Re: [Freesurfer] longitudinal study

Hi Ken, you should always look at the output from the …long.base directories, those are the final outputs. Looks to me that you are looking at the cross sectional produced surfaces from the first stage. Those will be - in different spaces (as the heads are in different positions in the

Re: [Freesurfer] starting longitudinal pipeline after mri_robust_template

Hi Marisa, That should be possible. You can run the long pipeline up to that step, replace the corresponding files with your version and continue from there. Best, Martin > On 1. Oct 2020, at 10:32, Marisa Johanna Nordt wrote: > > External Email - Use Caution > Hello, >

Re: [Freesurfer] lta files longitudinal pipeline

Hi Marisa, the -affine flag was only for some debugging and is currently not supported. It may also not do what you think it does. It will remove scaling difference between your time points. This makes sense if you have test-retest scans and want to remove scanner calibration scaling

Re: [Freesurfer] Question: Longitudinal Edits

Hi Suzan, (sending this also to the FS support list, where these questions fit best, but sometimes I miss emails there). If edits are necessary or not depends purely on the quality of your data. I.e. old scanners, low contrast, motion artefacts etc. It also depends on the number of

Re: [Freesurfer] --inittp 0 in mri_robust_template

Hi Marisa, usually a random time point is selected as an initial registration target. From there we map all images (including the initial target) to a common mid space and create the first template there, then we register to that template and iterate. This speeds things up, but is

Re: [Freesurfer] error message using mri_robust_template

Hi Marisa, the main goal of robust_template is to remove rigid motion between scans. So the first question is, do you really need (want) affine? The next question is, if this still occurs in FS 7.1.1 I remember dimly that I worked on this some years ago (basically allow a larger threshold, as

Re: [Freesurfer] intersubject longitudinal analysis

Hi Ken, Hmm, not sure. Does it give a reason why it cannot be loaded? Could be read permissions, could be corrupted. Generally the commands look good. You could also try to check the subject SPC on the base-template surface. Those files should also be there in the base dir. Best, Martin

Re: [Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

Hi Barbara, I think you are asking to run FastSurfer and source FS7.1 binaries instead of the recommended 6.0. for the surface processing part. This may work, but it is not recommended. We only tested FastSurfer in combination with 6.0. as described in the paper. So if you use 7.1 you are on

Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

Or should I merge unsmoothed data (e.g., > lh.thickness.fwhm0.fsaverage.mgh) and then smooth once merged? > > Thanks again, > Lara > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ma

Re: [Freesurfer] Error in long_mris_slopes

Hi Guillaume, not sure what is going on. It could be missing permissions or it could be that the disk is full? You could also try to drop the --do-label and see if that works. Best, Martin On Fri, 2020-02-14 at 10:12 +0100, Guillaume Carey wrote: > > Hello everyone, > I’m currently

Re: [Freesurfer] questions about batch running longitudinal data using long_submit_jobs on cluste

Hi, looks like someone changed the default python to version 3, and you are still using a script written for python 2. I think Andrew updated this recently, so obtaining a newer version of the long_submit_jobs script from dev may fix this. Best, Martin On Tue, 2020-02-11 at 18:03 +,

Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

Hi Lara, no, you should not use time point 1 as base. You need to distinguish between the image processing part and the statistics post processing analysis (LME). These are two separate things. For the image processing in the longitudinal pipeline, we create the base (=subject template). The

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

Hi Swati, - yes, you can treat the percent change maps (PC1) as the signal instead of the thickness and do a regular analysis (so either multiple comparisons or sim etc). - and yes, I would always recommend to use the linear mixed effects model instead as it is specifically designed for

Re: [Freesurfer] using different Freesurfer versions for cross-sectional & longitudinal processing

Hi, I have never tested compatibility with 5.1 and would recommend against it (5.1 was released almost 9 years ago). You can try it out on one subject and check results. There would be no support for this however. Best, Martin > On 17. Dec 2019, at 20:34, Greve, Douglas N.,Ph.D. >

Re: [Freesurfer] Question re: Longitudinal processing stream transforms.

Hi Jamie, looks like your command is wrong (reverse). Here are spaces: tp1 original space tp2 original space base = tp1.long.base = tp2.long.base space so the longitudinals and the base are in the same space (rigidly aligned and resliced to that space). The lta files map between tp1

Re: [Freesurfer] Contents of Freesurfer digest...

; absolute volume for any comparative analysis. > > Thank you again. This message board is of incredible value! > > Best regards, > David > > > > >> ------ >> >> Message: 1 >

Re: [Freesurfer] Questions re slice thickness, aseg and longitudinal analysis

Hi David, I am not very optimistic: 5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You will certainly get something, but it can be very unreliable and completely wrong. Especially longitudinally these thick slices will induce large variance due to different head positioning

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

Re: [Freesurfer] error in longitudinal stream command

Hi Alexandru, not sure what you mean with "unmatched" error. If this is still a problem, can you send details? Best, Martin On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote: > External Email - Use Caution > Hello Martin, > > I was wondering - how solved the

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

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

Re: [Freesurfer] mri_robust_template in FMRIprep rotation should not scale error

Hi, To debug this, I would need the 4 input images and the command. Of course the error would need to also come up when using those images.Best MartinAm 14.08.2019 20:01 schrieb "Greve, Douglas N.,Ph.D." :I have not seen it before; I've cc'ed Martin in case he has seen it. Have you checked the

Re: [Freesurfer] Applying Pial edits to Longitudinal

Hi Sierra, the long command should be recon-all -long C002d C002.base -mprage ….. same way as you called it the first time when using the -all flag. Best, Martin > On 8. Jun 2019, at 20:28, Sierra Ann Jarvis wrote: > > External Email - Use Caution > > > Hello

Re: [Freesurfer] Advantage of having skull for longitudinal processing?

Hi Adam, the longitudinal registration should not care, but the regular stream would like to have the skull in the image. This will help for a couple steps (full head talairach registration -> eTIV etc). Best, Martin > On 5. Jun 2019, at 03:57, Adam Martersteck wrote: > >

Re: [Freesurfer] Geometric distortion

Hi Martin, probably the reviewer does not mean anything related to FS. Rather, there is distortion during image acquisition (e.g. gradient non- linearities). The reviewer probably wants to know if gradient unwarparing was done prior to running FS. That is why Matthew asked what MRI data was

Re: [Freesurfer] Longitudinal processing

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

Re: [Freesurfer] Longitudinal Gray/white Contrast Measure

Hi William, you can use freesurfer's pctsurfcon to compute the gray/white contrast on the longitudinal directories. This will produce a surface overlay at: tp.long.base/surf/?h.w-g.pct.mgh I don't think the long_mris_slopes script can deal with those files directly, so you have two options: -

Re: [Freesurfer] Issue with longitudinal surfaces

Hi Maxime, also how do the surfaces look on their respective time point images from long? Do they look accurate there? Could be that there are differences across the time points that cause the surfaces to differ this much. Was the same hardware (scanner, coil) and same protocol used for both

Re: [Freesurfer] freesurfer longitudinal issue

Hi Maxime, please keep previous conversation in the email (so that it is easier to check the original question). Also let’s keep this on the list. I do not understand what you mean with “there is not strict alignment”. If you open the norm.mgz from base, tp1.long.base and tp2.long.base they

Re: [Freesurfer] freesurfer longitudinal issue

Hi Maxime, the longitudinal stream aligns images across time. This registration can (and should) be checked by opening the base/mri/norm.mgz and the norm.mgz from the tp.long.base (longitudinal) directories. They should all align. Your example looks like you might have openend the images from

Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

Hi Arsenije, the file name should be (with a starting “.” and no file extension): $SUBJECTS_DIR/qdec/.Qdecrc Best, Martin > On 22. Feb 2019, at 00:22, Arsenije Subotic > wrote: > > Dear Freesurfer experts, > > I am having issues choosing the spc option for my QDEC two stage

Re: [Freesurfer] Longitudinal QDEC

also note the file name starts with a “.” .Qdecrc > On 18. Mar 2019, at 21:16, Martin Reuter wrote: > > Hi Theo, > > the file should be : > $SUBJECTS_DIR/qdec/.Qdecrc > > it is important that it is at that location and should not have an extension > (no

Re: [Freesurfer] Longitudinal QDEC

Hi Theo, the file should be : $SUBJECTS_DIR/qdec/.Qdecrc it is important that it is at that location and should not have an extension (not .txt !) Best, Martin > On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS > wrote: > > External Email - Use Caution > Dear All, > > I am

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

ut this effect would > > be compensated by LME modeling ? > > > > Would there be proportion of early drop outs to respect in order to > > compensate bias with LME ? > > > > Thanks, > > Matthieu > > > > > > Le ven. 19 oct. 2018 à 16:

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

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

Re: [Freesurfer] Longitudinal Stream - LONG step

It says "Could not find file ..". I wonder which one it is looking for. Did you try to completely delete this long subject dir and re-run from scratch? Do other time points with this base go through? If not, you could re- run the base also. Also when you open orig of all time points (from the

Re: [Freesurfer] Longitudinal processing and paralllel flag

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

Re: [Freesurfer] longitudinal analyses after lesion segmentation

Hi Kathleen, if you map one image to the other, this introduces interpolation artefacts, which will bias your analysis (any type of analysis, so this is already a problem in the lesion segmentation part). Technically you run longitudinal freesurfer on these images but (similar to the lesion

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

Hi David, there is no need to worry. Whenever we change the pipeline, there will be consistent differences. Since we do not have ground truth thickness it is unclear which method is “more right”. A comparison between cross and long does not make sense here with respect to absolute values. It

Re: [Freesurfer] ICV normalization (longitudinal pipeline)

Hi Martin, ICV is head size. It is unlikely that anything except head growth in children changes head size. I don’t know of drugs that do that ;-). So it is best to assume that head size is fixed for adults. Usually results should have less variance if you remove the noise from the ICV

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

Hi, Looks like the input is a multi frame image. Should only be single frame. Best Martin > On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio > wrote: > > It seems like a problem with mri_robust_register. > Martin, any ideas? > > -- > Juan Eugenio Iglesias > Centre for Medical Image

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

gt; between both groups are still valid accounting for this bias ? Is LME > method robust enough for compensating this kind of drop-out ? > > Best, > Matthieu > > > Le mer. 17 oct. 2018 à 18:33, Martin Reuter edu> a écrit : > > Hi Matthieu,  > > > > 1) surv

Re: [Freesurfer] Adding longitudinal time points to clean dataset {Disarmed}

Hi Molly, no one can really tell you that. My feeling is, that it is pretty safe, given that you have already 4 time points in the base. The base will be very stable and the main reason for the base is that it is an independent space different from any single time point. Which remains true.

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

al neuroimaging data ? > > Thanks in advance for helping. > > Best, > Matthieu > > Le mer. 14 déc. 2016 à 22:14, Martin Reuter edu> a écrit : > > Hi Matthieu, > > > > 1. yes, LME needs to be done first so that values can be sampled > > from

Re: [Freesurfer] longitudinal hippocampal aseg editing

Hi Rebecca, I see. Generally, it should behave in the same way as cross sectional processing: If both aseg.mgz and aseg.auto.mgz exist, and they are different, then  the file aseg.manedit.mgz is created from the differences (and if an  aseg.manedit.mgz file also exists, then its contents are

Re: [Freesurfer] Fwd: longitudinal hippocampal aseg editing

Hi Rebecca, aseg edits to subcortical structures need to be done in the -long stage. (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits ) Best, Martin On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote: > External Email - Use Caution > HELP > --

Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

s of tp2 from tp1 for each subject > in a tabular form. > > Best, > > Anwar > > On 2018-08-30, 3:22 AM, "Martin Reuter" .edu> wrote: > > Hi Anwar, > > what FS version are you using? > > Also what ha

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

Hi Xiaoyu, please keep the previous conversation as inline citation below so I know what we discussed before. What I mean is to process every subject only once and not twice (with flipped images, if that is what you did?). Then run xhemi analysis on the subject-level. Invert the sign of

Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

Hi Dani, the regular FreeSurfer stream samples everything to 1mm isotropic. This is of course problematic, if you have one group scanned at 1mm and the other at a different resolution (as group differences could be affected by the different resolutions). You would never know how much of what

Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

Hi Anwar, what FS version are you using? Also what happens if you omit the --out-pc1 but keep the --do-pc1 ? Also no output with that ending? It should write it to the default location. Best, Martin On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote: > External Email

Re: [Freesurfer] error in longitudinal stream command

0-05152013 > > Thank you! > Valeria > > From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-bounces@nmr. > mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard. > edu] > Sent: Wednesday, August 29, 2018 12:14 PM &

Re: [Freesurfer] LME Univariate pvalue inconsistent

Hi Xiaoyu, again (see also other email) you should not run left hemispheres on the right. This could introduce a processing bias, especially when you force all left to be healthy and right to be diseased (or vice-versa). Instead run your images normally and then for the univariate , simply

Re: [Freesurfer] error in longitudinal stream command

Hi Valeria, what version of FS are you using (also is it a local install or the system install)? Also try to re-type the command in the shell (don't run it from a script) could be that there are invisible characters , like tab etc from copy paste that mess things up. Best, Martin On Wed,

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal Comparison

Hi Xiaoyu, I don't think it makes sense to model the hemisphere each as a different group. Do you mean different time point? The problem is that left hemispheres are probably anatomically slightly different than right hemispheres (on average in healthy people). I would run every subject only

Re: [Freesurfer] correlation between blood biomarkers and longitudinal decrease in cortical thickness

Hi Foad, if all subjects have 2 time point and same time delta, you can compute the difference between time points, divide by 2 (for yearly change) and run a standard GLM analysis on that measure instead of thickness. Or you can model this with linear mixed effects models (which makes sense

Re: [Freesurfer] recon-all with mri_ca_normalize (longitudinal)

Hi Paul, you will need aseg and maybe more in the -long runs anyway. But if you really want to stop after norm … -autorecon1 -gcareg -canorm passing autorecon2 will do the whole block : https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0

Re: [Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits

Hi Kaley, the problem is,, when you re-run the base with different images, it will create the median image at a different location. That means that all your edits will be at the wrong location. I currently don’t see a way to fix this easily without a lot of tweaking of the recon-all script.

Re: [Freesurfer] error with mri_ca_register in long

Hi Paul, Does this happen in the base or in the long step? -bigventricle has never been tested within the long stream and this is bug that needs to be fixed at some point (assuming the big ventricle is supported in the next release ) We should put this on our known issues list. Best,

Re: [Freesurfer] Resample data for longitudinal comparisons

Hi James, I would not run upsampled data through the highres pipeline. (not even sure I would run highres data through that). So you should sample to 1mm resolution. To be fair you should also resample the 1mm image to a new position (to also introduce interpolation artefacts there). You

Re: [Freesurfer] Longitudinal Processing question

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

Re: [Freesurfer] Missingness and recent developments in longitudinal pipeline for pediatric samples

Hi Laurel and Johannes, Pediatric: if the time distance is small it should also work in paediatric images. You can just test it on a couple cases and if too many edits would be required, then simply use the cross sectional processed results. There is no thorough analysis, but missingness is

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

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

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

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

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 Process

Hi Samir, you can first conform all inputs to 1mm isotropic using mri_convert --conform input output It may make sense to add a covariate in the statistics for the different acquisition to control for a linear effect. Best, Martin > On 25. May 2018, at 08:29, Samir Rekic wrote: > > >

Re: [Freesurfer] Longitudinal errors, Voxel size differs

> > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Martin Reuter > mailto:mreu...@nmr.mgh.harvard.edu>> > Sent: 15 May 2018 23:39 > To: Freesurfer suppor

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

Hi Tudor, 5.3 had some difficulties reporting image geometry differences even when they were tiny. That was fixed in 6.0. However Bruce’s recommendation (to reslice the second time point exactly as the first) should do the trick. Alternatively (in order to avoid processing bias) you could

Re: [Freesurfer] Longitudinal errors, Voxel size differs

Hi Erik, you should investigate why this is the case. Any difference in acquisition will cause effects and it will be impossible to distinguish these from real effects. Also you should never just resample one time point, as that will introduce processing bias. I would advise to - find out

Re: [Freesurfer] ICV adjustment of volumes in longitudinal pipeline

Hi Tamir, ICV is fixed across time (derived from the template image), so that data can be compared directly, but for cross subject analysis you still need to adjust for ICV of course. Best, Martin > On 15. May 2018, at 03:19, Tamir Eisenstein wrote: > > > > Hello

Re: [Freesurfer] Longitudinal LME cluster value extraction

Hi Emmanuel, I think this should be identical to the cross sectional situation, you map that cluster (defined on FSAVERAGE) to each subject_time_point and then use mri_segstats to get stats on that region. Probably others can help you with what tools exactly you need for this (or probably

Re: [Freesurfer] Problem with template longitudinal pipeline

Hi Laura, it could be that 9 years of severe aging or neundegenerative disease are too far apart for the method to cover the distance. The base would look blurry or show ghosting (in 2 time points the median is equal to the mean and the mean will not look good with too much change). I would

Re: [Freesurfer] mri_vol2surf

Hi,Yes the longitudinal images after the long run are all aligned in the base space. You will find the map from each time point to the base in the base MRI transforms dir (maybe also in the long MRI transforms). Naming should make clear what reach one is.Best MartinAm 09.05.2018 21:11 schrieb

Re: [Freesurfer] Longitudinal processing with different FS versions

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

Re: [Freesurfer] reruns recon-all -long after edits

Hi Anna, yes, long can still be edited, but usually this is not necessary. What kind of edits did you need to do in the long? You would need to call with the long flag, and passing the cross and base name. So just like the regular processing of the -long step, only replace -all with

Re: [Freesurfer] Longitudinal Freesurfer Analysis

Hi Katie, yes, you should check the base (subject-template) if further editing is necessary there, so that surfaces look good on the base. Best, Martin > On 4. Apr 2018, at 15:54, Mckay, Katie Geraldine > wrote: > > Hi, > I have a question regarding the longitudinal

Re: [Freesurfer] Longitudinal strean including more than an image per time point

Hi Maria, you can include all time points per subject in the longitudinal processing. For the statistics I would add a time-varying co-variate with the head coil type. Best, Martin > On 13. Mar 2018, at 11:45, Maria Paternina Die wrote: > > Dear all, > > We want to run

Re: [Freesurfer] ASEG and APARCSTATS2TABLE on longitudinal data

Hi Lisa, 1. It all depends on what kind of analysis you want to do. You can run aparcstats2table without the long_stats_slopes. Then you will get an entry for each time point. If you run long_stats_slopes it will compute the within-subject difference first, put the result into each base

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

s N Greve) > 2. Re: Extracting the centroids from Desikan-Killiany atlas >(zuxfoucault Wong) > 3. Unsubscribe Mailing List (Duy Nguyen) > 4. Unknown Label in following postprocessing with mne-python >(Daniel van de Velden) > 5. Re: Surface Err

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

# pbcmd = ... with a hashtag. you can also simplify the slurm command (remove the --mail flags and the -o logfile location flags) your cluster partition may not be called "work" either. Best, Martin Am 22.02.2018 um 16:43 schrieb Martin Reuter: Hi Lea, I wrote that script to

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

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

foreach? surfreg --s $subject --t fsaverage_sym --lh --xhemi foreach? end Thanks, Lanbo On Tue, Jan 16, 2018 at 4:46 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: Hi Lanbo,

Re: [Freesurfer] Freesurfer longitudinal templates failed - time points from different scanners

Hi Sara, the base (subject template) is pretty robust. Not sure what goes on that it fails on 50% of your images. You should debug to see why it fails? - look at the input images, e.g. the norm.mgz from both your time points from the cross sectional processing - check the log file for the

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

. Secondly, how I can get the change rate after construct left -right registration. Thanks, Lanbo On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: Hi Lanbo, you could look at longitudinal changes of th

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Lanbo, you could look at longitudinal changes of the left-right difference in volume per ROI. Or do you mean on the cortical thickness map (I have never done that, but probably works similarly, construct left -right registration, compute difference, then run the LME on that). Best,

Re: [Freesurfer] Longitudinal MRI but different scanner

Hi Shane, not really. You can of course run images through the stream. You will get measurements, but you will not know how much of that is caused by the scanner or by disease (or drug,etc). If you have 2 groups, you could model the scanner as a co-var, but there could be a group scanner

Re: [Freesurfer] Intracranial Volume

Hi Tamara, yes, it is in the aseg stats . You can extract that information for all subjects using asegstats2table Best, Martin Am 23.11.2017 um 20:43 schrieb Tamara Tavares: Hello, Just a quick question regarding the computed intracranial volume. I have ran Freesurfer version 5.1 and I

Re: [Freesurfer] feeding data not processed with longitudinal pipeline into Linear Mixed Effects (LME) model

Hi Lara, yes that is possible (and it also makes sense in early childhood as the longitudinal stream assumes no (or only minimal) head growing). Best, Martin Am 14.11.2017 um 19:03 schrieb Lara Foland-Ross: > Hello Freesurfer experts, > > I have two longitudinal datasets. In each dataset,

Re: [Freesurfer] longitudinal base error. (not a netCDF file)

Hi Paul, you can try to re-run from scratch (ensure there is enough space on the disk) and if you can replicate the problem start dropping some of the flags (like the parallel and the bigventricles etc, to find out if this is caused by one of the flags.) Anyway it looks more like an IO

Re: [Freesurfer] significant of long_mris_slopes

Hi Lanbo, the first command computes the slope of within-subject linear fits (the rate, so the unit is mm/time). You use —generic time which means that the time is 1 2 3 … It is better to put the real time, e.g. in years for a longitudinal study. the second command is a

Re: [Freesurfer] Fwd: running cross sectional analysis on .long outputs only

Hi Garret, sure, there is no need to run qcache at all. Assuming you do a thickness analysis, you can directly use mris_preproc to register all thickness maps from only the first time point to fsaverage and smooth them (there you need to pass a list of only the first longidutinal time points:

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

Hi Chris, thanks, can you send the images and the exact commands. We have had success in the past, could be that you have a special case (e.g. maybe we never tested registration across different resolutions or whatever?). Thanks, Martin https://gate.nmr.mgh.harvard.edu/filedrop2/

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

Re: [Freesurfer] qdec.table_ref

Hi Amy, please send your questions to the freesurfer email list . Try replacing ID with fsid , also you may need to fix the white spaces (replace multiple spaces with a single space or tab). Best, Martin > On 9. Oct 2017, at 03:09, 田阿敏 <237416...@qq.com> wrote: > > > Hi~ > > I am Amy from

Re: [Freesurfer] failed -base processing with 1 tp

Hi Michelle, it should work like this. I don't know if it was tested with the -3T and -mprage flags. You can try to omit these flags (for testing only). Also the SB017 has been processed cross sectionally before, right? For debugging, you can also look at the individual steps in the base

Re: [Freesurfer] freesurfer longitudinal pipeline

the timepoints. Is there a command to perform this operation? Also, will the "-qdec-long" flag replace the "--s" flag because the qdec table will contain the names of the fsid? Best, Paul On Wed, Sep 27, 2017 at 11:38 AM, Martin Reuter <mreu...@nmr.mgh.h

Re: [Freesurfer] freesurfer longitudinal pipeline

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

Re: [Freesurfer] Longitudinal increase in thickness/volume

Hi Caleb, is this in a single subject or a group result? In a single subject almost anything is expected. E.g. small motion can cause thickness changes , so can hydration levels. Best, Martin Am 21.09.2017 um 16:53 schrieb Huang, Caleb (NIH/NINDS) [F]: Hello, I'm tracking atrophy in

Re: [Freesurfer] longitudinal freesurfer- different scanners

Yes, see also my answers from 08 and 11 of September on the list. Best, Martin Am 17.09.2017 um 19:42 schrieb Martijn Steenwijk: The longitudinal pipeline will not overcome (contrast) differences due to scanner differences. If you register the scans to eachother you will see that there

Re: [Freesurfer] Longitudinal processing -qcache ERROR

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

Re: [Freesurfer] longitudinal freesurfer- different scanners

below I meant you could run it only on the first two time points. Maybe there is already enough power to see effects. Best, Martin Am 08.09.2017 um 09:13 schrieb Martin Reuter: Hi Michelle, when scanners (or even scanner hardware, like head coil or software upgrades etc) change

Re: [Freesurfer] longitudinal freesurfer- different scanners

Hi Michelle, when scanners (or even scanner hardware, like head coil or software upgrades etc) change in a longitudinal study you will have difficulties finding out whether the changes you see are real anatomical changes or scanner effects. This is true for any software pipeline (longitudinal

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