should be fixed for all time points per subject). You have the time_from_baseline variable to model the time. (maybe that is what you are already doing). I don't know why more survives with the voxelwise model, I usually see the

Re: [Freesurfer] longitudinal generic-time and spc

Hi Kasper, 1) yes correct 2) for generic the time delta is always 1 ( 2-1, 3-2, 4-3 ..) Best, Martin Am 16.08.2017 um 08:22 schrieb Kasper Jessen: Dear Freesurfer, The following is a follow-up, on a previous discussion

Re: [Freesurfer] Cortical thickness map for a pediatric case

Hi Sneha, I don’t know why this fails. There could be many reasons. Firstmost, the longitudinal stream assumes that head size is constant, which is probably not the case in your data. Looking at the log file however, it seems that recon-all stops in the NU correction step that comes before

Re: [Freesurfer] Univariate Linear Mixed Effects

Hi Amanda, the C matrix below has 14 columns ( 3 + 5 + 6 ). To find out what hypothesis are tested, look at the corresponding columns. column 4 for example is the MCIs slope delta with respect to controls (so slope difference MCIs and CN) the next test is slope difference between MCIs and

Re: [Freesurfer] Clarification for aseg edits in longitudinal phase

-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

Re: [Freesurfer] SPC in surface area

Hi Alejandra, the script creates an SPC stack, where you have all the SPC values for each vertex for each subject. Even in without the stack the SPC values are stored in each base directory. There are probably ways to define a label based on your ROI, then you can do an ROI analysis on the

Re: [Freesurfer] FS Version 6 Long Processing

Hi Allison, seems like autorecon2-pial has been removed from FreeSurfer (also in the cross sectional stream). I don't know when, why and what would be the equivalent command, but someone on the list will know. About brainmask edits, they are described here:

Re: [Freesurfer] Freesurfer Template Creation

Hi Daniele, as others commented, the stream is unbiased so the order does not affect results, so you are fine. That said, if you switch the order around you will get slightly different results due to numerical reasons (small differences affected by the order that accumulate to produce

Re: [Freesurfer] Longitudinal stats: target space

Hi Cris, in your case, fsaverage may not be optimal, but often it does it's job even if ages are far away. Still I would recommend c) or you can also select a specific subject from your data as the template and exclude it from the analysis. For c) you'd have to build the template, but I

Re: [Freesurfer] LME correction in longitudinal analysis

Hi Livia, I cannot help you, as I don’t know about the cluster analysis etc, maybe someone else does. Here some quick answers as far as what I know: 1. when running the test with F_lhstats = lme_mass_F(lhstats,CM); you get a structure F_lhstats which should also contain the F . Also take a

Re: [Freesurfer] Longitudinal Pipeline

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

Re: [Freesurfer] leaving out one timepoint from a longitudinal analysis

Hi Paola, the official answer is: no one knows. The practical answer is: it should be OK to take only the first 3 time point without creating the base. The base is mainly used as an unbiased space for initializing the longitudinal processing. The base does not change much by adding a 4th

Re: [Freesurfer] LME correction in longitudinal analysis

Hi Livia, [1] only the intercept is used as random effect in the model [1 2 ] both intercept and time (slopes) are used as random effect in the model. Here many more parameters get estimated so you need to have sufficient data. Often the more simple approach is better (but that can be tested

Re: [Freesurfer] LME correction in longitudinal analysis

Hi Livia, yes, 0 0 0 1 is the interaction (if longitudinal slopes = atrophy rates, differ across groups). When interpreting these, it makes sense to look at your model: Y_ij = b0 + b1 t_ij + b2 g_i + b3 t_ij g_i where t is time, g is group. For group=0 you have Y_ij = b0 + b1 t_ij so b0 is

Re: [Freesurfer] LME correction in longitudinal analysis

Hi Livia, groups should be 0 and 1, e.g. 0 for controls, 1 for disease. Order of groups does not matter (as long as both X and Y are ordered that way). You can do FDR or FDR2 on your final sig values. It is best to combine results from left and right hemisphere and do a single FDR2

Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

Hi, sorry to dig up this old email (just came across it). We have stopped with the gcut, because in some cases it cropped brain. Also passing a T2 via the -T2 flag (which is supposed to remove dura) sometimes crops cortex. It should be made clear that at the stage of the brainmask this should

Re: [Freesurfer] UPDATE: error in long_mris_slopes

Hi Clara, more likely there is a problem with your sever (e.g. disk IO problems). The label intersection works like this: For each subject it copies the of the first time point to rh.cortex.label to the base directory as: rh.long.cortex.label it then intersect the label with the one from the

Re: [Freesurfer] ADNI longitudinal brain volume in normal subjects

Hi Emory, Lots of publicly available Datasets have controls OASIS, ADNI, MIRIAD the problem is that these images were scanned on different scanners with different protocols, so the measurements are not comparable to your patients. Best, Martin On 05/24/2017 12:10 AM, shi yao wang wrote:

Re: [Freesurfer] Two group two time longitudinal analysis

Hi Livia, I am not very familiar with the paired analysis (never used it and did not develop it). From a glance (others may know better) your files look OK, the first creates the paired differences, the second is for the group comparison to test if the group mean of the paired differences

Re: [Freesurfer] Differences for the longitudinal processing with FreeSurfer 6.0 versus 5.3 ?

Hi Lisa, there are big differences in the cross sectional stream (see release notes). Most of these affect the longitudinal stream directly. Regarding the longitudinal pipelines, there are no big changes to the pipeline, but as lots of the cross sectionally processed results and tools from

Re: [Freesurfer] Longitudinal study concept question

Hi Gregory, If looking at longitudinal changes, I would use uncorrected ROI volumes. You could consider including ICV as a covariate (for offset and slope interaction, to test if ICV has an effect on your slopes). Best, Martin On 05/19/2017 04:44 PM, Gregory Book wrote: In writing a paper

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

with increasing score: more atrophy or less brain growth, depending on b1. Best Martin On 05/18/2017 01:12 PM, Matthieu Vanhoutte wrote: Hi Martin, Thank you this helps ! Please find last question below inline. Best, Matthieu Le 18 mai 2017 10:33 AM, "Martin Reuter&q

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

performance) ? Many thanks for your time and lights ! Best, Matthieu Le 17 mai 2017 1:46 PM, "Martin Reuter" <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> a écrit : Hi Matthieu, replacing time by score is very different from adding score as

Re: [Freesurfer] Question of longitudinal processing

here a way to display the bar in effect size? > And is this sig.mgh already statistically corrected? (FDR?) > > Best, > Jahanvi > > On Thu, May 18, 2017 at 1:55 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: > Hi J

Re: [Freesurfer] Question of longitudinal processing

thickness-pc1.fwhm15/osgm/sig.mgh > > I got a red to yellow sig.mgh, does it mean I got a increased percent > thickness change (pc1)? and the color bar showing 2 to 5 means? > > Best, > Jahanvi > > > > On Sun, May 14, 2017 at 10:11 PM, Martin Reuter <mreu...@

Re: [Freesurfer] long_stats results for group analysis

Hi Maria, That command creates a stack of the percent changes , with one entry per subject (it reduces the longitudinal data of a subject to a single number, e.g. the percent change computed in different ways). Make sure you know what the difference is between pc1, pc1fit (in your case this

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

with cognitive score. In context of AD which method would be the best for you ? Best, Matthieu Le 16 mai 2017 11:17 AM, "Martin Reuter" <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> a écrit : Hi Matthieu, one option is to replace time with score in

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

? Could you provide me an example of design matrix, I don't manage to see what does it look like to. Best regards, Matthieu Le 14 mai 2017 8:08 PM, "Martin Reuter" <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> a écrit : Hi Matthieu, yes, tha

Re: [Freesurfer] 2 stage model longitudinal data analysis

Development (ABCD) Study *From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] *Sent:* Sunday, May 14, 2017 1:14 PM *To:* Freesurfer

Re: [Freesurfer] 2 stage model longitudinal data analysis

Hi Maria, yes, the example on the wiki is a simple “one sample group mean” (osgd). You can find examples with more than one group here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Best, Martin > On 13 May 2017, at 00:24,

Re: [Freesurfer] Question of longitudinal processing

Hi Jahanvi, 1. yes, you need to create this table to then perform the stats 2. no, the format is as I described it below fsidfsid-base tp1_subA templatesubA tp2_subA templatesubA tp1_subB templatesubB tp2_subB templatesubB this is assuming that you called your base templatesubA

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Matthieu, yes, that is possible. Instead of group, you use a variable for your score (and interaction etc). Sometimes it may also makes sense to use score instead of time. Best, Martin > On 12 May 2017, at 10:51, Matthieu Vanhoutte > wrote: > > Dear

Re: [Freesurfer] Longitudinal hippocampal subfields analysis

Hi Manuel, smoothing is usually only necessary for surface data. You should have crated the subfields on top of the longitudinal directories, so: > recon-all -long -hippocampal-subfields-T1 > Else they will only be available in the cross dirs. The longs will have better reliability.

Re: [Freesurfer] Mri_segstats on longitudinal data (NVoxels)

Also, unless something is wrong with your processing or time point naming, you should get different volumes also for each time point in the longitudinal stream. Manually open the aseg.stats and check to determine if the problem is in way you processed the longitudinal data or when creating the

Re: [Freesurfer] Question of longitudinal processing

Hi Jahanvi, long.testretest.qdec is a qdec table in the longitudional format (with the fsid-base as the second column). For test-retest (e.g. same session with subject removal), you usually don't need a time column, that is why --generic-time is specified. the qdec table would just look

Re: [Freesurfer] Two group two time longitudinal analysis

Hi Livia, the Paired Analysis wiki page that you cite, contains the steps to create the differences and then run a glm analysis on the difference files. In your case you would to the first steps exactly as on the wiki and then you can create a more complex Second FSGD File with more than one

Re: [Freesurfer] Consistent volume increases for some regions when using longitudinal stream

Hi Melanie, whenever you change anything consistently in the processing pipeline (extra steps) you can expect a consistent change in the results. The longitudinal pipeline goes through many different steps than the cross-sectional. E.g. for surfaces, they get initialized from the subject

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

Not sure what is going on, maybe Eugenio knows. On 04/27/2017 10:29 PM, Salil Soman wrote: Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are

Re: [Freesurfer] Long-stream comparing differing resolutions

Hi Adam, the long stream is designed to reduce processing noise across longitudinal data. On one hand this can help when comparing arcoss scanners or acquisition, as the methods will be more sensitive to the scanner/acquisition induced differences. However, when switching resolutions, this

Re: [Freesurfer] Additional processing flags when using the longitudinal pipeline

Hi Gustav, use -all and -mprage for all steps use -qcache and -hippo..subfields only in the -long step. Best, Martin On 04/25/2017 12:51 PM, Gustav Mårtensson wrote: Hi, I have a question regarding the longitudinal pipeline. We are following the workflow summary as outlined in

Re: [Freesurfer] REPOST: Two stage model question

Hi Clara, the SPC (or any percent change) could be problematic, as the base value (either the volume at the baseline timepoint, or the average volume) will change depending wich interval you look at. You could check if the rate (mm/time_unit) or mm^3/time_unit is changing. I am not sure how

Re: [Freesurfer] Longitudinal Pipeline

t; > Thanks Martin. Should I be worried about affine transform masking out the > global atrophy if I am using the whole brain (no skull stripping)? > > Arman > > On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@

Re: [Freesurfer] Longitudinal Pipeline

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

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

se protected by law. If you received this e-mail in > error or from someone who was not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MA

Re: [Freesurfer] Can anyone help with this error - trying to compare 2 scans in same person

Hi Brad, the base commands needs a space before -tp recon-all -base 005_IHD_1_base -tp 005_IHD_1 -tp 005_IHD_1_post -all check if the directory 005_IHD_1_base exists. Also check if this file exits: /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm Best, Martin

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

. Thank you for your cooperation. *From: *Martin Reuter <mreu...@nmr.mgh.harvard.edu> *Date: *Tuesday, March 28, 2017 at 1:27 PM *To: *<freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams This is how it

Re: [Freesurfer] Comparing LME models

australia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 30 Mar 2017, at 12:18 am, Martin Reuter <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.har

Re: [Freesurfer] eTIV estimation on same subject over time

Hi Mel, when manually checking the talairach transform, make sure you are checking the one that is actually used for the eTIV computation (that changed over the years and versions). http://www.freesurfer.net/fswiki/eTIV so I think currently it is the talairach.xfm you can use lta_diff

Re: [Freesurfer] Comparing LME models

Hi Bronwyn, is this for a mass univariate approach? What do you mean with segmentation? ROI or vertex-wise vs region-wise? Best, Martin On 03/29/2017 01:23 AM, Bronwyn Overs wrote: Hi Mailing List, If you are comparing two matlab based linear mixed effects models (vertex-wise) with the

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

This is how it should work: WM edits in the base should affect surfaces in the base, these surfaces should be used as initialization for the long processing and fix most of the things there. If not , you need to edit the cross, because WM edits are copied into long from cross. Using the

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Hi David, first I think it makes sense to - replicate the problem in the regular (cross sectional) stream - then fix it there (if it exists) or look for it in long. So you see the problem in the S02_t1 and S02_t2 also, right? Best, Martin > On 13 Mar 2017, at 16:55, David Semanek

Re: [Freesurfer] Intensity normalization in longitudinal processing

_robust_register failed. We were advised by Dr. > Martin Reuter to either replace mri_robust_register & mri_robust_template > binary with the ones from v5.3 or to run all the bases and longs in v5.3. We > chose to run the longitudinal stream in v6.0 as it was released by then. &g

Re: [Freesurfer] LME mass univariate model

itter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> >> On 4 Mar 2017, at 12:43 am, Martin Reuter <mreu...@nmr.mgh.harvard.edu >> <mailto:mreu...@nmr.mgh.harvard.edu>> wr

Re: [Freesurfer] LME mass univariate model

Hi Bronwyn, I think years-between-scans should be years-from-baseline-scans . You may need to compute that if what you have is really years between neighbouring scans. 1. Usually people use intercept and maybe years-from-baseline as random effects. I would not include too many random effects,

Re: [Freesurfer] Hippocampus eTIV correction (LONGITUDINAL)

Hi Sebastian, the etiv is estimated in the base/subject-template, so it is constant for all time points. And if you want to include it into a longitudinal design depends on what you want. If you look at percent changes , you don't have to, but if you look at yearly rates, it is probably a

Re: [Freesurfer] 答复: Longitudinal proceesing for Pediatric data

would fail if the difference in head size exceeded any certain value? Best, Dong *发件人:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *代表 *Martin Reuter *发送时间:*2017年2月15日2:40 *收件人:*Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *

Re: [Freesurfer] REPOST: QDEC cluster as ROI

Hi Clara, I don't know, but this is not specific to longitudinal question. You don't need to warp to individual time points. The SPC is defined in each base and everything is a cross sectional analysis. So you have a cluster in QDEC and want to do an ROI analysis. I am sure someone else

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

> > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun..

Re: [Freesurfer] Longitudinal proceesing for Pediatric data

Hi Dong, it can work, if time points are close to each other (so not much head growth). Feel free to try, but make sure you are carefully looking at the surfaces, that no gray matter is clipped in later time points. The alternative is to only do cross sectional processing. Best, Martin >

Re: [Freesurfer] Analysis of rates or percent changes

nalysis of rates or percent changes > > Hi Martin, > > Thanks a lot. > > Best, Katarina > > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Mac

Re: [Freesurfer] recon-all -localGI with longitudinal pipeline output

Hi Mihaela, probably you are trying to run the localGI on a longitudinal directory. As the help text output says, you need to make sure you tell that to recon-al by passing the original command again (including the -long ….) and instead of -all you specify -localGI. Renaming hides from

Re: [Freesurfer] Edits to Aseg in the Longitudinal Stream

Hi Tamara, that depends on where you edit. Cross or base or long. Generally when editing in the longitudinal stream you always use the same recon-all command that you used initially, and only replace the -all with the new flag to tell it to start later in the process (here -autorecon2-noaseg

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, > >

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

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

Re: [Freesurfer] Attrition in longitudinal analysis

Hi Jonathan, I would recommend to run all subjects to the longitudinal stream only once and include as many time points for each subject as possible. That way you have only one measure per time point. Then I would use a linear mixed effects model (which can deal with missing data) and analyze

Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream

Hi Antonin, it would help with editing, but the problem is that we decided initialising from a single aseg is not working in situations with longitudinal changes and non-linear deformations because structures change/move too much. So accuracy will suffer and we decided to allow more

Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream

Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

scaling you need to do more detective work to find out where it is coming from. You also mentioned a brightness difference between time points. This could also indicated protocol of scanner differences. Best, Martin > On 12 Jan 2017, at 16:20, Martin Reuter <mreu...@nmr.mgh.harvard.edu&

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

m > not very familiar with transformations, thus any information or directions to > resources I can use would be very much appreciated. > > Thank you in advance for you help. > > Best, > Tamara > > > Message: 6 > Date: Tue, 10 Jan 2017 21:18:34 +0100 > Fr

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

ooth > transition from time 1 to time 2 and a relatively smooth transition from the > template to the time points. Do you think this is problematic? > > Thank you again for your help. > > Best, > Tamara > > > > Message: 4 > Date: Wed,

Re: [Freesurfer] postdoc in computational neuroimaging (method development)

Forgot the link to the page: https://www.dzne.de/jobs-karriere/job/postdoc-fm-in-computational-neuroimaging-code-1427201612.html <https://www.dzne.de/jobs-karriere/job/postdoc-fm-in-computational-neuroimaging-code-1427201612.html> Cheers, Martin > On 28 Dec 2016, at 10:57, Mart

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Tamara, three out of how many? I would probably remove those three as whatever you measure in them could be driven by the acquisition differences, but it depends on what acquisition differences you have. If it is only small differences, like tiny deviations in the voxel size etc, it should

[Freesurfer] postdoc in computational neuroimaging (method development)

Hi all, I wish everyone a successful new year 2017! Please pass along this job offer for a postdoc position in my group in Bonn, Germany, to anyone interested and feel free to contact me with any questions. Thanks, Martin Reuter The German Center for Neurodegenerative Diseases (DZNE

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Tamara, first you need to make sure that this is not just a viewing setting, so in freeview copy the brightness setting to all inputs (there is buttons for that, like copy setting and apply to all, underneath the list of images). If you still see differences, check the original inputs. If

Re: [Freesurfer] Longitudinal base creating in version 5.1 vs 5.3

Hi Allison, you have two options: 1. replace the mri_robust_register and mri_robust_template executables with newer ones (but who knows if flags changed, so this may not work directly, in that case also the call in recon-all may need to be adjusted). 2. better: simply run all bases with 5.3

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

rigid). Best, Martin > On Nov 22, 2016, at 9:31 PM, Matthieu Vanhoutte <matthieuvanhou...@gmail.com> > wrote: > > Hi Martin, > > Please see inline below: > >> Le 22 nov. 2016 à 17:04, Martin Reuter <mreu...@nmr.mgh.harvard.edu >> <mailto:mreu

Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

Hi Antonin, we start slightly inside as surfaces expand more easily than shrink. This way even for the further atrophied time points there is a higher chance that it will be slightly inside it’s final position. The mris_longitudinal_surfaces is over 11 years old and was used for testing

Re: [Freesurfer] mris_make_surfaces - longitudinal stream - questions

Hi Antonin, I had answered that in my email from Nov. 18.. Thickness is not constrained to 3.5mm, but see my email for the full answer. Best, Martin > On Nov 22, 2016, at 12:15 PM, Antonin Skoch wrote: > > Dear experts, > > I am trying to understand what is the specificity

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

Hi Matthieu, (also inline) > On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte > <matthieuvanhou...@gmail.com> wrote: > > Hi Martin, > > Thanks for replying. Please see inline below: > >> Le 21 nov. 2016 à 20:26, Martin Reuter <mreu...@

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

Re: [Freesurfer] differences between OS recon all output, longitudinal data

And to add to this. In a longitudinal study you search for small longitudinal changes. There you should never switch versions or OS across time points, period. (Also in a cross sectional study you should never do it, but often the effect there, e.g. group differences, are much larger than

Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

Hi Antonin, max does not constrain thickness. The location of the max is constrained to be within 2*max for every iteration, so it will constrain how far outwards it searches. But it will be done at each scale, so it can still deform a long way. We initialize the surface processing in long

Re: [Freesurfer] Longitudinal surface analysis of PET data

> <mailto:matthieuvanhou...@gmail.com > > <mailto:matthieuvanhou...@gmail.com>> > > > <mailto:matthieuvanhou...@gmail.com > > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > > <mailto:matthieuvanhou...@gmail.com

Re: [Freesurfer] Questions about outputs in Longitudinal Stream

Hi Tamara, in the base it is good the check the brain mask, as it is used for all time points (it is fixed over time). To check alignment accuracy, you could use either brain mask or norm. It should not make a difference. It will be hard to find problems in that image (the blurriness will be

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

Re: [Freesurfer] Bug Reporting: mris_long_slopes qdec table not found

Quinn, Could be that the table has any strange character in it (e.g. strange white space etc. ) Try to create a table in a simple text editor by typing the header line and the first 1 or two rows (space separated). If it can read that, then it is probably the format of your table. Best,

Re: [Freesurfer] Error long_mris_slopes

Hi Tom, Could be the qdec table has weird characters. Try with a simplified table (only a few rows, created in a text editor from scratch, space separated). best, Martin > On Oct 12, 2016, at 11:59 PM, tom parker wrote: > > Dear FreeSurfers, > > I've been trying

Re: [Freesurfer] Questions about outputs in Longitudinal Stream

Hi Tamara, 1. brainmask.mgz 2. yes, as you will get your final measures from the long output stats. Take a look at how aseg edits are done in the regular cross stream. In long it would work the same (just with passing -long and then instead of -all you just do the last steps to recompute the

Re: [Freesurfer] Question regarding Checking Longitudinal Runs: Repost

Hi Tamara, if you have time and only few subjects, I would recommend to look at all those. For a large study it becomes difficult. Just open the base and both time points on top to see if they all align and if the base looks OK. We also usually recommend to check the surface in base, but if

Re: [Freesurfer] Two Stage Longitudinal Model

Hi Tim, yes, in the 2-stage approach, you first compute the slope per subject (e.g. mm/year thinning or q mm per year volume loss) and then do a regular GLM for each subject. For that the co-variates need to be fixed per subject. The long_qdec_table command below averages the covers for you.

Re: [Freesurfer] T2pial and [LONG]

Hi Antonin, almost, you need to use the existing transforms from the base (when the T1 template get’s created) and apply these to the co-registered T2 of each time point. In recon-all base code you will find a mi_robust_template call that takes existing lta transforms for each time points

Re: [Freesurfer] qdec long parsing table to look in non-existant directory

Hi Katherine, You need to run the data through all three steps of the longitudinal pipeline. The *.long.* directories are created in the last step (recon_all -long ... ). See also the wiki ( Google longitudinal processing freesurfer ) Best Martin On Oct 8, 2016 21:19, Katherine Damme

Re: [Freesurfer] Longitudinal surface analysis of PET data

Hi Matthieu, I never used PET data, but once you manage to resample you pet data onto the surface, you will have a file similar to the thickness file for each subjects. Instead of thickness it holds you PET information. From that point on everything should be identical to the thickness

Re: [Freesurfer] longitudinal spc over an ROI

Hi Rachel, yes, there is a difference if you compute SPC of the average thickness in an ROI or if you average the SPC computed on a vertex level. For the second, you can use long_mris_surf to map your third group to fsaverage and compute SPC, there is an option to write out the stack, then

Re: [Freesurfer] Analysis of rates or percent changes

- Skopje, Republic of Macedonia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor

Re: [Freesurfer] when to -qcache in longitudinal processing

, Linette Savage University of Calgary Brain Training Study www.braintrainingstudy.ca <http://www.braintrainingstudy.ca> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --

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