Re: [Freesurfer] longitudinal study

[Martin Reuter]

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 scanner)
- created independently and therefore will look more different from each other 
than the surfaces from the long stream.

Best, Martin

> On 25. Sep 2020, at 15:55, Douglas N. Greve  wrote:
> 
> What is your command line for visualization? Can you also show the base image 
> as an underlay?
> 
> On 9/24/2020 6:54 PM, KennethSPrice wrote:
>> External Email - Use Caution
>> 
>> Hello,
>> I am running a longitudinal study and am examining the pial surface for my 2 
>> timepoints. The surfaces are slightly offset. Will this effect my 
>> statistical analysis for volume and thickness? I have attached the pial 
>> surface for each time point to this email. Should I be examining 
>> timpoint1.long and timepoint2.long instead?
>> 
>> Thanks,
>> Ken
>> 
>> 
>> Sent with ProtonMail  Secure Email.
>> 
>> 
>> 
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Re: [Freesurfer] starting longitudinal pipeline after mri_robust_template

[Martin Reuter]

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, 
>  
> I have a question regarding the longitudinal pipeline: Is it possible to 
> start the longitudinal pipeline after a template (using mri_robust_template) 
> has already been created in a separate step? 
>  
> Thank you so much, 
>  
> Marisa 
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Re: [Freesurfer] lta files longitudinal pipeline

[Martin Reuter]

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 problems. It will not be the right 
tool, if heads grow (as a longitudinal analysis will only provide measurements 
after global scaling is removed between time points). 

Best, Martin


> On 7. Oct 2020, at 10:54, Marisa Johanna Nordt  wrote:
> 
> External Email - Use Caution
> Hi, 
>  
> I have a question about the lta files from the longitudinal pipeline (using 
> the –affine flag). Instead of just one .lta file from each timepoint to the 
> template 3 different .lta files are saved  
> -tp1_to_templ_norm.lta,  
> -tp1_to_templ_affine.lta,  
> -tp1_to_templ.lta 
>  
> Is the one created last (tp1_to_templ.lta) the final lta-file that I can use 
> to align additional files from tp 1 to the template? 
>  
> Thanks a lot! 
> Marisa 
> 
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Re: [Freesurfer] Question: Longitudinal Edits

[Martin Reuter]

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 subjects. If you want to quantify small 
changes in only a few subjects, you need to make sure that FS results are clean 
and correct. If you are running a population study with 30.000 people you 
cannot do manual edits at all and have to resort to a quality control paradigm. 

Furthermore, the longitudinal stream additionally benefits from having the 
subject template (aka “base”). Usually it is sufficient to edit that instead of 
all time points (e.g. for skullstrip or surface related problems). 

In short FreeSurfer does not require edits, it allows users to include edits if 
they like. It is recommended to check results. Never trust any automated tool 
blindly. 

Best, Martin


> On 22. Oct 2020, at 03:46, Suzan Maleki  wrote:
> 
> 
> Dear Martin,
> 
> The time and effort of the FreeSurfer team is really appreciated. I would be 
> grateful if you explain to what extent it is necessary to apply manual edits 
> for longitudinal processing ? 
> I have read the FS longitudinal tutorial and noticed so many manual edits 
> need to be done on Cross > Base >Long scans. For example, having two 
> time-points that are 3 months apart, is it really necessary to do manual 
> edits for all the individuals ? 
> I am wondering what are the reasons that necessitate several manual edits for 
> longitudinal pipeline, considering that FreeSurfer is one of the best 
> available and commonly used neuroimaging softwares and supposed to be fully 
> automated. 
> Also, how much those manual edits will affect the reproducibility of the 
> processing ?
> Thanks a lot for your help,
> Kind regards,
> Suzan 
> 
> -- 
> Suzan Maleki
> PhD Student
> 
>  <>Brain, Mind and Society Research Hub
> Turner Institute for Brain and Mental Health
> School of Psychological Sciences
> Monash University
> 770 Blackburn Road
> Clayton VIC 3800 Australia
> 
> E: suzan.mal...@monash.edu 
> W: www.brainmindsociety.com 
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Re: [Freesurfer] --inittp 0 in mri_robust_template

[Martin Reuter]

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 theoretically not totally unbiased (due 
to the special role of the initial target). Now since all get resampled, this 
potential bias is very small (i.e. could not be measured) , so I selected this 
to be the default in the interest of having a fast registration. Further the 
randomness across subjects will remove any potential remaining bias in a group 
analysis.

Now if you specify no init, we will first create a really bad looking template, 
register to that and iterate (so it is completely unbiased), but will take much 
longer to converge. I don’t recommend doing this. 

Best, Martin

> On 17. Sep 2020, at 15:12, Marisa Johanna Nordt  wrote:
> 
> 
> Hi, 
>  
> I have a question regarding the flag  -- inittp 0 (no init ) in 
> mri_robust_template. What does ‘no init’ mean in this context and which 
> consequences arise from using this flag? 
>  
> Thank you! 
> Best, 
> Marisa 
> 
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Re: [Freesurfer] error message using mri_robust_template

[Martin Reuter]

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 it was 
too tight and numerical instabilities often triggered this, when it was totally 
fine to continue). So try that first and let me know. 

Best, Martin


> On 16. Sep 2020, at 10:27, Marisa Nordt  wrote:
> 
> 
> 
> Hello,
>  
> I am using mri_robust_template with the ‘--affine’ option to create 
> individual templates (using freesurfer version 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). For each 
> timepoint I use that timepoint's T1.mgz as the input. For some subjects this 
> works well. However, for others I am receiving an error message (* WARNING: 
> TP 3 to 1 did not converge !!  MatrixLog Error: Result too imaginary to 
> ignore). I am attaching the full command and the error message below. 
> Do you have thoughts on how to trouble-shoot this issue? I have looked at the 
> input
> files and these seem to be ok.
> Thank you!
> Best,
> Marisa
> 
> mri_robust_template --template template.nii.gz --affine --satit \
> --mov Tp1T1.mgz Tp2T1.mgz Tp3T1.mgz \
> --lta Tp1totemplate.lta Tp2totemplate.lta Tp3totemplate.lta \
> --mapmov Tp1totemplate.nii.gz Tp2totemplate.nii.gz Tp3totemplate.nii.gz
> 
>  
> - running loop to estimate saturation parameter:
> * WARNING: TP 3 to 1 did not converge !!
>  
>  MatrixLog Error:
>   Result too imaginary to ignore! ( 6.23199e-16 )
>  A = 1.006576323240725 0.003084002656233406 -0.03645397216347104
> -0.006991580325416484 1.011866325424678 -0.05229335553407307
> 0.03777040431253831 0.04392492645068569 1.002740736902102
>  
>  T = (1.00563233346774,0.0606675705194677) 
> (0.001071185761943805,0.00660486005552916) 
> (0.006657281419514499,0.004121077514717164)
> (0,0) (1.009918718632024,-3.183217578417441e-16) 
> (-0.001219644877272269,-0.006241389920134279)
> (0,0) (0,0) (1.00563233346774,-0.06066757051946813)
>  
>  U = (0.06522427283350557,-0.4086418628970923) 
> (-0.4512115300813958,-0.6429736578063935) 
> (0.4435972821778756,0.1223605486029275)
> (0.1324402433691656,-0.5811769288411271) 
> (0.396861124383305,0.4645450375452963) 
> (0.5209342533284942,0.004429342327522456)
> (-0.6671781011025059,-0.1682972455202441) 
> (-0.001010631409214958,0.09844371568609764) 
> (-0.959193687357,0.7102764951350742)
>  
>  fro( real(U * T * U^*) - A) = 1.736855929375805e-15
>  
>  log(A) = (0.007247004124560403,-2.550043509685906e-16) 
> (0.003840124735798771,3.469446951953614e-17) 
> (-0.03616149457717018,1.07552855510562e-16)
> (-0.00594730233232413,1.249000902703301e-16) 
> (0.0129351237191556,-2.289834988289385e-16) 
> (-0.05197693653405921,5.334274688628682e-17)
> (0.03770072871406291,-2.432949675057472e-16) 
> (0.0434964642601452,7.199102425303749e-17) 
> (0.004553620359034822,-2.775557561562891e-16)
>  
>  fro( exp(real(log(A))) - A)  = 1.311226128713136e-15
>  
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Re: [Freesurfer] intersubject longitudinal analysis

[Martin Reuter]

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


> On 31. Aug 2020, at 04:02, KennethSPrice  wrote:
> 
> 
> 
> 
> Hello Freesurfers!
> 
> I am working through the longitudinal tutorial found here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial 
> 
> 
> To keep it simple, I ran longitudinal processing on 2 timepoints for one 
> subject. My qdec file had only two entries. I would like to look at pct 
> difference in thickness for one subject. I ran
> 
> long_mris_slopes --qdec qdec.dat --meas thickness --hemi lh --do-avg 
> --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache 
> fsaverage --sd $SUBJECTS_DIR
> 
> When I run the overlay I get an error saying that "the overlay cannot be 
> loaded", although the file exists.  
> 
> freeview -f 
> $FREESURFER_HOME/subjects/fsaverage/surf/lh.pial:overlay=$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh:overlay_threshold=2,5
> 
> First of all, is this method sound in order to visualize pct change in 
> thickness for one subject? If so, why is the overlay not loading?
> 
> Best,
> Ken
> 
> 
> Sent with ProtonMail  Secure Email.
> 
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Re: [Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

[Martin Reuter]

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 
your own. 

Eventually we plan to upgrade FastSurfer to also run with 7.1, which also 
requires to modify the surface processing script to better represent the steps 
that 7.1 is performing in recon-all. 
Initial tests of this however did not show improvements. So better stick with 
6.0 for now. 

Also please note that FastSurfer questions should currently be asked on the 
FastSurfer GitHub Issue page https://github.com/deep-mi/fastsurfer 
  

Best, Martin


> On 20. Aug 2020, at 15:59, Barbara Kreilkamp  wrote:
> 
>External Email - Use Caution
> 
> Dear all,
> 
> I noticed FastSurfer also seems to run with a 7.1.0 FS version.
> 
> Or is there any reason not to do this?
> 
> Thank you,
> 
> Kind wishes,
> Barbara
> 
> 
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Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

[Martin Reuter]

Hi Lara, 

if you are sure you will stick with 15fwhm, you can do either one. 
If you plan to also run analysis at different fwhm, you can first map
and then smooth at different levels. 

Either way, it should not make a big difference. 

Best, Martin

On Fri, 2020-02-21 at 15:41 +, Lara Foland-Ross wrote:
> External Email - Use Caution
> 
> Hi Martin, 
> 
> Thanks. This makes a lot of sense. I'll merge my subjects' surface
> files that have been registered to fsaverage, then follow the rest of
> the protocol listed at 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels.
> 
> One quick follow up question - when I use mris_preproc to merge
> thickness files, should I merge subjects' smoothed data (e.g.,
> lh.thickness.fwhm15.fsaverage.mgh) and skip the smoothing step (run
> using mri_surf2surf)? 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 Martin Reuter <
> mreu...@nmr.mgh.harvard.edu>
> Sent: Friday, February 21, 2020 1:10 AM
> To: Freesurfer support list
> Subject: 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 name base can be misleading and has
> nothing to do with "baseline". That is why we try to refer to it as
> "subject_template" in most documentation now.
> Anyway, one never analyzes results of the subject template, but of
> the
> final fine-tuned time points after the -long runs.
> 
> In your case, you can simply process the images independently (cross
> sectionally) and still perform the statistical LME analysis where you
> group results from the same subject.
> 
> For measures from the stats files (aseg, aparc...) you just obtain
> those from the cross dirs with asegstats2table. For surface results
> you
> simply map everything to fsaverage (mris_preproc) and then run the
> LME.
> 
> Best, Martin
> 
> 
> On Thu, 2020-02-20 at 21:53 +, Lara Foland-Ross wrote:
> > External Email - Use Caution
> > 
> > Hi there,
> > 
> > Reposting this message (below). Would appreciate any guidance you
> > can
> > provide.
> > 
> > Thanks,
> > Lara
> > 
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu <
> > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-
> > Ross
> > 
> > Sent: Friday, February 7, 2020 12:46 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] some basic questions regarding longitudinal
> > analyses  in Freesurfer
> > 
> > External Email - Use Caution
> > 
> > Hello,
> > 
> > I'm analyzing a large dataset using an LME model to examine
> > longitudinal changes in brain structure that vary as a function of
> > group (patients vs controls). Because some participants were
> > scanned
> > several years apart in early childhood, the intra-subject
> > registration failed in the longitudinal processing stream. For this
> > reason, my data were not initially processed using the longitudinal
> > processing stream within Freesurfer. However, per this thread -
> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html
> >  - I still plan to use the LME model. As I understand it, this
> > model
> > assumes that the longitudinal processing stream was
> > conducted.  Therefore, I have the following questions:
> > 
> > 1. would the "base" (aka within-subject template) for each subject
> > be
> > = time point 1?
> > 2. would the "long run" for each subject be = each subject's
> > individual time points?
> > 3. assuming #1 and 2 are correct, would I need to set my directory
> > structure to match that used in the longitudinal processing stream?
> > For example, if I have 2 time points for subject 1234, and they are
> > initially labeled "1234.time1" and "1234.time2", then in order to
> > run
> > the LME model, I would create a copy of "1234.time1" and rename the
> > copy as "1234" to indicate to the software 

Re: [Freesurfer] Error in long_mris_slopes

[Martin Reuter]

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 working on a longitudinal FreeSurfer pipeline in order
> to compare cortical thickness changes across the time. I’m using
> FreeSurfer version 6.0.0 (OS: Scientific Linux 7.3). I already
> processed the recon-all, -base and -long processing steps.
> Now I’m trying to run the “long_mris_slopes“ processing in order to
> prepare the data for a two stage model analyze. But there is an
> error. 
> The command:
> long_mris_slopes --qdec ./qdec.dat --meas thickness --hemi lh  --do-
> spc --do-label --time month --qcache fsaverage --sd $SUBJECTDIR
> 
> At first everything seems to work well for the 1st subject and then:
>  ==
> SUBJECT CBTPD-001/template_CBTPD-001  mapping label to QCache
> (…)
> Writing label file /data/guillaume/ParkAnx3/freesurfer/results/CBTPD-
> 001/template_CBTPD-001/label/lh.long.cortex.fsaverage.label 167889
> mri_label2label: Done
> 
> Traceback (most recent call last):
>   File "/opt/mumc/apps/freesurfer-6.0.0/bin/long_mris_slopes", line
> 868, in 
> dirname = tempfile.mkdtemp('',prefix,'')
>   File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp
> _os.mkdir(file, 0700)
> OSError: [Errno 2] No such file or directory: './tmp-CBTPD-
> 001/template_CBTPD-001_lh_thickness_wuK7ZI'
> 
> It seems like the output “lh.long.cortex.fsaverage.label” has been
> created for this subject. But then there is a missing “tmp” folder.
> I haven’t find this error in the archives. Does anyone have an idea
> of how to fix it ?
> 
> Best,
> Guillaume 
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Re: [Freesurfer] questions about batch running longitudinal data using long_submit_jobs on cluste

[Martin Reuter]

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 +, Huang, Yiting wrote:
> Hi there,
> 
> I am trying to run some longitudinal data using freesurfer
> long_submit_jobs command on cluster. I have double checked my
> directory and files setup according to freesurfer longitudinal
> preprocessing wiki:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts. And it
> seems there is no problem with my setup.
> However, when I run the command it keeps sending me error as below:
> 
> launchpad:yh917[21] long_submit_jobs --qdec long.qdec.table.dat --
> cdir $PWD/../ --cross --base --long --pause 5 --max 200 --queue
> max100
> File "/usr/local/freesurfer/stable6_0_0/bin/long_submit_jobs", line
> 94
> print "job submission failed, maybe unknown host "+hostname
>^
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print("job submission failed, maybe unknown host "+hostname)?
> 
> I can't figure out the reasons. Any help please?
> 
> Thanks,
> Yiting
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Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

[Martin Reuter]

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 name base can be misleading and has
nothing to do with "baseline". That is why we try to refer to it as
"subject_template" in most documentation now. 
Anyway, one never analyzes results of the subject template, but of the
final fine-tuned time points after the -long runs. 

In your case, you can simply process the images independently (cross
sectionally) and still perform the statistical LME analysis where you
group results from the same subject. 

For measures from the stats files (aseg, aparc...) you just obtain
those from the cross dirs with asegstats2table. For surface results you
simply map everything to fsaverage (mris_preproc) and then run the LME.

Best, Martin


On Thu, 2020-02-20 at 21:53 +, Lara Foland-Ross wrote:
> External Email - Use Caution
> 
> Hi there, 
> 
> Reposting this message (below). Would appreciate any guidance you can
> provide.
> 
> Thanks,
> Lara
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-Ross 
> 
> Sent: Friday, February 7, 2020 12:46 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] some basic questions regarding longitudinal
> analyses  in Freesurfer
> 
> External Email - Use Caution
> 
> Hello,
> 
> I'm analyzing a large dataset using an LME model to examine
> longitudinal changes in brain structure that vary as a function of
> group (patients vs controls). Because some participants were scanned
> several years apart in early childhood, the intra-subject
> registration failed in the longitudinal processing stream. For this
> reason, my data were not initially processed using the longitudinal
> processing stream within Freesurfer. However, per this thread - 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html
>  - I still plan to use the LME model. As I understand it, this model
> assumes that the longitudinal processing stream was
> conducted.  Therefore, I have the following questions:
> 
> 1. would the "base" (aka within-subject template) for each subject be
> = time point 1?
> 2. would the "long run" for each subject be = each subject's
> individual time points?
> 3. assuming #1 and 2 are correct, would I need to set my directory
> structure to match that used in the longitudinal processing stream?
> For example, if I have 2 time points for subject 1234, and they are
> initially labeled "1234.time1" and "1234.time2", then in order to run
> the LME model, I would create a copy of "1234.time1" and rename the
> copy as "1234" to indicate to the software that this should be used
> as the base. And, I would also need to rename "1234.time1" and
> "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to
> indicate that these folders should be used as the longitudinal time
> points.
> 
> Does this seem appropriate?
> 
> Thanks in advance for your help,
> Lara
> 
> Lara Foland-Ross, Ph.D.
> Senior Research Associate and Imaging Lab Manager
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
> 
> 
> 
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> 
> 
> 
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> 
> 

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Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

[Martin Reuter]

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 longitudinal data. The percent 
change (2 step approach) is a remainder of the time before we had the LME. Both 
models are similar only if the longitudinal data has the same number of time 
points for each subject and if those time points are equally spaced. That is 
rarely the case and LME can account for that. 

Best, Martin



> On 17. Jan 2020, at 00:59, Swati Rane  wrote:
> 
> External Email - Use Caution
> 
> 
> It is the file computed longitudinal processing that represents the rate with 
> respect to the thickness at the first time point computed by long_mris_slopes.
>  
> Swati
>  
>  
>  
>  
> 
> Swati Rane Levendovszky, PhD
> Interim Director, Diagnostic Imaging Sciences Center
> Assistant Professor, Integrated Brain Imaging Center
> Radiology
> University of Washington
> Box 357115 | AA035 HSB | Seattle, WA 98195
> srle...@uw.edu  | Ph: 206 543 6159  
> Web: https://sites.google.com/site/uwswatirane/ 
> 
> 
>  
>  
> From:  on behalf of "Greve, Douglas 
> N.,Ph.D." 
> Reply-To: Freesurfer support list 
> Date: Thursday, January 16, 2020 at 3:26 PM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines
>  
> Sorry, what is "pc1"? 
> 
> On 1/14/2020 9:44 AM, Swati Rane wrote:
>> External Email - Use Caution
>> Hello,
>>  
>> I was wondering if someone could answer my question below
>>  
>> Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.
>>  
>> Are there any set of parameters that should be set differently when using 
>> pc1 instead of thickness files?
>>  
>>  
>> Thanks!
>> Swati
>>  
>>  
>>  
>> 
>> Swati Rane Levendovszky, PhD
>> Interim Director,Diagnostic Imaging Sciences Center
>> Assistant Professor,Integrated Brain Imaging Center
>> Radiology
>> University of Washington
>> Box 357115 | AA035 HSB | Seattle, WA 98195
>> srle...@uw.edu  | Ph: 206 543 6159 
>> Web: https://sites.google.com/site/uwswatirane/ 
>> 
>> 
>>  
>>  
>> From:  
>>  on behalf of Swati Rane 
>>  
>> Reply-To: Freesurfer support list  
>> 
>> Date: Friday, January 10, 2020 at 10:06 AM
>> To: "freesurfer@nmr.mgh.harvard.edu"  
>>  
>> Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines
>>  
>> External Email - Use Caution
>> Hello FreeSurfer Developers,
>>  
>> I'm attempting to compare longitudinal cortical thinning rates (pc1) between 
>> 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that 
>> you could use the multiple comparisons corrections that come with it but 
>> does not comment on using the mri_glmfit-sim option. 
>>  
>> I just want to confirm whether there is anything prohibiting me from using 
>> mri_glmfit-sim. Are there any set of parameters that should be set 
>> differently when using pc-1 instead of thickness files?
>>  
>> Also, would you do a stricter correction and stick to the longitudinal model 
>> or prefer the linear mixed effects model and do a FDR? How do you decide 
>> between the two?
>>  
>> Thanks!
>> Swati
>>  
>>  
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> 
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Re: [Freesurfer] using different Freesurfer versions for cross-sectional & longitudinal processing

[Martin Reuter]

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.  
> wrote:
> 
> I think it should be ok in principle, though it might fail because the v6 
> long stream expects there to be certain files with certain names, and they 
> might not be there with 5.1.
> 
> On 12/16/2019 2:49 PM, Morgan Botdorf wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer Experts,
>> 
>> We have child data that was previously processed cross-sectionally using 
>> version 5.1. We are now interested in looking at the data longitudinally. 
>> Can the longitudinal processing stream in version 6.0 be used on data that 
>> was processed cross-sectionally using 5.1? Or is it better that we reprocess 
>> the data using 6.0. We appreciate any help you can provide!
>> 
>> Thank you,
>>  
>> Morgan Botdorf, M.S.
>> Doctoral Candidate
>> Neurocognitive Development Lab
>> University of Maryland, College Park
>> mbotd...@terpmail.umd.edu 
>> Office: 301.405.5922 
>> 
>> 
>> 
>> 
>> ___
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>> 
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Re: [Freesurfer] Question re: Longitudinal processing stream transforms.

[Martin Reuter]

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 original and the base space. 

Your command uses as mov the tp1.long.base brain.mgz file, which is already in 
base space. No need to map it to the template=base space again. In fact 
applying that transform will move it away. If you want to go from base back to 
original tp1 space, you need to invert the transform. 

Best, Martin


> On 16. Oct 2019, at 20:10, Jamie Hanson  wrote:
> 
> Dear FS List,
> 
> My group was trying to look at the overlap between cortical labels in the 
> longitudinal processing stream and I had a question re: use of transform 
> files. In brief, we followed the commands for the longitudinal processing 
> stream, creating a "subject-specific" template for each participant 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSummary
>  
> ,
>  using FS v.6.0). We processed T1w images multiple times and now, we wanted 
> to transform the time 1 and time 2 (native space) scans to their 
> subject-specific template. 
> 
> We used the following commands--
> mri_vol2vol --mov 
> $INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz
>  --o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta 
> $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta
>  --targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz
> 
> But when we did this for time 1 and time 2 scans, they were poorly aligned. I 
> also used the lta file for template to 001, but again things were poorly 
> aligned. Should we be using m3z files? Or combining different transforms? Any 
> guidance or suggestions are deeply appreciated.
> 
> Thanks much,
> Jamie.
> 
> 
> --
> Jamie Hanson
> Assistant Professor, Psychology
> Research Scientist, Learning Research and Development Center
> University of Pittsburgh
> Personal website: jamiehanson.org 
> 
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Re: [Freesurfer] Contents of Freesurfer digest...

[Martin Reuter]

Hi David, 

nobody can really tell you what will happen if you use the software outside its 
tested use cases. 5mm thick slices, with tumor resection is not what it has 
been designed to work with. And as I said, gad enhanced also not. It might give 
you meaningful results or not. The only way to find out is to try it and make 
sure to carefully inspect the segmentation visually (in all three views). Don’t 
be fooled by the nice looking within-plane images. They are smooth averages 
across 5mm. Missing resolution in the 3rd direction will allow you do only 
detect large volume changes due to loss of sensitivity. How much you loose is 
unclear. 

Best, Martin


> On 10. Oct 2019, at 21:11, David Kamson  wrote:
> Martin, thank you for these comments. These are extremely valuable!
> 
> Although my patients had tumors, these are cured (this is why I have so few 
> of them…) and have no residual mass effect/deformity beyond biopsy tracks / 
> small resection cavities. Thus far, I was able to get pretty accurate looking 
> segmentations of deep nuclei on aseg. Segmentation issues were associated 
> with the surface structures (e.g.  dura/falx being misclassified as gray or 
> brain tissue adjacent to resection cavities are correctly classified as brain 
> but GM/WM often misclassified).  
> 
> I’m OK restricting the analysis to ventricular and deep GM volume, since what 
> I’m trying to measure is marked atrophy of these structure after chemotherapy 
> which I guess is in the range of 1-5%/year. The changes are mostly marked 
> enough to enable a visual qualitative analysis, however, quantitative data 
> would be clinically more helpful to clarify when, and how much change to 
> expect after treatment.
> 
> Do you think increasing the number of time points analyzed (I have 4-6 scans 
> per year for each patient) could eliminate the noise from head 
> positioning/slicing as long as the volumetric trends remain consistent? 
> Again, the data would be normalized per individual and I would not use 
> absolute volume for any comparative analysis. 
> 
> Thank you again. This message board is of incredible value!
> 
> Best regards,
> David
> 
> 
> 
> 
>> ------
>> 
>> Message: 1
>> Date: Wed, 09 Oct 2019 10:48:48 +0200
>> From: Martin Reuter > <mailto:mreu...@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] Questions re slice thickness, aseg and
>> longitudinal analysis
>> To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Message-ID:
>> <7a4d059cb5cb42f390e03f523677a3362d17cb81.ca...@nmr.mgh.harvard.edu 
>> <mailto:7a4d059cb5cb42f390e03f523677a3362d17cb81.ca...@nmr.mgh.harvard.edu>>
>> Content-Type: text/plain; charset="UTF-8"
>> 
>> 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 (and different
>> slice angulations) in the scanner.
>> 
>> Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will
>> not work if tumor lesions are present. 
>> 
>> About your questions:
>> 
>> 1. Surfaces update the aseg, but if you are only interested in the
>> volumes, you can skip this expensive step (potentially at the cost of
>> slightly higher noise levels in your measurements).
>> 
>> 2. I think not (see above). 5mm is too low.
>> 
>> 3. Theoretically yes, but I have never tested if the scripts will do
>> it. You could run up to the aseg in the cross, then create base (up to
>> aseg) and then run the longs up to aseg. Not even sure you really need
>> the base aseg. You might be able to just run the initial base
>> registration step, obtain the transformations and median norm.mgz
>> image, could be sufficient for the long runs. 
>> 
>> 4. No. Gad images won't work. 
>> 
>> Best, Martin
>> 
>> 
>>>External Email - Use Caution
>>> Freesurfers,
>>> 
>>> First of all, I'd like to express my gratitude to the community for
>>> the support that keeps researchers like myself afloat!
>>> 
>>> 
>>> I have a unique set of oncology patients that I want to evaluate for
>>> brain atrophy in a retrospective longitudinal analysis.
>>> I was thinking about using Aseg.auto results to assess longitudinal
>>> volume changes, but before I invest all the time I 

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

[Martin Reuter]

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 (and different
slice angulations) in the scanner.

Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will
not work if tumor lesions are present. 

About your questions:

1. Surfaces update the aseg, but if you are only interested in the
volumes, you can skip this expensive step (potentially at the cost of
slightly higher noise levels in your measurements).

2. I think not (see above). 5mm is too low.

3. Theoretically yes, but I have never tested if the scripts will do
it. You could run up to the aseg in the cross, then create base (up to
aseg) and then run the longs up to aseg. Not even sure you really need
the base aseg. You might be able to just run the initial base
registration step, obtain the transformations and median norm.mgz
image, could be sufficient for the long runs. 

4. No. Gad images won't work. 

Best, Martin


On Mon, 2019-10-07 at 18:12 +, David Kamson wrote:
> External Email - Use Caution
> Freesurfers,
> 
> First of all, I'd like to express my gratitude to the community for
> the support that keeps researchers like myself afloat!
> 
> 
> I have a unique set of oncology patients that I want to evaluate for
> brain atrophy in a retrospective longitudinal analysis.
> I was thinking about using Aseg.auto results to assess longitudinal
> volume changes, but before I invest all the time I wanted to check
> with the community whether this makes any sense at all:
> 
> The dataset that looks like this:
> - 22 patients (no control dataset [yet])
> - 10-25 MRIs per patient acquired over 2-8 years in relatively
> uniform intervals
> - Patients had most of their scans on the same scanner, but
> scanners differed widely between patients
> - All patients have axial T1 post gadolinium scans of 1x1x5mm
> resolution (3D acquisition available in <10%)
> - About 80% of scans have an axial pre-contrast T1 sequence
> - All scans are skullstripped (third party algorithm)
> 
> I'm looking for crude changes, no subtleties; volumes of interest
> are:
> - Whole brain volume
> - White matter volume
> - Ventricular volume (mainly lateral ventricle)
> - Subcortical gray matter volume (whole thalamus most importantly)
> 
> I ran a few test analyses and to my surprise I was able to generate
> pretty acceptable surfaces, however, topology fixing took about 24H
> per scan, and I feel aseg.auto contained all the volumetric data I
> was really interested in.
> 
> My concrete questions are:
> 1) Does the full autorecon pipeline affect Aseg.auto? If there is no
> benefit, I could reduce the per scan analysis time from 28 hours to
> 1-2 h.
> 2) Would this low-resolution dataset be accepted by reviewers if used
> for Aseg? Should I do any quantitative validation beyond a visual
> quality analysis of Aseg?  
> 3) Can I perform a longitudinal analysis only for the Aseg results?
> 4) Is it OK to use T1-gad images for the analysis?
> 
> I'd appreciate any input!
> 
> Best regards,
> David O. Kamson, MD PhD
> Neuro-oncology fellow 
> Johns Hopkins Hospital &
> National Institutes of Health
> 
> 
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Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

[Martin Reuter]

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 cross, base and long
locally 

2. if that looks good, run cross do finalsurf edits if necessary and
complete cross runs. Then run base, do finalsurf edits and complete
base run. Finally run long. All should be fine.

Depending on the type of problem you are editing, usually it is
sufficient to edit these only in the base. 

And make sure you use fs60 (not sure which version you used). 

Best, Martin



On Fri, 2019-09-13 at 16:41 +, Douglas Merkitch wrote:
> External Email - Use Caution
> Hey all,
>  
> I have a group of subjects with 2 time points that I've run thru the
> longitudinal processing stream. All goes OK until I run the recon-all 
> -long and the resulting .long. subject dirs have the finalsurfs
> misaligned (i.e. one subject has the edits moved inferior and the
> other has them moved superior, causing drastic consequences to the
> pial/wm surfaces).
>  
> FYI these subjects were processed on a Linux-based high performance
> computing cluster and edits were made locally on a Linux virtual
> machine with subject dirs being transferred back and forth via scp.
> Not sure if this is relevant, but thought I’d mention it just in
> case.
>  
> I’ve uploaded a .tar file containing one of these longitudinal
> subject’s directories (i.e. both cross tps, base, and both resulting
> long tps) called ‘merkitch_upload_201980913.tar’ via the filedrop
> website.
>  
> Any help would be appreciated!
>  
> Thanks,
>  
> Doug
>  
> Douglas Merkitch
> Clinical Research Coordinator
> 
> 355 E. Erie St, Chicago, IL 60611
> 312-238-5911 office
> dmerki...@sralab.org
> 
> 
> sralab.org
> 
> Facebook   |   Twitter   |   YouTube
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Re: [Freesurfer] error in longitudinal stream command

[Martin Reuter]

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 "Unmatched" error ?
> 
> In our case, this error appears for both 5.3, 6.0 and dev, on 2
> different clusters.
> 
> All folders exist, are filled with data and reecon-all finished
> without error, plus hippocampus and brainstem
> all folders and readable: drwxrwsrwx (chmod 777 -R)
> In the base-tps - all time points are listed correctly.
> Re-running -base - did not solve the issue.
> Name has no underscores '_'
> 
> I didn't have this error on the local installation, so, I suspect it
> might be linked to sourcing some libraries/folders, since we had to
> source the mni folder to make it work.
> 
> Best,
> Alexandru.
> 
> 
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Re: [Freesurfer] [FREESURFER] longitudinal processing base_tmps does not exist error

[Martin Reuter]

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 resolve this error? I looked up the previous
> postings, but the recommendation (copying files in the same folder
> etc.) did not help.
> Thank you.
>  
>  
> $ recon-all -base template -tp 002_S_0295_S32678 -tp
> 002_S_0295_S567612 -sd $SUBJECTS_DIR
> Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> INFO: SUBJECTS_DIR is /Users/seonjoolee/ADNI_long/tmp
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin Seonjoos-iMac.nyspi.local 18.5.0 Darwin Kernel Version 18.5.0:
> Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64
> x86_64
>  
> Started at Wed Aug 7 10:24:55 EDT 2019 
> Ended   at Wed Aug 7 10:24:56 EDT 2019
> #@#%# recon-all-run-time-hours 0.000
> recon-all -s template finished without error at Wed Aug  7 10:24:56
> EDT 2019
> done
>  
>  
> $ recon-all -long 002_S_0295_S32678 template -all
> ERROR: file /Users/ll/ADNI_long/tmp/template/base-tps does not exist!
>  
>  
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Re: [Freesurfer] mri_robust_template in FMRIprep rotation should not scale error

[Martin Reuter]

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 underlying data to make sure that there are no 

artifacts, etc?



On 8/13/19 8:02 AM, Dylan Nielson wrote:

>

> External Email - Use Caution

>

> Hi Freesurfer folks,

>

> I'm running Freesurfer's longitudinal pipeline as part of FMRIprep and 

> I've got two subjects generating similar errors in the 

> mri_robust_template step, one of which I've copied below. I've defaced 

> these subjects and saved the working directories so I can share them 

> with you on the ftp site if you'd like.

>

> Thanks for your help,

>

> Dylan Nielson

>

> Error for subject 22477:

> RuntimeError: Command:

> mri_robust_template --satit --mov /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz --inittp 1 --iscale --template sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz --subsample 200 --lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta

> Standard output:

> $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

>

> --satit: Will estimate SAT iteratively!

> --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume.

> --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume.

> --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume.

> --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume.

>  Total: 4 input volumes

> --inittp: Using TP 1 as target for initialization

> --iscale: Enableing intensity scaling!

> --template: Using sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz as template output volume.

> --subsample: Will subsample if size is larger than 200 on all axes!

> --lta: Will output LTA transforms

> Setting iscale ...

> reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'...

> converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ...

> MRItoBSpline degree 3

> reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'...

> converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ...

> MRItoBSpline degree 3

> reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'...

> converting source 

Re: [Freesurfer] Applying Pial edits to Longitudinal

[Martin Reuter]

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 Freesurfers, 
> 
> I am trying to apply Pial edits to my longitudinal time point. I have tried 
> the command,
> 
> recon-all -long C002d.long.C002.base/ C002.base -mprage -3T -norm2-b 20 
> -norm2-n 5 -autorecon2 -autorecon3
> 
> But receive the error, 
> 
> Unmatched “.
> 
> I am using  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> 
> Do you know what could be the reason for this?
> Sierra 
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Re: [Freesurfer] Advantage of having skull for longitudinal processing?

[Martin Reuter]

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:
> 
> External Email - Use Caution
> 
> 
> Hi Freesurfer team,
> 
> I'm thinking of pre-skullstrip'ing my brains prior to being input into 
> FreeSurfer.
> 
> My fear was this information in the skull might be useful during 
> mri_robust_register or mri_robust_template for longitudinal analyses:
> 
> Martin discusses this in his Freesurfer workshop talk at 9 minutes in 
> (youtube: http://www.youtube.com/watch?v=vxJODPBLd3M=9m21s 
> ) where the heatmap 
> covers parts of the skull and the Freesurfer wiki which mentions that the 
> Tukey biweight will deweight regions of noise like tongue/eye/neck 
> differences.
> 
> But it appears the longitudinal stream registers everything on each 
> cross-sectional's norm.mgz to create the fused norm -- which is skullstripped 
> and missing neck/tongue/eyes/skull already.
> 
> Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz, 
> etc. do not have a skull for longitudinal processing?
> 
> Thanks,
> Adam 
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Re: [Freesurfer] Geometric distortion

[Martin Reuter]

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 collected exactly (sequence, scanner etc). 

Best, Martin

On Mon, 2019-05-13 at 21:06 -0700, Martin Juneja wrote:
> External Email - Use Caution
> Thank you Matthew for your reply.
> 
> I just ran recon-all to get cortical thickness, area and volume
> values for specific ROIs using the steps here: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
> and correlated the morphometric values with behavioral data.
> I am not sure how can I address reviewer's comment.
> 
> Any help would be really appreciated.
> 
> On Mon, May 13, 2019 at 5:41 PM Glasser, Matthew 
> wrote:
> > External Email - Use Caution
> > There are different kinds of geometric distortion that affect your
> > data to differing extents.  What kind of MRI data was in your
> > study?
> > 
> > Matt.
> >  
> > From:  on behalf of Martin
> > Juneja 
> > Reply-To: Freesurfer support list 
> > Date: Monday, May 13, 2019 at 6:53 PM
> > To: Freesurfer support list 
> > Subject: [Freesurfer] Geometric distortion
> >  
> > External Email - Use Caution
> > Hi experts,
> >  
> > I have following question from one of the reviewers regarding
> > recon-all pipeline:
> > "Was geometric distortion corrected? If not, this should be
> > discussed or mentioned in the study limitation."
> > I was wondering if the reviewer is referring to following step in
> > the recon-all pipeline. Could you please help me in addressing this
> > concern by the reviewer?
> >  
> > Thanks.
> > MJ
> > Cortical Parcellation (-cortparc, -cortparc2)
> > Assigns a neuroanatomical label to each location on the cortical
> > surface. Incorporates both geometric information derived from the
> > cortical model (sulcus and curvature), and neuroanatomical
> > convention. Calls mris_ca_label. -cortparc creates
> > label/?h.aparc.annot, and -cortparc2 creates
> > /label/?h.aparc.a2005s.annot.
> >  
> > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature.
> > If you are not the intended recipient, be advised that any
> > unauthorized use, disclosure, copying or the taking of any action
> > in reliance on the contents of this information is strictly
> > prohibited. If you have received this email in error, please
> > immediately notify the sender via telephone or return mail.
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> 
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Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

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 ? 

If you re-scan in short time interals (and if these are young and
healthy, then even for mid to long intervals), you would not expect
anatomical aging effects. Then the variance is probably mainly
acquisition noise (e.g. induced by motion etc, see eg 
https://www.ncbi.nlm.nih.gov/pubmed/25498430) plus some processing
noise (different surface placement etc). Maybe there are also hydration
effects (see https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). 

Best, Martin


On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
> Dear all,
>  
> I’m a beginner in using the longitudinal processing pipeline (as well
> as statistical analysis) and it would be great to get some insights
> or hints to analyze my data.
>  
> I have a dataset consisting of 11 subjects each acquired at 7
> different time points with an isotropic resolution of 1 and 0.8 mm at
> 3T using a 64-channel head coil. Using that dataset I want to
> investigate short term differences in e.g. cortical thickness with
> the goal to assess the degree of biological variance during that time
> period.
>  
> I have plotted the mean cortical thickness of each time point of
> every subject (using lme_timePlot and lme_lowessPlot) showing a
> somewhat random distribution across time and from my perspective
> fairly high standard deviation. I wanted to have a look at the
> individual percent change by overlaying the symmetric percent change
> on fsaverage, but wasn’t quite sure of the scale. Is it in percent?
> So in case I set the scale bar between 1 and 5, the color relates to
> 1 to 5 percent?
>  
> What other ways would make sense to have a look at? I definitely
> cannot compare groups, as there is just one. The days and time of
> acquistion are rather randomly choosen, so I potentially cannot use
> either as a covariate.  
>  
> Best,
> Falk
>  
> ...
>  
> 
> University Clinic for Neurology
>  
> Otto-von-Guericke-university Magdeburg
> Medical faculty
> Leipziger Str. 44
> 39120 Magdeburg
>  
> Phone +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de
> http://www.kneu.ovgu.de/kneu.html
>  
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Re: [Freesurfer] Longitudinal Gray/white Contrast Measure

[Martin Reuter]

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:

- take a look at that script and run the same commands manually for the
w-g.pct.mgh files

- convert the pct.mgh  files to thickness format, rename volume to
something else, rename the w-g.pct to volume , run long_mris_slopes and
rename everything back. 

Best, Martin



On Mon, 2019-05-06 at 16:41 -0700, WON JONG CHWA wrote:
> External Email - Use Caution
> Dear FreeSurfer experts,
> 
> I am currently running a longitudinal analysis in FreeSurfer v5.3 to
> look at changes in volume and gray/white contrast. I ran all the
> processing steps and used this command below to look at results for
> volume:
> 
> long_mris_slopes --qdec ./qdec/qdec.table.dat --meas volume --hemi lh
> --do-label --do-rate --time years --qcache fsaverage --sd
> $SUBJECTS_DIR
> 
> We also would like to look at change in gray-white matter intensity
> ratio over time (between 2 timepoints) as well, but there is no
> separate measure defined for it. I was wondering what we can do to
> calculate this.
> 
> Thank you.
> William
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Re: [Freesurfer] Issue with longitudinal surfaces

[Martin Reuter]

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 time points?

Best, Martin


On Tue, 2019-04-09 at 11:04 +, maxime GUILLAUME wrote:
> External Email - Use Caution
> Dear freesurfer experts, 
> 
> I re-send this question because i didn't received (or missed) the
> answer from the first time i sent it.
>  
> I am performing a longitudinal study (2 time points, 1 year apart) in
> patients with Multiple Sclerosis using freesurfer 6.0.
>  
> After following the tutorial for the CROSS, the BASE (where I only
> performed few manual edits of the surfaces) and the LONG steps, I am
> facing a problem with the results of the longitudinal pipeline:
>  
> If I overlay the final surfaces of the different time points (the
> white and pial surfaces of the LONG step) on the BASE template using
> the command given in the fs tutorial, there are important differences
> between the two time points (see figure attached). This happened only
> on a subset of my subjects.
> One of our collaborators in this study suggested that this might be
> because the patient was positioned differently in the two time
> points, in particular with respect to the z axis (and indeed the
> major differences between the two surfaces are in the topmost area of
> the brain).
> Does anybody have experienced the same problem? And how can I correct
> for it?
>  
> Thank you in advance for your help.
> 
> (*in the captures surfaces of the first visit are in red and blue and
> in lighter tones for the second visit) 
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Re: [Freesurfer] freesurfer longitudinal issue

[Martin Reuter]

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 should all be 
perfectly aligned. If that is not the case something went wrong with your 
processing - maybe the way you called recon-all or maybe the 
editing/re-reunning process. 

I would recommend to 
- rename base and the 2 long directories
- re-run the base and inspect surface
- re-run both the long (with recon-all -long …) and inspect if everything is 
aligned. 

Best, Martin



> On 11. Apr 2019, at 11:43, maxime GUILLAUME  wrote:
> 
> Hi Martin,
> 
> Thank you for your answer, but (un)fortunatelly, I double checked, I didn't 
> made these mistakes. 
> The overlay of the surfaces (opened from each tp.long.base directories) is 
> still wrong.
> I noticed that there is not a strict alignment between the norm volume from 
> base and the one from the tp1, whereas the alignment is correct between base 
> and tp2..
> 
> Have you ever faced this situation ? And if so, is there anything else to try 
> ?
> 
> Hope a made myself clear, if you need more captures/informations just ask me.
> 
> Best,
> 
> Maxime
> 

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Re: [Freesurfer] freesurfer longitudinal issue

[Martin Reuter]

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 the
CROSS directories instead of the long? The CROSS time points are in
original space and therefore do not align. Please double check you are
looking at the right files and that the norm.mgz are aligned. 

Best, Martin


On Tue, 2019-03-26 at 13:05 +, maxime GUILLAUME wrote:
> External Email - Use Caution
> Dear freesurfer experts,
>  
> I am performing a longitudinal study (2 time points, 1 year apart) in
> patients with Multiple Sclerosis using freesurfer 6.0.
>  
> After following the tutorial for the CROSS, the BASE (where I only
> performed few manual edits of the surfaces) and the LONG steps, I am
> facing a problem with the results of the longitudinal pipeline:
>  
> If I overlay the final surfaces of the different time points (the
> white and pial surfaces of the LONG step) on the BASE template, there
> are major differences between the two time points (see figure
> attached). This happened only on a subset of my subjects.
> One of our collaborators in this study suggested that this might be
> because the patient was positioned differently in the two time
> points, in particular with respect to the z axis (and indeed the
> major differences between the two surfaces are in the topmost area of
> the brain).
> Does anybody have experienced the same problem? And how can I correct
> for it?
>  
> Thank you in advance for your help.
> 
> (*in the capture surfaces of the first visit are in yellow and in
> green for the second visit)
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Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

[Martin Reuter]

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 longitudinal 
> analysis as it is not there. The spc files are all present in my participants 
> files and the Qdecrc file is in the qdec subdirectory containing the line 
> long.thickness-spc. Is there a way to bypass this problem somehow?
> 
> Thank you,
> Arsenije
> 
> ---
> Arsenije Subotic | MSc Student 
> Department of Clinical Neurosciences
> Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
> Tel: (403) 918-6970 
> arsenije.subot...@ucalgary.ca  
> 
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Re: [Freesurfer] Longitudinal QDEC

[Martin Reuter]

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 
> (not .txt !)
> 
> Best, Martin
> 
>> On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS > <mailto:t.akudje...@nuigalway.ie>> wrote:
>> 
>> External Email - Use Caution
>> Dear All,
>> 
>> I am running a longitudinal (2-time points) group cortical analysis in 
>> Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
>> cross-sectional form, I added a text file containing the lines
>> MEASURE1 = long.thickness-avg
>> MEASURE2 = long.thickness-rate
>> MEASURE3 = long.thickness-pc1
>> MEASURE4 = long.thickness-spc
>> in the qdec directory to guide qdec to know about the newly created files 
>> (e.g. lh.long.thickness-spc...). However, it doesn't seem to be 
>> recognizing/picking up the new files or not reading the text file named 
>> Qdecrc.txt (which has the lines above. 
>> 
>> Will be glad if you could offer any help. 
>> 
>> Thanks 
>> 
>> Theo
>> 
>> 
>> 
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Re: [Freesurfer] Longitudinal QDEC

[Martin Reuter]

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 running a longitudinal (2-time points) group cortical analysis in 
> Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
> cross-sectional form, I added a text file containing the lines
> MEASURE1 = long.thickness-avg
> MEASURE2 = long.thickness-rate
> MEASURE3 = long.thickness-pc1
> MEASURE4 = long.thickness-spc
> in the qdec directory to guide qdec to know about the newly created files 
> (e.g. lh.long.thickness-spc...). However, it doesn't seem to be 
> recognizing/picking up the new files or not reading the text file named 
> Qdecrc.txt (which has the lines above. 
> 
> Will be glad if you could offer any help. 
> 
> Thanks 
> 
> Theo
> 
> 
> 
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Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Martin Reuter]

Hi Matthieu, 

no, sorry. Maybe you can find a local biostatistician who knows. 

A slope estimate with less time points is more uncertain than one with
more time points (obviously). Also a slope estimate with time points on
a line is more certain than one with time points values all over the
place. This information is used in the LME model. But I don't know to
what extend any potential biases are removed. For example, if one group
has only 2 time points and the other had 5, I would be very suspicious.
You can, of course, always reduce the number of time points in the
second group to match the first and see if your results remain stable. 

Best, Martin



On Fri, 2018-12-07 at 22:33 +0100, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> Hi Martin,
> 
> I come back on my previous question concerning survival bias in LME.
> 
> Do you have an advice ?
> 
> Best,
> Matthieu
> 
> > Le 19 oct. 2018 à 16:30, Matthieu Vanhoutte  > l.com> a écrit :
> > 
> > Hi Martin,
> > 
> > Do you mean that high attrition (less time points with time) would
> > induce more variance on the slope estimates but this effect would
> > be compensated by LME modeling ?
> > 
> > Would there be proportion of early drop outs to respect in order to
> > compensate bias with LME ?
> > 
> > Thanks,
> > Matthieu
> > 
> > 
> > Le ven. 19 oct. 2018 à 16:19, Martin Reuter  > d.edu> a écrit :
> > > Hi Matthieu, 
> > > 
> > > in LME it is OK if subjects have differently many time points in
> > > general. You need to ask a statistician about your specific
> > > setup, but
> > > I think it might be OK (basically less time points, means more
> > > variance
> > > on the slope estimates, but that should be considered in LME).
> > > But I am
> > > not a statistician. 
> > > 
> > > Best, Martin
> > > 
> > > 
> > > On Wed, 2018-10-17 at 18:46 +0200, Matthieu Vanhoutte wrote:
> > > > External Email - Use Caution
> > > > Hi Martin,
> > > > 
> > > > Thanks for your answer.
> > > > 
> > > > I actually compare neurospychological scores at baseline
> > > between
> > > > drop-out subjects and subjects with full time-points. If I ever
> > > find
> > > > that drop-out subjects are more severely affected than the
> > > subjects
> > > > with full time-points, then there might be a bias in the
> > > results of
> > > > my LME study ?
> > > > 
> > > > How could I argue that significant patterns found in my LME
> > > study
> > > > 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  > > rvard.
> > > > edu> a écrit :
> > > > > Hi Matthieu, 
> > > > > 
> > > > > 1) survival analysis is typically used if you want to detect
> > > if the
> > > > > time to an event is longer in one group vs the other (e.g.
> > > one
> > > > > group
> > > > > gets placebo the other drug and we want to know if recurrence
> > > is
> > > > > later
> > > > > in the drug group). Not sure this is what you need. The nice
> > > thing
> > > > > is,
> > > > > it can deal with drop-outs
> > > > > 
> > > > > 2) No, you can directly test that (e.g. do more dieseased
> > > drop out
> > > > > than
> > > > > healthy, or are the dropouts on average more advanced (test-
> > > scores,
> > > > > hippo-volume etc) than the diseased at baseline... many
> > > options.
> > > > > you
> > > > > could also test interactions with age , gender etc. However,
> > > not
> > > > > finding an interaction may not mean there is no bias, it is
> > > just
> > > > > small
> > > > > enough to go undetected with your data size. 
> > > > > 
> > > > > 3) Survival analysis is a different analysis than LME. 
> > > > > 
> > > > > Best, Martin
> > > > > 
> > > > > On Tue, 2018-10-16 at 16:15 +, Matthieu Vanhoutte wrote:
> > > > > > 

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

[Martin Reuter]

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 input is in and then this can happen. 

One thing you can try is to open the orig.mgz from both time points in
freeview. Are they in the same orientation? If so , there might be a
different problem. If not, you should go back to the original scans
(dicom) and convert them to nifti directly (if possible) using
mri_convert. 

Best, Martin


On Fri, 2018-12-07 at 11:32 +1100, Elena Pozzi wrote:
> External Email - Use Caution
> 
> Dear FreeSurfer Experts,
> 
> I have some baseline and follow-up MRI scans that I would like to
> process through the longitudinal stream.
> 
> Some of the baseline images were originally in Analyze format (LAS
> orientation) and were converted into nifti (keeping the LAS
> orientation) and then processed through the recon-all stream (and
> edited). A few other baseline images were instead in nifti format
> (RAS orientation). The follow-up images were all in nifti format (RAS
> orientation) and were as well processed through the recon-all stream
> and edited. 
> 
> For all the images that were originally in Analyze format at baseline
> and converted in nifti, the within subject template (base)
> failed,  i.e., the surfaces clearly do not properly follow the WM and
> GM boundaries. Instead, for the baseline images that were in nifti
> format the template looks fine.
> 
> Given that the problem arose only with the Analyze images, could the
> different orientation (LAS and RAS) explain the issue? If so, is it
> possible to flip the orientation after the preprocessing, keeping the
> edits that were made on the pial of the baseline images?
> 
> Apologies if any of these questions was already asked but I couldn’t
> find an answer.
> 
> Thank you very much,
> 
> Elena
> 
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> 
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Re: [Freesurfer] Longitudinal Stream - LONG step

[Martin Reuter]

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 long dirs), are
they nicely registered?

Best, Martin


On Thu, 2018-12-06 at 18:06 +, Figueiro Longo, Maria Gabriela
wrote:
> yes.
> The images have lower SNR but we ran other subjects with similar
> acquisition parameters and we didn't have problems.
> From: freesurfer-boun...@nmr.mgh.harvard.edu  mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.  vard.edu>
> Sent: Thursday, December 6, 2018 3:46:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Longitudinal Stream - LONG step
>  
> Does the orig.mgz file look ok?
> 
> On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote:
> >
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to run the longitudinal stream, but in the [LONG]
> step 
> > of one time-point of on of my subjects, I have the following error:
> >
> > MRInormInit():
> > INFO: Modifying talairach volume c_(r,a,s) based on average_305
> > MRInormalize():
> > MRIsplineNormalize(): npeaks = 11
> > Starting OpenSpline(): npoints = 11
> > MRInormFindControlPoints: could not find enough control points
> > building Voronoi diagram...
> > performing soap bubble smoothing, sigma = 8...
> >
> > Iterating 2 times
> > -
> > 3d normalization pass 1 of 2
> > No such file or directory
> > MRInormFindControlPoints failed
> > No such file or directory
> >
> > The segmentation of the this time-point for this subject ([CROSS] 
> > step) looks good and I couldn't find any error.
> > I didn't find any similar error in the email list. Does anyone
> have 
> > any thoughts on how to trouble-shoot this one? I attached the 
> > recon-all.log.
> >
> > FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8
> >
> > Thanks, Gabriela
> >
> >
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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Re: [Freesurfer] Longitudinal processing and paralllel flag

[Martin Reuter]

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 longitudinal process with three time points per subject
> and was wondering if you can advise on the typical time to process?
> Can the -parallel flag be added to the base and long steps? I'm
> running this on a cluster that has 16 core nodes with 32gigs of ram
> so it might give me a good tme saving if these steps can be
> parallelized.
> 
> Thanks and regards
> 
> Erik
> 
> 
> Postdoctoral Research Fellow 
> Dept. Of Psychiatry
> Royal College of Surgeons in Ireland
> ERC Building
> Beaumont Hospital
> Dublin
> &
> Dept. Of Psychiatry
> Trinity College Institute of Neuroscience
> The Llyod Institute 
> Trinity College Dublin
> D2
> 
> Erik O'Hanlon 
> Postdoctoral researcher
> 
> RCSI Psychiatry 
> Royal College of Surgeons in Ireland 
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740 
> E: erikohan...@rcsi.ie W: www.rcsi.com
> 
> Transforming Healthcare Education, Research and Service: RCSI
> Strategic Plan 2018-2022
> 
> 
> 
> 
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Re: [Freesurfer] longitudinal analyses after lesion segmentation

[Martin Reuter]

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 analysis) you will never know if changes across
time are due to the processing bias or if they are real. 

Get the original data, not the mapped images, and work with those. (And
you may want to warn your colleague that lesion change estimates are
probably biased, if one image is mapped to the other). 

Best, Martin

On Thu, 2018-11-29 at 11:50 -0500, kathleen Gerbino wrote:
> External Email - Use Caution
> Sorry, I was thinking that my question may not have been very clear.
> Baseline T1 images were rigidly registered to 1mm^3 MNI template and
> then all follow-up images were rigidly registered to the individual's
> baseline T1. My question is whether I could still apply the
> Freesurfer longitudinal pipeline (i.e. using  recon-all -base
>  -tp    -tp  -all) to these images as they are
> (i.e. rigidly registered to the baseline scan) or if you had any
> guidance as to how to best proceed. 
> 
> thank you in advance and sorry to email twice!
> 
> Kathleen
> 
> On Thu, Nov 29, 2018 at 6:35 AM kathleen Gerbino  ail.com> wrote:
> > Hi FreeSurfer experts:
> > 
> > I hope you are well. I need to segment quite a few longitudinal T1
> > scans from patients with multiple sclerosis. A colleague has
> > applied an automated lesion segmentation algorithm to segment and
> > fill the lesions. During this process, the follow-up scans were
> > registered to the baseline scan. My question is whether I could
> > still apply the Freesurfer longitudinal pipeline to these images or
> > whether your had any recommendations on the appropriate steps to
> > take if this is not appropriate. 
> > 
> > Kind regards,
> > Kathleen 
> > 
> 
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Re: [Freesurfer] Consistent volume increases for some regions when using longitudinal stream

[Martin Reuter]

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 does make sense with 
respect to test-retest reliability and group differentiation sensitivity where 
long performs better.  

However, as you noted and as we say in our tutorials, it is absolutely 
important to run single time point subjects through the longitudinal stream so 
that those images undergo the same processing steps as other images from 
subjects with more than 1 time point. That way the values are comparable again 
and can be included in the linear mixed effects analysis to estimate cross 
subject variances. 

Simply run 
cross
base with only one time point
and long 
for all single time point subjects 


Best, Martin



> On 9. Nov 2018, at 15:04, Pagliaccio, David (NYSPI) 
>  wrote:
> 
> 
> 
> Hello,
> Our lab has been running a set of data from a pre/post-treatment study 
> through the FreeSurfer v6 pipeline. I was comparing the pre-treatment 
> structural values initially run through the cross-sectional pipeline with the 
> same pre-treatment data later run through the longitudinal pipeline and was 
> seeing the same issue as has been previously posted about (msg52994). 
> Particularly, one cortical region of interest shows on average 0.24mm (8.8%) 
> larger cortical thickness values processed in the longitudinal pipeline vs. 
> the cross-sectional pipeline. While all participant’s data showed increased 
> thickness in this area with the longitudinal vs. cross-sectional pipeline, 
> this was not at all consistent across participants (ranging from 0.08 to 
> 0.47mm differences [3-18%]). While the longitudinal pipeline would increase 
> reliability and sensitivity comparing the pre to post-scans, we are just very 
> concerned about these major and inconsistent differences analyzing the same 
> baseline data with the different pipelines. Particularly, we have some 
> attrition so most participants have 2 but some have only 1 scan and thus this 
> feels like it could introduce systematic bias in overall thickness.
> Any input would be appreciated!
> David
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Re: [Freesurfer] ICV normalization (longitudinal pipeline)

[Martin Reuter]

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 estimate, thus 
smaller p-values. Not sure what happens in your case, but I would not trust 
that.

(also how large is your dataset, how far apart are the time points, and what 
kind of treatment will change head size??)

Best, Martin



> On 1. Nov 2018, at 16:13, Martin Juneja  wrote:
> 
> Hello FS experts,
> 
> I am using longitudinal processing pipeline 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing 
> ) to 
> calculate the cortical volume (CV) over a course of treatment (two 
> conditions: pre condition and post condition). In fact, I am interested in 
> comparing normalized CV (NCV) i.e. raw CV/ ICV between pre- and 
> post-condition.
> 
> (1). Now, longitudinal pipeline assumes that there is no change in ICV so it 
> gives me identical ICV for pre and post condition. That way, when I compared 
> NCV between pre and post condition, it gives me differences at significant 
> level of 0.16.
> (2). However, when I checked ICV (from cross-sectional pipeline i.e. each 
> time-point separately) and compared between pre and post-conditions, ICV 
> values are different. Its possible that these values could be different 
> because of treatment (may be !). When I compared NCV between pre and post 
> condition (calculated by dividing raw CV from longitudinal pipeline with ICV 
> values form cross-sectional pipeline), it gives me significant differences at 
> 0.02.
> 
> Could you please share your thoughts on this i.e. (a) whether I can use 
> approach 2 or (b) if I am using longitudinal pipeline, dividing raw CV from 
> longitudinal pipeline and dividing by ICV calculated from cross-sectional is 
> in correct way to do this analysis?
> 
> Thanks.
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Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

[Martin Reuter]

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 Computing (CMIC)
> Department of Medical Physics and Biomedical Engineering
> University College London
> http://www.jeiglesias.com 
>  
>  
>  
> From:  on behalf of "Chen Guoyang 
> (IMH)" 
> Reply-To: Freesurfer support list 
> Date: Friday, 26 October 2018 at 11:35
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
>  
> External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
>  
> 
> I am currently attempting to include an additional T2 MRI scan in the 
> segmentation of our T1 scan. The freesurfer version that I'm using is the 
> freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).
> 
>  
> 
> However, I ran into this issue, ERROR: cannot find transform file. I've 
> pasted the output below.
> 
>  
> 
> Will like your advices for the this matter.
> 
>  
> 
> Thanks!
> 
>  
> 
> Sincerely,
> 
> Guoyang
> 
>  
> 
> OS Darwin
> Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 
> 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
> --
>  
> #
> #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018
> --
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is 
> .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:
> Registering norm.mgz to additional volume
> /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass 
> single frame MRI target 
> /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.
>  
> /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov 
> /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz
>  --maskmov 
> /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz
>  --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta 
> /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
>  --noinit --cost NMI -nosym >/dev/null: Signal 127
> ERROR: cannot find transform file 
> /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
> gunzip: can't stat: 
> /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz
>  
> (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz):
>  No such file or directory
> ERROR: problem reading fname
> SWITCH expression must be a scalar or string constant.
>  
> Error in myMRIread>load_mgh (line 550)
>  
>  
>  
> Error in myMRIread>myMRIread_aux (line 92)
>  
>  
>  
> Error in myMRIread (line 63)
>  
>  
>  
> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)
>  
>  
>  
> MATLAB:badSwitchExpression
> Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 
> 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
>  
> T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

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

[Martin Reuter]

Hi Matthieu, 

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

Best, Martin


On Wed, 2018-10-17 at 18:46 +0200, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> Hi Martin,
> 
> Thanks for your answer.
> 
> I actually compare neurospychological scores at baseline between
> drop-out subjects and subjects with full time-points. If I ever find
> that drop-out subjects are more severely affected than the subjects
> with full time-points, then there might be a bias in the results of
> my LME study ?
> 
> How could I argue that significant patterns found in my LME study
> 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) survival analysis is typically used if you want to detect if the
> > time to an event is longer in one group vs the other (e.g. one
> > group
> > gets placebo the other drug and we want to know if recurrence is
> > later
> > in the drug group). Not sure this is what you need. The nice thing
> > is,
> > it can deal with drop-outs
> > 
> > 2) No, you can directly test that (e.g. do more dieseased drop out
> > than
> > healthy, or are the dropouts on average more advanced (test-scores,
> > hippo-volume etc) than the diseased at baseline... many options.
> > you
> > could also test interactions with age , gender etc. However, not
> > finding an interaction may not mean there is no bias, it is just
> > small
> > enough to go undetected with your data size. 
> > 
> > 3) Survival analysis is a different analysis than LME. 
> > 
> > Best, Martin
> > 
> > On Tue, 2018-10-16 at 16:15 +, Matthieu Vanhoutte wrote:
> > > External Email - Use Caution
> > > Hi Martin,
> > > 
> > > It's been a long time since this discussion but I return on this
> > from
> > > now... The problem is that I followed longitudinal images of two
> > > groups where I had mainly missing time points at the end. Than
> > you
> > > suggested:
> > > If you have mainly missing time points at the end, this will bias
> > > your analysis to some extend, as the remaining ones may be
> > extremely
> > > healthy, as probably the more diseased ones drop out. You may
> > want to
> > > do a time-to-event (or survival-analysis) which considers early
> > drop-
> > > out.
> > > 
> > > 1) I know the survival analysis toolbox on matlab, but now I
> > would
> > > like to know what information will this survival analysis give to
> > me
> > > ? 
> > > 2) Will this analysis tell me if there is a bias ?
> > > 3) How to consider early drop-out with this type of analysis
> > based on
> > > mass-univariate LME analysis of longitudinal neuroimaging data ?
> > > 
> > > Thanks in advance for helping.
> > > 
> > > Best,
> > > Matthieu
> > > 
> > > Le mer. 14 déc. 2016 à 22:14, Martin Reuter  > ard.
> > > edu> a écrit :
> > > > Hi Matthieu,
> > > > 
> > > > 1. yes, LME needs to be done first so that values can be
> > sampled
> > > > from the fitted model for the SA.
> > > > 
> > > > 2. yes, I was talking about gradient non-linearities etc that
> > could
> > > > be in the image from the acquisition. We currently don’t use
> > non-
> > > > linear registration across time points (only rigid). 
> > > > 
> > > > Best, Martin
> > > > 
> > > > 
> > > > > On Nov 22, 2016, at 9:31 PM, Matthieu Vanhoutte
> >  > > > > e...@gmail.com> wrote:
> > > > > 
> > > > > Hi Martin,
> > > > > 
> > > > > Please see inline below:
> > > > > 
> > > > > > Le 22 nov. 2016 à 17:04, Martin Reuter  > vard
> > > > > > .edu> a écrit :
> > > > > > 
> > > > > > Hi Matthieu, 
> > > > > > (also inline)
> > > > > > 
> > > > > > > On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte
> >  > > >

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

[Martin Reuter]

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. 

You can take a couple cases and run them from scratch and using the old
base and compare yourself. The base will be at a different location so
visual comparison will be tricky. It is (technically) possible to
create a new base (including the new time points) at the same location
as the old. That could help preserve edits. But I think there are no
scripts for that. Also in your case that may not need to be necessary.

Best, Martin


On Tue, 2018-10-16 at 17:47 +, Molly Prigge wrote:
>   
> Hello Freesurfer experts,
> 
> We have a large longitudinal dataset (n=~200) of up to 4 time points
> per participant.  All images were processed using Freesurfer v6.0 and
> have already undergone QA, and editing the cross, Base or long where
> needed. 
> 
> We are finishing up collection of a 5th time point and will begin
> collecting a 6th time point next year (average interscan interval 2.5
> years).  We are running the new scans through the same Freesurfer
> v6.0 and same workstation as the previous time points.  
> 
> Is it appropriate to use the Bases already created with Times 1-4 for
> the 5th and 6th timepoint long file creation?  We are hoping to avoid
> losing all the QA editing already done on the Base and long files
> from Times 1-4 and not have to redo all QA on Times 1-5 long files
> when time 6 is complete.
> 
> We appreciate any guidance.
> 
> Thanks!
> Molly
> 
> ---
> Molly DuBray Prigge, PhD
> Research Associate
> Department of Pediatrics
> molly.prigge at hsc.utah.edu
> MRI Study Phone: 801.585.9061
> 
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Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Martin Reuter]

Hi Matthieu, 

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

2) No, you can directly test that (e.g. do more dieseased drop out than
healthy, or are the dropouts on average more advanced (test-scores,
hippo-volume etc) than the diseased at baseline... many options. you
could also test interactions with age , gender etc. However, not
finding an interaction may not mean there is no bias, it is just small
enough to go undetected with your data size. 

3) Survival analysis is a different analysis than LME. 

Best, Martin

On Tue, 2018-10-16 at 16:15 +, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> Hi Martin,
> 
> It's been a long time since this discussion but I return on this from
> now... The problem is that I followed longitudinal images of two
> groups where I had mainly missing time points at the end. Than you
> suggested:
> If you have mainly missing time points at the end, this will bias
> your analysis to some extend, as the remaining ones may be extremely
> healthy, as probably the more diseased ones drop out. You may want to
> do a time-to-event (or survival-analysis) which considers early drop-
> out.
> 
> 1) I know the survival analysis toolbox on matlab, but now I would
> like to know what information will this survival analysis give to me
> ? 
> 2) Will this analysis tell me if there is a bias ?
> 3) How to consider early drop-out with this type of analysis based on
> mass-univariate LME analysis of longitudinal 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 the fitted model for the SA.
> > 
> > 2. yes, I was talking about gradient non-linearities etc that could
> > be in the image from the acquisition. We currently don’t use non-
> > linear registration across time points (only rigid). 
> > 
> > Best, Martin
> > 
> > 
> > > On Nov 22, 2016, at 9:31 PM, Matthieu Vanhoutte  > > e...@gmail.com> wrote:
> > > 
> > > Hi Martin,
> > > 
> > > Please see inline below:
> > > 
> > > > Le 22 nov. 2016 à 17:04, Martin Reuter  > > > .edu> a écrit :
> > > > 
> > > > Hi Matthieu, 
> > > > (also inline)
> > > > 
> > > > > On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte  > > > > hou...@gmail.com> wrote:
> > > > > 
> > > > > Hi Martin,
> > > > > 
> > > > > Thanks for replying. Please see inline below:
> > > > > 
> > > > > > Le 21 nov. 2016 à 20:26, Martin Reuter  > > > > > vard.edu> a écrit :
> > > > > > 
> > > > > > Hi Matthieu, 
> > > > > > 
> > > > > > a few quick answers. Maybe Jorge knows more. 
> > > > > > Generally number of subjects / time points etc. cannot be
> > > > > > specified generally. All depends on how noisy your data 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
> > > > > > subject / time points would be needed. There are some tools
> > > > > > for that in the LME toolbox:
> > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffect
> > > > > > sModels#Poweranalysis 
> > > > > > 
> > > > > > 1. see above
> > > > > > 2. yes, also time points can miss from the middle. If you
> > > > > > have mainly missing time points at the end, this will bias
> > > > > > your analysis to some extend, as the remaining ones may be
> > > > > > extremely healthy, as probably the more diseased ones drop
> > > > > > out. You may want to do a time-to-event (or survival-
> > > > > > analysis) which considers early drop-out.
> > > > > 
> > > > > Is there any way to do with Freesurfer this kind of analysis
> > > > > ?
> > > > 
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis 
> > > > Yes, there is also a paper where we do this. It is a
> > > > combinat

Re: [Freesurfer] longitudinal hippocampal aseg editing

[Martin Reuter]

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 merged with
the newly created aseg.manedit.mgz).  If aseg.manedit.mgz exists, then
its contents are merged with aseg.auto.mgz (which is the output of the 
automatic segmentation program mri_ca_label).  The default action, if 
neither aseg.manedit.mgz nor aseg.mgz exist, is to copy aseg.auto.mgz
to aseg.mgz. 

Can you check (with a simple edit) in a cross sectional run, if it
behaves as expected, then check what happens in the long if you do the
same steps? Could be that there is a bug in the code for -long
processing, but not sure.

Best, Martin


On Fri, 2018-09-07 at 09:55 -0700, Rebecca Ray wrote:
> External Email - Use Caution
> Martin,
> That is the point.  I have edited the hippocampus in the -long 2
> times and the recon does not maintain my edits. 
> I would love any help to changes I should be making to my recon
> statement to maintain my edits.
> 
> Rebecca
> 
> 
> Hi Rebecca,
> 
> aseg edits to subcortical structures need to be done in the -long
> stage.
> (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdit
> s
> )
> Best, Martin
> 
> 
> 
> On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote:
> > External Email - Use Caution
> > HELP
> > -- Forwarded message --
> > From: Rebecca Ray 
> > Date: Thu, Sep 6, 2018 at 12:05 PM
> > Subject: longitudinal hippocampal aseg editing
> > To: freesurfer at nmr.mgh.harvard.edu
> > 
> > 
> > I have 2 time points on 60 subjects with most being in some form of
> > AD.  There are considerable differences in hippocampal volume
> between
> > time points.  I edited the raw images before making the template. I
> > then had to edit the aseg template image and there were still
> > problems on the -long images.  I tried to edit and rerun
> autorecon2-
> > noaseg and autorecon3 and it does not appear to be keeping my
> edits.
> > 
> > What am I doing wrong?
> > 
> > Rebecca
> > 
> > ___
> 
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Re: [Freesurfer] Fwd: longitudinal hippocampal aseg editing

[Martin Reuter]

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
> -- Forwarded message --
> From: Rebecca Ray 
> Date: Thu, Sep 6, 2018 at 12:05 PM
> Subject: longitudinal hippocampal aseg editing
> To: freesurfer@nmr.mgh.harvard.edu
> 
> 
> I have 2 time points on 60 subjects with most being in some form of
> AD.  There are considerable differences in hippocampal volume between
> time points.  I edited the raw images before making the template. I
> then had to edit the aseg template image and there were still
> problems on the -long images.  I tried to edit and rerun autorecon2-
> noaseg and autorecon3 and it does not appear to be keeping my edits.
> 
> What am I doing wrong?
> 
> Rebecca
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Martin Reuter]

Hi Anwar, 

I see, you want to convert the mgh file back to some text table. Not
sure how that worked, but I think mri_convert could do it (but maybe
only for a single subject with several structures, not sure about
multiple subjects - this is a stacked file). Another way is to open the
mgh in matlab or python and then you get a vector and output it to a
text file.

Best, Martin


On Tue, 2018-09-04 at 20:05 +, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> 
> Hi Martin/Doug:
> 
> Still looking for an answer. Could not find a way to list the
> percentage change values for each subject in a tabular form.
> 
> Thanks,
> 
> Anwar
> 
> On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat"  ybrook.ca> wrote:
> 
> External Email - Use Caution
> 
> Hello Martin:
> 
> I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42
> (that came with it by default).
> 
> If I omit --out-pc1 but keep --do-pc1 still do not get any output
> as a .dat or .stats file. I only get .mgh file in surf folder.
> 
> I need percentage change values 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 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 - Use Caution
> > Dear Doug:
> >
> > I am trying to get a table containing pc1 values for each
> subject in
> > a longitudinal study and failed to extract this. I use the
> code
> > below:
> >
> > long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas 
> thickness
> > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
> --do-label
> > --time years --qcache fsaverage --sd
> > /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-
> pc1.dat
> >
> > It says
> > long_mris_slopes: error: no such option: --out-pc1
> >
> >
> > However in the --help file it says:
> >
> > Within-Subject Output:
> > Pass these to overwrite the default names:
> >
> > --out-avg=OUT_AVG   filename to store temporal average
> in
> > /stats/
> (default:
> > long..-avg.dat)
> > --out-rate=OUT_RATE
> > filename to store rate in
> > /stats/
> > (default: long..-
> rate.dat)
> > --out-pc1fit=OUT_PC1FIT
> > filename to store pct. change (to
> tp1fit) in
> > /stats/
> (default:
> > long..-pc1fit.dat)
> > --out-pc1=OUT_PC1   filename to store pct. change (to
> tp1) in
> > /stats/
> (default:
> > long..-pc1.dat)
> > --out-spc=OUT_SPC   filename to store sym. pct. change
> in
> > /stats/
> (default:
> > long..-spc.dat)
> > --out-resid=OUT_RESID
> > filename to store residual in
> > /stats/
> (default:
> > long..-
> resid.dat),
> > requires
> > --resid 
> > --out-stack=OUT_STACK
> > filename to store stacked measure
> file
> > /stats/
> (default:
> > long..-stack.dat)
> >
> >   Stacked Tables:
> > To output tables with results from all subjects
> >
> > --stack-avg=STACK_AVG
> > full filename to stack temporal
> average
> > tables
> > (default no stacking)
> > --stack-rate=STACK_RATE
> > full filename to stack rate tables
> (default
>    

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

[Martin Reuter]

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 the left-right 
difference depending on which is the diseased hemi. Then do a regular analysis 
on that. Nothing paired. 

Best, Martin



> On 30. Aug 2018, at 18:29, Wang, Xiaoyu  
> wrote:
> 
> 
> 
> 
> Thanks Martin,
>  
> Yes, I did mean to have the right hemisphere added to the left hemisphere as 
> a new time point.
>  
> Can you explain on what you mean by run every subject only once?
> Do you mean to run xhemi for all of the subjects and then run a paired 
> analysis?
>  
> Xiaoyu
>  
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Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

[Martin Reuter]

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 you get is group and how 
much is resolution. 

Similarly this is problematic if you switch scanner, software, head-coil, 
resolution in a longitudinal study. Effects cannot be separated any longer and 
all you can report in a paper is that what you find is longitudinal effect plus 
resolution effects and you don’t know how much is which. 

FreeSurfers longitudinal stream therefore requires inputs to be the same 
resolution. This safety feature (to prevent potentially meaningless analysis) 
can be circumvented by manually sampling images first - at your own risk. If 
you go that way, you should at least also interpolate the 1mm images to a new 
position (at least then both images will have interpolation artefacts, so that 
differences are only the acquisition resolution and not additionally 
interpolation artefacts in one of the time points). 

As an example, taking the same image twice, mapping one to a different location 
and back again produces interpolation artefacts that are significant and at 
orders comparable with 1 year of neurodegenerative disease. 

Best, Martin





> On 30. Aug 2018, at 18:22, Daniel Ferreira  wrote:
> 
> 
> 
> 
> Dear colleagues,
> 
> I was wondering if resampling voxel size is done during recon-all.
> 
> Also, I have data with voxel resolution of 1x1x1 mm at baseline and 
> 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation 
> by default (or can be performed by any way) that minimizes these differences 
> in somehow.
> 
> Thank you very much
> 
> Dani
> 
> -- 
> Daniel Ferreira, PhD, Assistant Professor
> 
> Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences 
> and Society
> 
> Karolinska Institutet (Sweden)
> 
> Address: Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: 
> daniel.ferreira.padi...@ki.se 
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Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Martin Reuter]

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 - Use Caution
> Dear Doug:
> 
> I am trying to get a table containing pc1 values for each subject in
> a longitudinal study and failed to extract this. I use the code
> below:
> 
> long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time years --qcache fsaverage --sd
> /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat
> 
> It says 
> long_mris_slopes: error: no such option: --out-pc1
> 
> 
> However in the --help file it says:
> 
> Within-Subject Output:
>     Pass these to overwrite the default names:
> 
>     --out-avg=OUT_AVG   filename to store temporal average in
>                         /stats/ (default:
>                         long..-avg.dat)
>     --out-rate=OUT_RATE
>                         filename to store rate in
> /stats/
>                         (default: long..-rate.dat)
>     --out-pc1fit=OUT_PC1FIT
>                         filename to store pct. change (to tp1fit) in
>                         /stats/ (default:
>                         long..-pc1fit.dat)
>     --out-pc1=OUT_PC1   filename to store pct. change (to tp1) in
>                         /stats/ (default:
>                         long..-pc1.dat)
>     --out-spc=OUT_SPC   filename to store sym. pct. change in
>                         /stats/ (default:
>                         long..-spc.dat)
>     --out-resid=OUT_RESID
>                         filename to store residual in
>                         /stats/ (default:
>                         long..-resid.dat),
> requires
>                         --resid 
>     --out-stack=OUT_STACK
>                         filename to store stacked measure file
>                         /stats/ (default:
>                         long..-stack.dat)
> 
>   Stacked Tables:
>     To output tables with results from all subjects
> 
>     --stack-avg=STACK_AVG
>                         full filename to stack temporal average
> tables
>                         (default no stacking)
>     --stack-rate=STACK_RATE
>                         full filename to stack rate tables (default
> no
>                         stacking)
>     --stack-pc1fit=STACK_PC1FIT
>                         full filename to stack pct. change to tp1fit
> tables
>                         (default no stacking)
>     --stack-pc1=STACK_PC1
>                         full filename to stack pct. change to tp1
> tables
>                         (default no stacking)
>     --stack-spc=STACK_SPC
>                         full filename to stack sym. pct. tables
> (default no
>                         stacking)
>     --stack-resid=STACK_RESID
>                         full filename to stack residual tables
> (default no
>                         stacking)
> 
> 
> Am I writing the code wrong?? I never got any long..-
> pc1.dat file in /stats/ folder except bunch of mgh files
> in /surf/ folder.
> 
> Thanks,
> 
> Anwar
> --
> 
> Anwar S. Shatil
> 
> Research Assistant
> Department of Medical Imaging
> Sunnybrook Health Sciences Centre
> Room AB204, 2075 Bayview Avenue
> Toronto, ON M4N 3M5
> Tel: 416.480.6100 ext. 89617
> Email: anwar.sha...@sunnybrook.ca
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Re: [Freesurfer] error in longitudinal stream command

[Martin Reuter]

Hi Valeria, 

that is a local install (a frozen version of 5.3 or some modified
version from 2013). 

Can you source the system wide install of 5.3 and test that.
source /space/freesurfer/nmr-stable53-env

If that fails, try 6.0
source /space/freesurfer/nmr-stable60-env

Also make sure all directories exist, are filled with data and are
readable. You can also check the base-tps file in the base and see if
all time points are listed there correctly. 

As a last resort, you can try to re-run the base from scratch and then
the long again from scratch. If all that fails, it could be a bug in
recon-all (maybe it get's confused with all the _ in the name, but that
is unlikely. I also remember we had difficulties with really long names
in 5.3 but then it should work with 6.0. 

Best, Martin


On Wed, 2018-08-29 at 17:41 +, Barletta, Valeria wrote:
> Hi Martin, thanks for your reply.
> I tried to re-type the command in the shell but I still have the
> error.
> I don't know what you mean with system install, but we are using the
> version 5.3 and this is the path, if it can help:
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-
> stable5_3_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
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: 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, 2018-08-29 at 13:51 +, Barletta, Valeria wrote:
> > Dear Freesurfers,
> > I am trying to re-launch a longitudinal time point after edits by
> > using the command:
> > 
> > recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base
> > MS069_base -all
> > 
> > But I am obtaining this type of error:
> > 
> > Unmatched ".
> > 
> > I also tried to launch it on Launchpad but I have an error all the
> > same and the process immediately aborts.
> > Do you know what could be the reason?
> > Thank you,
> > Valeria
> > 
> > 
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> > 
> > 
> 
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Re: [Freesurfer] LME Univariate pvalue inconsistent

[Martin Reuter]

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
compute the diff between the left and right ROI's (always healthy -
diseased). Then do a normal GLM analysis on this signed difference. 

Best, Martin


On Tue, 2018-08-28 at 21:27 +, Wang, Xiaoyu wrote:
> External Email - Use Caution
> Hello Freesurfer Developers,
>  
> I’m attempting to use Univariate LME analysis to compare the
> symptomatic and asymptomatic hemispheres of early stage Parkinson’s
> disease patients.
>  
> I re-organized the data so that the symptomatic hemisphere is the
> left hemisphere and the Asymptomatic is the right (by flipping the
> orig.mgz before recon-all).
>  
> I followed the LME model tutorial for univariate on the freesurfer
> wiki and created my qdec.tabel.dat to have the same layout as in the
> example with group 1 as left hemisphere and group 2 as right
> hemisphere.
>  
> I have a design matrix to do a simple linear model containing a group
> by time interaction with the contrast of [0 0 0 1 0 0]
>  
> After running the F-test however, I noticed that the p-value was
> really inconsistent across atlases.
> I used multiple atlases and noticed that the p-value can be as low as
> 1.00E-30 for many structures.
> This is too good to be true especially since after sending the
> thickness value to a statistician she came back with values greatly
> different from mine.
> However, the Bhat values were similar.
>  
> Can someone give me a hint as to what is going on?
>  
> Xiaoyu
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Re: [Freesurfer] error in longitudinal stream command

[Martin Reuter]

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, 2018-08-29 at 13:51 +, Barletta, Valeria wrote:
> Dear Freesurfers,
> I am trying to re-launch a longitudinal time point after edits by
> using the command:
> 
> recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base
> MS069_base -all
> 
> But I am obtaining this type of error:
> 
> Unmatched ".
> 
> I also tried to launch it on Launchpad but I have an error all the
> same and the process immediately aborts.
> Do you know what could be the reason?
> Thank you,
> Valeria
> 
> 
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> 
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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal Comparison

[Martin Reuter]

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 once, then do a x-hemi analysis (I think
there are tools for that, which try to keep stuff unbiased with respect
to the hemi) and then perform your statistic on that.

Since not all diseased hemispheres are on one side, it makes sense to
attach a sign to the x-hemi difference so that you always have, e.g.
healthy-diseased. Then simply do a GLM on that. 

Best, Martin


On Tue, 2018-08-28 at 22:18 +, Wang, Xiaoyu wrote:
>   
> Hello Freesurfer Experts,
>  
> I am trying to compare the left and right hemisphere of a group of PD
> patients with Mass-Univarate LME.
>  
> From what I can see in the wiki tutorial, the mris_preproc only
> assembles data from one hemisphere at a time, which is not very
> usefull if I am doing a hemisphere comparison where each hemisphere
> is a different group.
>  
> I am thinking of getting around this issue by flipping each subject
> time point so that the right hemisphere is on the left and adding it
> as a new timepoint.
> For example:
> S01_1    s01_base
> S01_1f  s01_base
> S01_2    s01_base
> S01_2f  s01_base
>  
> However, Can I still create the base file the same way using this?
>   recon-all -base  -tp  -tp  ... -all
>  
> also for the fsaverage, would make_average_subject still work?
>  
> Xiaoyu
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Re: [Freesurfer] correlation between blood biomarkers and longitudinal decrease in cortical thickness

[Martin Reuter]

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 if 
time deltas are very different or if you have different many time points per 
subject). 

Best, Martin



> On 20. Aug 2018, at 22:27, Foad Taghdiri  
> wrote:
> 
>External Email - Use Caution
> 
> Hello,
> 
> I have done freesurfer (v6) longitudinal preprocessing for 20 subjects 
> (baseline and 2-year follow-up). We also have levels of some blood biomarkers 
> (e.g. tau, neurofilament light) for these subjects at the baseline. I am 
> interested to figure out if the level of blood biomarkers at the baseline is 
> related to the amount of cortical thinning over time, and if so, which brain 
> regions’ cortical thinning are significantly correlated with the blood 
> biomarker. I was wondering if you could please guide me through this analysis 
> and let me know how I can do it.
> 
> Thanks
> Best,
> Foad
> 
> 
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Re: [Freesurfer] recon-all with mri_ca_normalize (longitudinal)

[Martin Reuter]

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 


Best, Martin


> On 10. Aug 2018, at 18:01, miracle ozzoude  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello FreeSurfer team, 
> 
> In order to create the longitudinal base after norm.mgz, Is the command below 
> the right way to end recon-all after creating norm.mgz? 
> 
> recon-all -s subjectID -autorecon1 -autorecon2  -i T1image -canorm. 
> 
> Thank you. 
> 
> Best, 
> Paul
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Re: [Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits

[Martin Reuter]

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. One potential approach could 
be to manually create the new template with the correct images at the same 
location as before, by passing the old template into the mri_robust_template 
code as an initial target (not even sure there is a flag for that). Then start 
recon-all from a later stage after that. I cannot support you for this and it 
requires some coding skills and good knowledge of the individual steps in the 
base pipeline. 

Best, Martin



> On 31. Jul 2018, at 18:35, KALEY E ELLIS  wrote:
> 
> Dear FreeSurfer Developers,
>  
> I posted this question last week, but did not receive a response. Please let 
> me know if I can provide any additional information.
> 
> We are using your longitudinal processing pipeline (version 6.0) for our 
> study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the  a 
> filter was used on the raw images to adjust for hyperintensities in the 
> images due to using a multi-channel coil. 
>  
> At this point, our bases have already been processed and consist of three 
> timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. 
> Since we have invested many resources into the manual editing process, we 
> want to try to retain all the manual edits that have been done to the base. 
> We still have the original scan and the filtered scan for each subject. We 
> have some ideas on how we might be able to retain the edits, but would you be 
> able to provide  input regarding whether this seems reasonable? Your feedback 
> is greatly appreciated!
>  
> Plan A:
> 1) Create a new T3 cross-sectional with the correct nifti
> 2) Run recon-all on the existing base
> Q: Will this retain the previous manual edits AND incorporate the new 
> cross-sectional image?
>  
> Plan B:
> 1) Create a new T3 cross-sectional with the correct nifti
> 2) Create a new base
> Q: Is it possible to transfer data from old manual edits to a new base? If 
> so, how?
> 
> Thank you!
> Kaley
> 
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
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Re: [Freesurfer] error with mri_ca_register in long

[Martin Reuter]

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, Martin


> On 5. Jul 2018, at 18:23, miracle ozzoude  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello All, 
> 
> When running the longitudinal pipeline for version 6, i encountered this 
> error " TransformSample: gcam has not been inverted!; Numerical result out of 
> range". I found a thread with similar error but the problem wasn't solved. 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html 
> .
>  
> Just like the previous thread, it happens whenever I include the 
> "-bigventricle" flag. Below is a sample of my recon-all scripts from 
> cross-sectional to longitudinal. The error.log and recon.log files are too 
> large to send. Thank you. 
> 
> Best, 
> Paul
> 
> Cross-sectional
> recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} 
> -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time
> 
> Longitudinal 
> recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 
> 20 -bigventricles -3T -time 
> 
> recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles 
> -3T -time
> recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles 
> -3T -time
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Re: [Freesurfer] Resample data for longitudinal comparisons

[Martin Reuter]

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 could use my make_upright script for that, which uses mri_robust_register 
to map the image to an upright and straight head position. 

Best, Martin


> On 20. Jul 2018, at 22:15, James Gullickson  wrote:
> 
> External Email - Use Caution
> 
> 
> All,
> 
> I would like to compare cortical thickness between two timepoints.
> 
> Timepoint 1 has 1mm^3 data.
> Timepoint 2 has 0.8mm^3 data.
> 
> I realize that there are limitations with this change in resolution between 
> timepoints and that no analysis is going to be perfect, but I am trying to 
> come up with the best possible solution.
> 
> Would it work to resample both timepoints' raw data into 0.9mm^3 ( 
> mri_convert --conform_size 0.9 invol outvol ), and then run the 0.9mm data 
> through Freesurfer 6.0 submilimeter recon? If so, are there any special 
> considerations I need to take into account after the initial recon, or would 
> longitudinal processing after this point be per normal?
> 
> Thanks,
> 
> James
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Re: [Freesurfer] Longitudinal Processing question

[Martin Reuter]

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 it worked. I have no idea 
how large the time delta is for it to fail but I guess if you scan a 4 year old 
and then again when they are 12 that could be problematic. 

You should use eTIV from the cross stream. In the long stream eTiv is fixed 
across time.


Best, Martin

> On 9. Jul 2018, at 20:51, Nillo, Ryan Michael R  
> wrote:
> 
>External Email - Use Caution
> 
> Hello FreeSurfer experts,
> 
> I have a few questions on the longitudinal processing stream. I am interested 
> in studying longitudinal morphometry changes in a pediatric population. The 
> age range of this population is between 4-20 years with age deltas between a 
> few months to < 2 years. I want to know what are appropriate/acceptable age 
> deltas used for longitudinal processing. I looked through the archives and 
> one researcher asked about age deltas. One of the answers was that “if the 
> time delta is relatively small, this has good chances to work”. What does 
> “relatively small” mean? If the time points exit the longitudinal pipeline 
> without errors and the surfaces look correct, does this mean the data is 
> relevant?? When I correct for head size, should I use the eTIV values from 
> the cross-sectional directories or the longitudinal directories?
> 
> Thanks in advance,
> 
> Ryan Michael Nillo
> Staff Research Associate I
> University of California San Francisco
> Department of Radiology and Biomedical Imaging
> 
> 
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Re: [Freesurfer] Missingness and recent developments in longitudinal pipeline for pediatric samples

[Martin Reuter]

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 not a big problem if you use 
Linear Mixed Effects Modeling. You can even include subjects with a single time 
point (but make sure you run it also through the longitudinal stream so that 
that single image undergoes the same processing steps as the rest). 

Best, Martin

> On 9. Jul 2018, at 15:50, Mohn, Johannes  wrote:
> 
> 
> Dear FS Experts and Community,
>  
> we are working on a longitudinal dataset of structural T1w images in a 
> pediatric sample assessed at 2 waves, 2 years apart (aged 6/7 and 8/9).
> As far as we know, it is yet unresolved whether the Freesurfer longitudinal 
> pipeline is robust in pediatric samples, where the head size is still 
> changing or have there been any recent developments?
> Also, is there any documentation on how missingness affects this Pipeline?
>  
> We look forward to your response
>  
> Thank you,
>  
> Laurel and Johannes
>  
> Jacobs Entwicklungsstudie
>  
> Max-Planck-Institut für Bildungsforschung
> Max Planck Institute for Human Development
> Lentzeallee 94
> 14195 Berlin
>  
> Tel.: 030-824 06 371
> E-Mail: jacobs-stu...@mpib-berlin.mpg.de 
> 
>  
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Re: [Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log

[Martin Reuter]

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 cases and fails in others. The reason is that in 6.0 the 
position of the base image could be (slightly?) different than 5.3. So your 
edits, e.g. control points, would not be at the right anatomical spot. This is 
not a problem when re-running cross runs. 

You should check if the norm.mgz is at the same location in 5.3 base and the 
6.0 base. 
Also I would re-run the long from scratch. (probably there are no edits in long 
anyway)?
Optimally re-run bases also from scratch, could be you don’t need any edits 
because 6.0 is awesome (maybe). 

Best, Martin


> On 25. Jun 2018, at 18:41, KALEY E ELLIS  wrote:
> 
> Hello FreeSurfer experts,
> 
> I previously emailed regarding processing longitudinal data in v6.0 using 
> bases with manual edits that had been completed in v5.3. I went ahead and ran 
> recon-all -all on the base of a subject (originally generated in v5.3) in 
> v6.0, but it looks like the header of the recon-all.log still indicates v5.3. 
> Looking at the /stats output, all files indicate v6.0. Below is the head of 
> the log from running recon-all -all on this subject. Is this what you would 
> expect if you ran recon-all -all on a subject_base in v6.0 that was generated 
> in v5.3? If so, is this okay?
> 
> Recon-all log:
> setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects
> FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest
> Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6
> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Linux c139.keck.waisman.wisc.edu  
> 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 11:12:41 CST 2017 x86_64 x86_64 
> x86_64 GNU/Linux
> 
> Thank you!
> Kaley Ellis
> 
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
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Re: [Freesurfer] Longitudinal processing: cannot find input volume error

[Martin Reuter]

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


> On 16. Jun 2018, at 19:21, Arsenije Subotic  
> wrote:
> 
>
> 
> Dear Freesurfer experts,
> 
> I’m having problems with one of my participants when I am trying to create 
> the base template for my longitudinal analysis. I get an error saying that 
> the input volume (norm.mgz) for my followup time-point cannot be opened, even 
> though the volume is not missing and loads perfectly fine in Freeview. Is 
> this a bug or is something wrong with my norm.mgz volume by any chance? 
> Please let me know.
> 
> Thank you,
> Arsenije
> 
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> 
> 


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Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions

[Martin Reuter]

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 effects remain small for the 
regions of interest (of course this would not help i there is an interaction, 
e.g. with diesease or age) but at least it could help convince reviewers. Also 
if you only analyse the first 2 time points  and find large differences, you 
could argue that they are real, because the same scanner should not course 
large effects. But who knows (different head coils? Different callibrations, 
software versions?…). Better to test with a few subjects. 

Best, Martin



> On 7. Jun 2018, at 20:15, zalewk  wrote:
> 
> 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 type of 
> scanner, there was an effort made to match them) at time point 1 and 2 with a 
> Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal 
> analysis on this cohort?  
> 
> Best, 
> Kody Zalewski
> 
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Re: [Freesurfer] Longitudinal Process

[Martin Reuter]

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:
> 
> 
> 
> 
> Dear FreeSurfers,
> I am trying to run the longitudinal process including (recon-all -base and 
> -long) for 5 different timepoints.
> But in my original data one the of five differs in the acquisition 
> orientation and in the size of the field of view, so the results and 
> especially the statistic is distorted.
> Four of my data sets have RPI as acquisition Parameter and a FOV of 230,
> the last data set has LPI and a FOV of 257.
> Does it even make sense to include this last dataset – is it even possible 
> (due to different Parameters)?
> Do I have to pre-process this different data set?
>  
> Thank you in advance!
> Sam
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Re: [Freesurfer] Longitudinal errors, Voxel size differs

[Martin Reuter]

Hi Erik, 

better late then never: 
you should use mri_convert --conform input output



Best, Martin 


> On 16. May 2018, at 12:19, Erik O'Hanlon  wrote:
> 
> External Email - Use Caution
> Thank Martin,
> 
> I've been looking into this and it appears that the slight changes in the 
> sequence may have occurred software updates to the scanner. So essentially 
> from what you say, this drastically impacts any longitudinal analyses as 
> there will be a systematic bias across the data. Is there any point in trying 
> to do longitudinal analyses with such data as it will be a factor in all 
> output? Is it worth resampling all three time points to 1mm and then rerun 
> the analysis as it will be difficult to say if any patterns of change arent 
> due to the acquistions as you said?
> 
> If I want to resample the data to a "standard 1mm3" voxel size, is there a FS 
> command for that or should I use something in FSL or AFNI tools and then feed 
> the resampled data back to the recon-all inistial step in FS.
> 
> Thanks for the help and guidance. Much appreciated
> 
> Erik  
> 
> 
> 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 support list
> Subject: 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 why, and you need to report this in any analysis so that people 
> are aware of this potential bias
> - resample both time points to some 3rd space. Probably here simply conform 
> them to 1mm isotropic. 
> 
> Best, Martin
> 
>> 
>> Erik O'Hanlon 
>> Postdoctoral researcher
>> 
>> RCSI Psychiatry 
>> Royal College of Surgeons in Ireland 
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740 
>> E: erikohan...@rcsi.ie <mailto:erikohan...@rcsi.ie> W: www.rcsi.com 
>> <http://www.rcsi.com/>
>> 
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
>> 2018-2022 <http://www.rcsi.ie/strategy2018>
>> 
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>> 
>> 
>> 
>> 
>> On 15. May 2018, at 07:20, Erik O'Hanlon > <mailto:erikohan...@rcsi.ie>> wrote:
>> 
>> Hi FS Experts,
>> 
>> I'm trying to run a longitudinal analysis across three timepoints and have 
>> run the cross steps for the data. I then ran the base step but found that my 
>> voxel dimensions are slightly different across the timepoints and I got the 
>> following error
>> 
>> ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
>>   Currently not supported, maybe first make conform?
>>   Debug info: size(2) = 0.881117, 0.881117, 0.881117   size(0) = 0.884507, 
>> 0.884507, 0.884507
>> MultiRegistration::loadMovables: voxel size is different 
>> /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz.
>> 
>> 
>> I assume I need to resample the data to the voxel size of the first time 
>> point and then rerun. Can you advise on what command to use to resample the 
>> images from time 2 and time 3 to those of time 1 before rerunning from 
>> scratch. I assume I can't avoid rerunning the initial reconall step once I 
>> resample my data.
>> 
>> Any guidance is much appreciated 
>> 
>> Best regards
>> 
>> Erik
>> 
>> Erik O'Hanlon 
>> Postdoctoral researcher
>> 
>> RCSI Psychiatry 
>> Royal College of Surgeons in Ireland 
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740 
>> E: erikohan...@rcsi.ie <mailto:erikohan...@rcsi.ie> W: www.rcsi.com 
>> <http://www.rcsi.com/>
>> 
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
>> 2018-2022 <http://www.rcsi.ie/strategy2018>
>> 
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>> 
>> 
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harva

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

[Martin Reuter]

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 also simply conform both inputs 
first 

mri_convert - - conform in out 
(I think)

The other problems that you report are strange and could be caused by partially 
processing things and maybe incorrect ways to call recon-all. 
You would need to completely remove (or move to backup) existing cross runs, 
base runs and long runs. 

Then re-run the cross sectionals first (and make sure the norm.mgz exists). If 
it does not, this has nothing to do with the longitudinal stream but some other 
problem. It also has nothing to do with the geometries. Once you have completed 
cross runs, do the base run. Since both time points were conformed in the 
pre-processing step, there should be no error message due to geometry 
differences and it should work 

Best, Martin



> On 13. Jun 2018, at 16:34, Tudor Popescu  wrote:
> 
> 
> 
> Hi Bruce,
> 
> I am guessing that Martin might be unavailable for now, judging by the date 
> of his last input to the list. 
> 
> However, my intuition is that there is something really trivial that's 
> causing this chain of (circular!) errors...
> 
> For any more ideas of what I could try, I'd remain really indebted!
> 
> Cheers,
> Tudor
> 
> On Mon, 11 Jun 2018 at 16:03, Bruce Fischl  > wrote:
> Hi Tudor
> 
> I think Martin is probably better able to sort this out than I am.
> 
> Bruce
> 
> 
> On Mon, 11 Jun 2018, Tudor Popescu wrote:
> 
> > 
> > External Email - Use Caution
> > 
> > Hi Bruce,
> > I assumed a subject-specific target for the mri_convert, so I used this 
> > command to realign
> > subject1's post to his pre:
> >   mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz
> > 
> > (and renamed the resampled file to 01_2). However, then the base step
> >   recon-all -base 01 -tp 01_1 -tp 01_2 -all
> > 
> > still gives the same warning about geometries differing across time; and 
> > also in addition, this
> > error message (which might have been there earlier too but had gone 
> > unnoticed):
> >   mghRead(/media/FS/01_1/mri/norm.mgz, -1): could not open file
> > MultiRegistration::loadMovables: could not open input volume 
> > /media/FS/01_1/mri/norm.mgz.
> > 
> > Inside /media/FS/01_1/mri/ (where /media/FS is my $SUBJECTS_DIR), there is 
> > indeed no norm.mgz, which
> > suggests something in my previous commands:
> >   recon-all -i 01_1.nii.gz -subjid 01_1
> > recon-all -i 01_2.nii.gz -subjid 01_2
> > recon-all -subjid 01_1 -all
> > recon-all -subjid 01_2 -all
> > 
> > ..has gone wrong despite these having produced no errors. Although I 
> > thought the base step already
> > does autorecon1 as part of the longitudinal pipeline, I tried doing it 
> > manually:
> >   recon-all -autorecon1 -subjid 01
> > 
> > however this returns:
> >   ERROR: It appears that this subject ID is an existing base/template 
> > from longitudinal
> >   processing (-base). Please make sure you pass all necessary flags. 
> > For example, if you
> >   are trying to re-run a -base: \' -base  -tp  ... \'
> > 
> > ..and running autorecon1 and 2 for the first timepoint instead,
> >   recon-all -autorecon1  -autorecon2 -subjid 01_1
> > 
> > returns
> >   mri_em_register: could not open input volume nu.mgz
> > 
> > 
> > Not sure what to do at this stage!.. Thanks again for any pointers!
> > 
> > Cheers,
> > Tudor
> > 
> > On Thu, 7 Jun 2018 at 18:16, Tudor Popescu  > > wrote:
> >   Hi Bruce,
> > Thanks for your answer! Before seeing this warning (rather: error, as no 
> > output is produced),
> > I'd not have thought the pre-post images have different geometries, as I'm 
> > pretty sure their
> > acquisition parameters were the same. The pre and post of any one subject, 
> > as well as the
> > different subjects' images, all seem to have identical voxel size (1x1x1) 
> > and image size
> > (176x224x160). Furthemore, the (0,0,0) point seems to always overlap 
> > well-enough on the
> > anterior commissure... 
> > 
> > This all suggests to me the geometry differences are trivial, so the 
> > resampling is worth a
> > try. However, I'm unsure whether, in the call to mri_convert -rl, the 
> > target would have to
> > be subject-specific (e.g. resample each 'post' to the 'pre' baseline), or 
> > if I should use a
> > single target for all the pre images in the study, a bit like the 
> > study-specific template
> > used by VBM?
> > 
> > Cheers,
> > Tudor
> > 
> > 
> > 
> > On 6 June 2018 at 16:37, Bruce Fischl  > > wrote:
> >   Hi Tudor
> >
> >   if you are sure that the differences are trivial you can resample the 
> > images to
> >   all have exactly 

Re: [Freesurfer] Longitudinal errors, Voxel size differs

[Martin Reuter]

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 why, and you need to report this in any analysis so that people are 
aware of this potential bias
- resample both time points to some 3rd space. Probably here simply conform 
them to 1mm isotropic. 

Best, Martin

> On 15. May 2018, at 07:20, Erik O'Hanlon  wrote:
> 
> Hi FS Experts,
> 
> I'm trying to run a longitudinal analysis across three timepoints and have 
> run the cross steps for the data. I then ran the base step but found that my 
> voxel dimensions are slightly different across the timepoints and I got the 
> following error
> 
> ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
>   Currently not supported, maybe first make conform?
>   Debug info: size(2) = 0.881117, 0.881117, 0.881117   size(0) = 0.884507, 
> 0.884507, 0.884507
> MultiRegistration::loadMovables: voxel size is different 
> /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz.
> 
> 
> I assume I need to resample the data to the voxel size of the first time 
> point and then rerun. Can you advise on what command to use to resample the 
> images from time 2 and time 3 to those of time 1 before rerunning from 
> scratch. I assume I can't avoid rerunning the initial reconall step once I 
> resample my data.
> 
> Any guidance is much appreciated 
> 
> Best regards
> 
> Erik
> 
> Erik O'Hanlon 
> Postdoctoral researcher
> 
> RCSI Psychiatry 
> Royal College of Surgeons in Ireland 
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740 
> E: erikohan...@rcsi.ie  W: www.rcsi.com 
> 
> 
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
> 2018-2022 
> 
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> 
> 
> 
> 
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Re: [Freesurfer] ICV adjustment of volumes in longitudinal pipeline

[Martin Reuter]

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 Freesurfer experts,
> 
> If I want to analyze the volume difference of regions (2 time points) after 
> performing all the 3 steps of the longitudinal pipeline, do I need to adjust 
> each volume in the "long" directories to its specific "tp.long" ICV or are 
> the data of the two "long" directories already "adjusted" to the template and 
> there is no need for the specific time-point ICV adjustment?
> 
> Thanks!
> Tamir
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Re: [Freesurfer] Longitudinal LME cluster value extraction

[Martin Reuter]

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 this can be found on the wiki 
or archive).

Best, Martin

> On 11. May 2018, at 07:44, Emmanuel Nwosu  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear FreeSurfer experts,
> 
> Am analysing longitudinal structural data with the LME model algorithm. I 
> will like to map the significant cluster after analysing the data to all 
> subjects at all time points, extract the values for all and perform further 
> statistical analyses. Please how do I go about extracting the cluster value 
> from all subjects at all time points? Any help will be appreciated.
> 
> Kind regards
> Emmanuel
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Re: [Freesurfer] Problem with template longitudinal pipeline

[Martin Reuter]

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 recommend to do your analysis 
only with the cross sectional stream until you get at least one more time point 
for this data. 

Best, Martin


> On 10. May 2018, at 07:12, Laura van Velzen  wrote:
> 
> 
> Dear FreeSurfer experts,
> 
> We are trying to run FreeSurfer v5.3 on our longitudinal imaging data using 
> the longitudinal pipeline. We first processed both time points 
> cross-sectionally. The output of this step looks fine for both time points. 
> 
> We then performed step 2: creation of a template from both time points and 
> step 3: longitudinally processing both time points. All steps run without 
> errors, but the output of steps 2 and 3 look abnormal (please see images 
> attached), so there appears to be something wrong in the creation of the 
> template. We also have some subjects with data from only one timepoint and 
> ran the longitudinal pipeline for these subjects as well (as was recommended 
> on the wiki) and the output of steps 2 and 3 look fine for these subjects, so 
> there appears to be an issue in creating the template based on both time 
> points. 
> 
> The acquisition parameters at both time points are the same as far as we 
> know. There is nine years between both measurements, and most of our subjects 
> are between 50 and 60 years old at the second measurement. 
> 
> We have attached the recon.all.log file for one of our subjects. 
> 
> We hope you have some suggestions what the problem might be and how we could 
> check this.
> 
> Many thanks in advance for your help!
> Kind regards,
> 
> Laura van Velzen & Julia Binnewies
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Re: [Freesurfer] mri_vol2surf

[Martin Reuter]

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 "Douglas N. Greve" :There is a registration file that gets created by the longitudinal 

processing that can be used with mri_vol2vol. I don't know where the LTA 

file is, but maybe Martin can weigh in.





On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:

>

>

> Hi,

>

> I figured that part out: I can't load surfaces as volumes in freeview, 

> but rather i need to load them as an overlay to the subject white, or 

> pial surfaces.

>

> I have another question for which I can't find an answer to. After 

> registering myelin maps to the individual subjects, how do I 

> register/transform them into the subjects' longitudinal T1s (obtained 

> after the recon-all long command)?

>

> The broad goal that I am trying to achieve is longitudinal myelin 

> analysis. Any feedback is appreciated. Thanks!

>

> On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque 

> > wrote:

>

> I did: mri_vol2surf --src Myelin_conformed.mgz --out

> C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5

>

> Now I'm just getting the error "freadFloat: fread failed" a whole

> bunch of times and the terminal gets stuck. Any suggestions?

>

> I checked Myelin_conformed.mgz and loaded it with orig.mgz in

> freeview and they look fine with great overlap and registration

>

> Thanks!

>

> On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve

> > wrote:

>

> Specify a file format for the output (eg, C01.mgz)

>

>

> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:

>>

>>

>> Hi,

>>

>> Thank you for the prompt response.

>>

>> I used the following command:

>>

>> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after

>> mri_vol2vol from the previous step) --out C01 --regheader C01

>> --hemi lh --projfrac 0.5

>>

>> This created two files called COR-.info and COR001. I tried

>> loaded the COR001 file into freeview and tksurfer, but I keep

>> the error "MRISalloc(8229512, 76): could allocated faces \

>> cannot allocate memory

>>

>> Am I making a mistake somewhere?

>>

>> Thanks,

>>

>> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve

>> > wrote:

>>

>> That all looks correct. For the registration, just use

>> --regheader C01

>>

>>

>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:

>>>

>>>

>>> Hi,

>>>

>>> It's my first time using FreeSurfer and I'd like some

>>> guidance regarding some of my steps.

>>>

>>> I'm attempting to perform myelin mapping as outlined in

>>> the paper by Righart (2017) Ann Neurol. Overall, I want

>>> to calculate myelin maps from each subject, sample them

>>> from the mid-cortical level to create cortical myelin

>>> surface maps, and perform vertexwise and ROI based analyses.

>>>

>>> Here's what I've done so far:

>>>

>>> 1. recon-all for all the subjects

>>> 2. Used bbregister to register the native T2 scans to

>>> the conformed T1 scans using this command: bbregister

>>> --s C01 --mov C01_T2.nii --init-fsl --reg register.dat

>>> --t2 (my understanding here is that this generates the

>>> .dat file that has the transformation to register the T2

>>> image to the conformed orig.mgz file from subject C01)

>>> 3. Applied the register.dat file to the native T2 using

>>> mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz

>>> --fstarg --reg register.dat (this registers the T2 to

>>> the orig.mgz file in the conformed space)

>>>

>>> The next step for me is to perform mri_vol2surf. My

>>> question here is, which file should I select for the

>>> --srcreg flag and what should the --trgsubject input be?

>>> Secondly, am I on the right track to complete the

>>> analysis i.e., correct file types and my understanding

>>> of the steps? Clarifications regarding these questions

>>> and any suggestions for further directions will be very

>>> helpful!

>>>

>>> Let me know. Thanks!

>>>

>>>

>>> ___

>>> Freesurfer mailing list

>>> Freesurfer@nmr.mgh.harvard.edu

>>> 

Re: [Freesurfer] Longitudinal processing with different FS versions

[Martin Reuter]

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 
processed with different software methods (here 5.3 an 6.0). You will not know 
if the differences that you find come from the methods or are real. 
Best, Martin


> On 13. Apr 2018, at 10:21, Susanna Carmona Cañabate 
>  wrote:
> 
> Dear Freesurfers,
> 
> We are running a longitudinal study with 4 time points. The first two time 
> points were processed and edited with the 5.3 version of Freesurfer and the 
> other two time points with FS6. I assume we have to re-run the first two time 
> points with the new versión, but is there a way to preserve the editings?
> 
> In the same line, on a transversal study, would it be a lot of bias if most 
> of the subjects of one group are processed with version 5.3 and most of the 
> subjects of the other group with FS6?
> 
> Thanks a lot for your time
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Re: [Freesurfer] reruns recon-all -long after edits

[Martin Reuter]

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 
-autorecon2 etc. 

recon-all -long 11904_T1_fs 11904_base  -autorecon2 -autorecon3

for this to work 11904_T1_fs.long.11904_base
needs to contain your edits, so maybe backup the old long run and call it 
backup, then edit this one and run it. You cannot simply append the _edit or 
you will confuse the naming convention. 

Best, Martin



> On 15. Apr 2018, at 23:07, Anna Daniels  wrote:
> 
> Dear FreeSurfer team,
> 
> using the longitudinal stream in v6.0.0, I edited the cross and base runs, 
> but still had to edit the long runs for some subjects. If I understood the 
> LongitudinalEdits Wiki correctly, the long can still be edited if necessary. 
> 
> Rerunning the respective recon-all command with -autorecon2 -autorecon3 and 
> the edited long run as input did not work. How do I rerun the long correctly 
> while incorporating the edits made directly to the long?
> 
> Here you see how I called the procedure:
> 
> 
> anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
>  ls -lisa
> total 20
> 8527874 4 drwxrwxr-x  5 anna anna 4096 Apr 15 21:18 .
> 8527873 4 drwxrwxr-x 34 anna anna 4096 Apr 15 12:18 ..
> 8544378 4 drwxrwxr-x 10 anna anna 4096 Mär 29 23:54 11904_base
> 8527875 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:02 
> 11904_T1_fs_edit.long.11904_base_edit
> 8527888 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:29 
> 11904_T2_fs_edit.long.11904_base_edit
> 
> anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
>  start=`date +%s`
> 
> anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
>  !recon
> recon-all -long 11904_T1_fs_edit.long.11904_base 11904_base -autorecon2 
> -autorecon3
> 
> Unmatched ".
> 
> anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
>  end=`date +%s`
> 
> anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
>  runtime=$((end-start))
> 
> anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
>  echo $runtime
> 10
> 
> As you can see, the process ends very quickly (10s) and only gives the error 
> 'Unmatched ".' though I did not open any double quotes when calling the 
> procedure.
> 
> Thanks a lot for your help!
> 
> Best,
> Anna
> 
> 
> 
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Re: [Freesurfer] Longitudinal Freesurfer Analysis

[Martin Reuter]

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 processing stream in FreeSurfer, 
> is it possible to use the processing stream if both baseline and endline data 
> have already been edited with control points? 
> Thanks! 
> Katie McKay
> 
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Re: [Freesurfer] Longitudinal strean including more than an image per time point

[Martin Reuter]

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 the longitudinal FS processing pipeline for our study, which 
> has 4 time points. The 1st one was acquired with a radiofrequency head coil 
> of 8 channels. Then, due to unexpected problems, some subjects at the 2nd 
> time point were acquired with a different head coil of 16 channels. 
> At time points 3 and 4, all subjects were scanned with the first head coil 
> and only the subjects with different head coil at time point two were 
> acquired twice (using both head coils). My question is: is there a way to do 
> the longitudinal processing pipeline including more than an image per time 
> point (one with the 16ch and the other with the 8ch)? If so, which will be 
> the best procedure to follow?
> 
> Thanks in advance for your time,
> 
> Maria
> 
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Re: [Freesurfer] ASEG and APARCSTATS2TABLE on longitudinal data

[Martin Reuter]

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 
directory and then you can stack that (this should be described on the 
wiki).


2. see also 1. You can also pass a qdec-long table and asegstats2table 
will automatically pull the data from the *.long.base dirs. Again you 
would get a single measurement per time point. You could then open that 
data in a stats software or matlab and do your statistics there, or use 
our LME matlab tools.


Best, Martin


Am 07.03.2018 um 12:46 schrieb Lisa Delalande:

Hi FreeSurfer experts,

I would like to use the asegstats2table and the aparcstats2table 
commands on my longitudinal data, which have been processing following 
the longitudinal pipeline (recon-all -cross, - base and finally 
-long). And I have two questions :


1) Am I obliged to do the ''long_stats_slopes --qdec 
./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas 
volume --do-avg --do-rate --do-pc1 --time months'' command before 
using the aseg/aparc commands ?


2) And I would like to know which subjectsID I have to choose for the 
command line, example :
asegstats2table --subjects *001_tp1 002_tp1*...etc. (cross)? OR 
*template_001 template_002*...etc (base)? OR 
*001_tp1.long.template_001 002_tp1.long.template_002*...etc (long)?
Knowing that it's for a comparison test-retest (microlongitudinal : 1 
month).



Thanks you in advance for your precious help,
Best regards,

Lisa



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

[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 
half the cross are already processed it may make sense to re-do 
everything with 6.0 to have a clean and easy setup.

2. Basically yes, but there are some situations where things can go 
wrong, for example

  - you restart long_submit_jobs, but not all scheduled jobs are running 
(e.g. some are still in the queue), it would then resubmit those jobs

- Jobs die and the is_running file still exists in the freesurfer 
scripts dir, in that case long_submit_jobs will not re-submit those jobs


Best, Martin


Am 27.02.2018 um 11:23 schrieb Backhausen, Lea:
> 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 
> steps with FS 6.0.0 or would this corrupt results?
> 2) Our HPC system is known to have problems from time to time and jobs end up 
> being killed. If the long_submit_jobs job gets killed prematurely would it 
> just resume processing the data that hasn't been processed yet if I submit 
> this job/script again?
>
> Thanks again for your help!
>
> Best,
> Lea Backhausen
> Research assistant
>
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie
>
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://www.uniklinikum-dresden.de
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
> freesurfer-requ...@nmr.mgh.harvard.edu
> Sent: Thursday, February 22, 2018 5:33 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 168, Issue 34
>
> Send Freesurfer mailing list submissions to
>   freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>   freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
>   freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific than "Re: 
> Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. Re: Search angle limitation in the flirt registration
>(Douglas 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 Errors (Emily Schwartz)
> 6. Re: Problem with cortical parcellation of rh but not lh
>(Amal Achaibou)
>     7. Re: Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)
> 8. Re: Longitudinal analysis using SLURM {Disarmed} (Satrajit Ghosh)
> 9. Re: Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)
>10. Re: Freesurfer equivalent to fslmaths? (Bruce Fischl)
>11. asymmetric parcellation error (Dijkshoorn, A.B.C. (Aicha))
>
>
> --
>
> Message: 1
> Date: Wed, 21 Feb 2018 18:26:32 -0500
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Search angle limitation in the flirt
>   registration
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <1e86b3d8-54c6-c9ad-54b3-7cc8df81c...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> you should post your question to the FSL list (they developed and support 
> flirt)
>
>
> On 02/21/2018 05:34 PM, Yixin Ma wrote:
>> Hi freesurfer developers and users,
>>
>> I'm writing to ask about the search angle limitation (--searchrx, --
>> searchry and --searchrz) in the flirt function. I use the search angle
>> option a lot for limited angle search, which usually generate a better
>> registration result compared with the broad angle search. But I still
>> don't quite understand how rx,ry and rz are defined and how negative
>> and positive angles affect the result. Because sometimes I find the
>> result after the angle limitation does not align 

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

[Martin Reuter]

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 = ...

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 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 issues a submit command (stored in 
pbcmd).  The examples there should help anyone who programs python to 
modify it for a slurm submission.



The wait_jobs scripts runs a different command (here qstat and grep 
user) to see how many jobs you are already running and waits until 
this number sinks below maxjobs, then it continues submitting new 
jobs. If you don't care about the number of submitted jobs (because 
your cluster does the scheduling anyway), you can just write



"return" as the first line (before the "users = os." line).


Still the submit block would have to be rewritten for slurm.


Best, Martin



Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:

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 
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts>


Unfourtunately it does only run on launchpad and I would do the 
analyses with SLURM using bash system.
Has anybody adopted the script so i will run with SLURM or does 
anybody know where I should look to get information on this?


I have little scripting experience so any help would be greatly 
appreciated!


Best,

Lea Backhausen, B.Sc.

Research assistant

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und 
–psychotherapie

Tel. +49 (0)351 458-7166
Fax +49 (0)351 458-5754

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
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Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

[Martin Reuter]

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 issues a submit command (stored in 
pbcmd).  The examples there should help anyone who programs python to 
modify it for a slurm submission.



The wait_jobs scripts runs a different command (here qstat and grep 
user) to see how many jobs you are already running and waits until this 
number sinks below maxjobs, then it continues submitting new jobs. If 
you don't care about the number of submitted jobs (because your cluster 
does the scheduling anyway), you can just write



"return" as the first line (before the "users = os." line).


Still the submit block would have to be rewritten for slurm.


Best, Martin



Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:

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 only run on launchpad and I would do the 
analyses with SLURM using bash system.
Has anybody adopted the script so i will run with SLURM or does 
anybody know where I should look to get information on this?


I have little scripting experience so any help would be greatly 
appreciated!


Best,

Lea Backhausen, B.Sc.

Research assistant

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und 
–psychotherapie

Tel. +49 (0)351 458-7166
Fax +49 (0)351 458-5754

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an der Technischen Universität Dresden
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Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[Martin Reuter]

Hi Lanbo and Doug,


What happens is this:

surfreg calls xhemireg (these are shell scripts)

xhemireg calls "recon-all -sb $subject/xhemi -talairach"

recon-all complains, because this $subject is a longitudinal time point.

recon-all expects longitudinal time point to be passed as

-long  

instead of -s .long.


This needs to be fixed in the calling scripts, by adding a -long flag. 
Or in recon-all we could potentially skip this sanity check in cases 
where the -sb flag is used (not sure what exactly that flag does, but it 
seems to be special to the xhemi stuff).



Best, Martin





Am 22.01.2018 um 17:47 schrieb lanbo Wang:

The problem is that the surfreg command is failing.

Thanks,
Lanbo

On Thu, Jan 18, 2018 at 5:14 PM, Douglas Greve 
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Is the problem that the surfreg command is failing or that you
don't know how to apply LME?


On 1/17/18 9:55 AM, lanbo Wang wrote:

Hi Martin,

I didn't try to run recon-all, I try to run flipped.
The code I used is:
foreach subject (subj_27_2.long.s27_base)
foreach?   surfreg --s $subject --t fsaverage_sym --lh
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,

what is the exact command you use for this? The problem is
that the script or your command does not pass the right flags
to recon all. Whenever recon-all is supposed to work on a
longitudinal directory it needs to know the base and the long
so the recon all command needs to show

-long subj_02_1 s02_base

as part of its arguments. So either adjust your command line,
or if the recon-all call is performed from within another
script, we need to change that script (add a -long flag so
that the script performs the correct recon-all call in those
cases when working on a longitudinal time point).

Once you have the left right difference (define on one of the
hemispheres), you can treat it similar as a thickness map and
run it through the Matlab LME code.
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
<https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>



Best, Martin


Am 27.12.2017 um 16:11 schrieb lanbo Wang:

Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal
data, it showed error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to
/HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz...
Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time
point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross
sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

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 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, Martin


Am 17.12.2017 um 17:54 schrieb lanbo Wang:

Hi, all experts.
I want to compare changes rate between left and right
hemisphere of longitudinal data, How should I do that,
how to combine xhemi with two stage or LME?

Best,
Lanbo


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

[Martin Reuter]

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 base run to see where it stops.

- also check the norm.mgz in the base, is it blurry or 2 ghosts? That 
could mean that the registration fails?


- search the log file for the mri_robust_template command (the 
registration) and see if that fails



On top of that, even if you get it to work, any changes you quantify 
between your two time points could be purely caused by the scanner 
change. Or are you trying to quantify scanner effects?



Best, Martin


Am 18.01.2018 um 11:32 schrieb Ambrosino di Bruttopilo-3, S.:


Dear  experts,

I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired 
with identical protocol (ADNI) but 2 different Philips 3T scanners 
(all time 1 with Achieva, all time 2 with Ingenia). Unfortunately ~ 
50% of the within-subjects templates completely failed. Is there 
anything I could try to fix this, or should just accept that is not 
possible to run FS longitudinal with this data?


Thanks a lot!

Sara



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

[Martin Reuter]

Hi Lanbo,

what is the exact command you use for this? The problem is that the 
script or your command does not pass the right flags to recon all. 
Whenever recon-all is supposed to work on a longitudinal directory it 
needs to know the base and the long so the recon all command needs to show


-long subj_02_1 s02_base

as part of its arguments. So either adjust your command line, or if the 
recon-all call is performed from within another script, we need to 
change that script (add a -long flag so that the script performs the 
correct recon-all call in those cases when working on a longitudinal 
time point).


Once you have the left right difference (define on one of the 
hemispheres), you can treat it similar as a thickness map and run it 
through the Matlab LME code. 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels



Best, Martin


Am 27.12.2017 um 16:11 schrieb lanbo Wang:

Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it 
showed error like this:

Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to 
/HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz...

Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

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 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, Martin


Am 17.12.2017 um 17:54 schrieb lanbo Wang:

Hi, all experts.
I want to compare changes rate between left and right hemisphere
of longitudinal data, How should I do that, how to combine xhemi
with two stage or LME?

Best,
Lanbo


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

[Martin Reuter]

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, Martin


Am 17.12.2017 um 17:54 schrieb lanbo Wang:

Hi, all experts.
I want to compare changes rate between left and right hemisphere of 
longitudinal data, How should I do that, how to combine xhemi with two 
stage or LME?


Best,
Lanbo


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Re: [Freesurfer] Longitudinal MRI but different scanner

[Martin Reuter]

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 
interaction and you have no way to test that.


You could scan a few people on both scanners to estimate scanner effects 
etc. If those are smaller than what you find above, you can argue that 
some of that could be real.


Best, Martin


Am 18.12.2017 um 16:49 schrieb Shane Schofield:

Hi Freesurfer Team,

I try to calculate a within-subject decrease in cortical thickness 
over 2 years, but the MRI scanner was changed during the project. Is 
it still possible to do that using the longitudinal stream in Freesurfer?


Thanks.

Best Wishes,
Shane


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Re: [Freesurfer] Intracranial Volume

[Martin Reuter]

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 have been using the intracranial 
volume from the aseg.stats file to correct for head size. I just want 
to ensure this is where I get the intracranial volume from.


Thank you in advance for your help.

Best,
Tamara


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

[Martin Reuter]

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, some participants have 
> only a single timepoint. For this reason, I aim to run the Linear Mixed 
> Effects (LME) Model described at 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels.
>
> I understand that it is recommended that before running LME, I process my 
> data using the longitudinal stream (e.g., 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). However:
>
> 1. in one dataset, some participants were scanned several years apart in 
> early childhood, which caused the intra-subject registration to fail in the 
> longitudinal processing stream
>
> and
>
> 2. in the second dataset, editing of longitudinal timepoints was time 
> prohibitive - several hours of edits were spent per brain at the 
> cross-sectional level due to the use of an older sub-optimal pulse sequence. 
> And, several more hours are required for the editing of each base or 
> longitudinal timepoint.
>
> Given each of these circumstances, is it feasible/appropriate to run LME 
> using data that was not initially processed using the longitudinal processing 
> stream within Freesurfer?
>
> Thanks in advance!
> Lara
>
> Lara Foland-Ross, Ph.D.
> Research Associate and Imaging Lab Manager
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
>
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>

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

[Martin Reuter]

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 problem 
ncopen: filename "./tmp.mri_nu_correct.mni.53099/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.53099/nu1.mnc
mincRead(): error reading volume from file 
./tmp.mri_nu_correct.mni.53099/nu1.mnc

is that file even there?

Best, Martin


> On 8. Nov 2017, at 19:56, miracle ozzoude  wrote:
> 
> Hello FreeSurfer, 
> 
> While running base step of the longitudinal pipeline, i got the following 
> error (please see the rec-all.log file for more details). How do i solve this 
> problem? Thank you
> 
> Best, 
> Paul
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Re: [Freesurfer] significant of long_mris_slopes

[Martin Reuter]

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 one-sample-group-mean (OSGM) analysis to test whether 
the slopes are significantly different from zero. The sig.table.dat shows the 
significances (log 10 , so 1 is p=0.1, 2 is p=0.01 etc, with a sign showing the 
direction). 

Now if you look at regular aging and if you have enough subjects and wait for a 
year or two all regions in the brain should show significant atrophy. So the 
OSGM is not very interesting usually. For a real study you usually need two 
groups (diseased vs control, or drug vs no-drug)

Best, Martin


> On 27. Oct 2017, at 20:13, lanbo Wang  wrote:
> 
> Dear freesurfer group,
> 
> Hi!
> I used long_stats_slopes and code to process my longitudinal data:
> long_stats_slopes --qdec sub_qdec_long.dat --stats lh.aparc.stats --meas 
> thickness --sd $SUBJECTS_DIR --do-rate --generic-time --stack-rate 
> thickness.lh.aparc-rate.stack.txt
> mri_glmfit --osgm --glmdir thickness.lh.aparc-rate --table 
> thickness.lh.aparc-rate.stack.txt
> I got results sig.table.dat in folder of 'thickness.lh.aparc-rate'. I want to 
> ask what's meaning of this results. Is it the significant results or just 
> directly result?
> 
> All best,
> Lanbo Wang 
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Re: [Freesurfer] Fwd: running cross sectional analysis on .long outputs only

[Martin Reuter]

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: 
sidtp1.long.base ) . Then you can run mri_glmfit the same way as in any 
other cross sectional analysis.


Take a look at this page (Uncached Data):

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

Usually it is a good idea to separate the mapping and smoothing steps 
(as described in the tutorial) by splitting into mris_preproc and 
mris_surf2surf (for smoothing). The reason is that you can later easily 
smooth at a different smoothing level and avoid a second time-consuming 
mapping of all the thickness files.


Best, Martin


Am 17.10.2017 um 16:59 schrieb Garret O'Connell:



Hello FreeSurfer experts,

I am trying to do a cross-sectional baseline analysis from the outputs 
of the longitudinal processing stream, following the advice on a 
previous question's thread:


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-March/044681.html 



From my reading of the issue, I need to run the following command, 
entering the cross-sectional title folder as the first input.


recon-all -long "subj_crossfolder" "subj_base" -qcache

For this step, i know it is necessary that recon-all knows where the 
cross folders are located, although from my understanding, it does not 
actually use data from these folders., instead using the data in the 
.long folders.


My issue is that I do not have access to the cross folders anymore, 
and was wondering if there was a work around to do the cross sectional 
analysis without them?


Thanks for any help!
Garret



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

[Martin Reuter]

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/ 
 


> On 16. Oct 2017, at 19:37, Christopher Markiewicz  
> wrote:
> 
> Doug,
> 
> Sorry if I muddied things by going into the significant digits - accurate to 
> 5 seems reasonable. I was simply meaning to say that the rotation and scaling 
> parameters are not the issue, to save the reader time inspecting them.
> 
> The translations (final three parameters) are off by anywhere 3 to 54mm, 
> though.
> 
> LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
> LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766
> 
> I'm guessing lta_convert has the wrong model of the origin in ITK style 
> affines, at least as applied by antsApplyTransforms.
> 
> Chris
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Monday, October 16, 2017 12:39:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that 
> are correctly applied by antsApplyTransforms
> 
> Not sure I understand. If the two transforms are only off by less than
> the 5th decimal, then why are the registrations off so much. As for why
> it would be off at the 5ht dec, it probably has to do with the way we
> store the matrix. When a volume is read in, the matrix is decomposed
> into translation, scale, and direction cosine, and then the matrix is
> thrown away. When a volume with the same geometry is written out, the
> matrix is recomputed. Some resolution is lost during the
> decomposition/recomposition, and we don't end up with the exact same matrix.
> 
> 
> On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
>> Hi,
>> 
>> I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` 
>> to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
>> 
>> The following produces a well-aligned output:
>> 
>> mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
>> 
>> As does the following:
>> 
>> lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
>> c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
>> bold2T1.txt
>> antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
>> bold2T1.txt
>> 
>> However, if one skips the FSL step, the registration is quite far off:
>> 
>> lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
>> antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
>> bold2T1.txt
>> 
>> Comparing the ITK transform files:
>> 
>> LTA-FSL-ITK
>> 
>> #Insight Transform File V1.0
>> #Transform 0
>> Transform: MatrixOffsetTransformBase_double_3_3
>> Parameters: 0.9895096215486424 0.011126830936108464 
>> -0.00042204653562094823 -0.01079971161879626 0.872329255299452 
>> -0.42602926756857834 -0.004755964529051335 0.42420535065804454 
>> 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749
>> FixedParameters: 0 0 0
>> 
>> 
>> LTA-ITK
>> 
>> #Insight Transform File V1.0
>> #Transform 0
>> Transform: AffineTransform_double_3_3
>> Parameters: 0.98950976133346558 0.011126830242574215 
>> -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
>> -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
>> 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 
>> 11.744022369384766
>> FixedParameters: 0 0 0
>> 
>> 
>> To 5 significant digits, these are the same, except the last three 
>> (translation) parameters. And the `AffineTransform_double_3_3` is different 
>> from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether 
>> this has any effect.
>> 
>> Here is the original LTA:
>> 
>> type  = 1 # LINEAR_RAS_TO_RAS
>> nxforms   = 1
>> mean  = 0. 0. 0.
>> sigma = 1.
>> 1 4 4
>> 1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
>> -2.332115173339844e+00
>> 1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
>> 2.507942199707031e+00
>> 4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
>> -1.201664733886719e+01
>> 0.000e+00 0.000e+00 0.000e+00 
>> 9.98807907104e-01
>> src volume info
>> valid = 1  # volume info valid
>> filename = 
>> /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
>> volume = 64 64 34
>> voxelsize = 3.125e+00 3.125e+00 
>> 4.000e+00
>> xras   = 

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

[Martin Reuter]

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 decimal places). I don’t 
see a good reason or mapping all follow-ups to 6 years when the exact date is 
known.

3) No idea. Does it even matter? The single time points are mainly used to 
estimate cross subject variance for that I don’t even know how much the time is 
used. You could try out to put 6 (or better if you know the exact date, put the 
exact time distance to the subject clinical baseline visit). 

Best, Martin


> On 13. Oct 2017, at 16:16, Christoph Abé  wrote:
> 
> 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 follow-up). We are also dealing with 
> several cases (100 out of 300) with only one time point. The model is set up 
> with “time” between scans, group, group*time, sex, and age as regressors. 
> But, dealing with only two time points raised some questions:
> 
> 
> 
> 1) I have read mixed opinions about fitting random slopes when dealing with 
> two time points. Even though it seems to make sense to model individual 
> random slopes, a fit through two time points may actually cause a problem. It 
> also seems redundant to include 2 random factors (intercept and slope) in 
> that case, as fitting random intercepts seems to be sufficient for the 
> covariance estimation. So my question: Is it recommended to model only one 
> random factor (intercept), or even wrong to model two (intercept and slope), 
> when dealing with 2 TPs (especially when dealing with drop outs)?
> 
> 
> 
> 2) This question is regarding how to set up the time variable. We have a 
> large variance in that measure, meaning the follow-up scans were done between 
> 5-7 years after baseline. As this contributes to the variance of the 
> dependent variable, I would like to include the exact time interval as 
> continuous number in the model (thus a slightly different number for each 
> participant), rather than using time as a two-level factor (e.g. “0” for 
> baseline and “6” for all follow-up cases). I am wondering which approach is 
> recommended and whether there are any significant benefits of using one 
> method (time as two-level factor) over the other (time as continuous) in a 
> LME model with two time points.
> 
> 
> 
> 3) We have several cases with data at one single time point (ca 100 out of 
> 300). In the design matrix, I include single rows for drop out cases, with 
> time=0. I assume that their number of repeated measures (1) will be handled 
> by the ni-vector generated by the sorting procedure (sortData in matlab). 
> However, we also have cases who were scanned only during clinical follow-up 
> intervention (6 years after the baseline data was collected). Ideally, I 
> would like to avoid assigning those to the baseline time point, for several 
> reasons (e.g. treatment effects, potential scanner drifts over 6 years, etc). 
> Instead, I want to assign them to the follow-up time point. If the better 
> choice in point 2) is to use the actual (continuous) numbers for “time”, I am 
> thinking about assigning the population median of the time difference between 
> scans to those cases. Is this a reasonable approach? Does not seem to be the 
> cleanest way of doing it, as we introduce some error, but may be a reasonable 
> trade off to avoid dropping data of ca. 50 individuals. What is your opinion 
> on that matter? 
> 
>  
> 
> Thanks for any help and opinions.
> 
> Best,
> 
> Christoph
> 
> 
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Re: [Freesurfer] qdec.table_ref

[Martin Reuter]

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 Zhejiang University in China. When I run QDEC to load the file 
> qdec.table.dat, I always get this info:
> 
> Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
> ERROR: QdecDataTable::Load did not find a column named 'fsid', 'ID', or 
> 'Subject' in the first column of 
> /Applications/freesurfer/subjects/qdec/qdec.table.dat!
> Error loading the data table.
> 
> 
> Attached are the files that I made to load the subjects information.
> What's wrong?
> --
> 田阿敏  Tian Amin
> 13071892606
> amint...@zju.edu.cn, 237416...@qq.com 
> Master Degree Candidate,
> Zhejiang University Interdisciplinary Institute of Neuroscience and 
> Technology, ZIINT.
> Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang 
> Province, China, 310029.
>  
>  
> 

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

[Martin Reuter]

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 
processing (like the orig.mgz, nu.mgz, norm.mgz to see if they all look OK.


Best, Martin


Am 28.09.2017 um 21:13 schrieb Michelle VanTieghem:

Hello,

I am running the -base processing so that I can create a 
subject-specific template for the -long processing. I have some 
subjects with only 1 timepoint. According to the website, all versions 
5.2 and higher can handle 1 time point when making the base. I am 
using freesurfer 5.3.


However, when I run the -base commands, it's working fine for subjects 
with 2-3 scans but fails  mid way through processing for subjects with 
only 1 scan. I cannot determine why this is happening,  and it happens 
at *different stages* of processing. (e.g. fix topology or CA Reg)


 the recon-all.error log does not provide useful information. Is there 
an extra flag that i am missing:


Here is an example command:

recon-all -base SB017templatebaseline -tp SB017 -all -3T -mprage


Here is a recon-all.error log:

--

SUBJECT SB014templatebaseline

DATE Thu Sep 28 15:00:02 EDT 2017

USER mrv2115

HOST casablanca.cc.columbia.edu 

PROCESSOR x86_64

OS Linux

Linux casablanca.cc.columbia.edu  
2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 
x86_64 x86_64 GNU/Linux


$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $

/vega/psych/app/freesurfer/bin/recon-all

PWD 
/vega/psych/users/mrv2115/fsdata/processed/CLEAN/SB014templatebaseline/scripts


CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 
SB014templatebaseline rh







--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu 


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Re: [Freesurfer] freesurfer longitudinal pipeline

[Martin Reuter]

Hi Paul,

step 4 basically means that you should take results from the 
*.long.baseid directories and not look at the original cross sectional 
directories or the base output. The page on statistic describes 
different tools to do that.


Yes, --s is replaced. All information on the subject ids is taken from 
the longitudinal qdec table file.


(Note here the naming is a little confusing, the longitudinal qdec table 
format follows and extends the original qdec table format, but it cannot 
be used in the Qdec too).


Best, Martin





Am 27.09.2017 um 18:02 schrieb miracle ozzoude:
Thank you very much Martin for your response. I do understand the 
statistical analysis ascept, my question was more in line with the 
last step (i.e. step 4) of the work flow summary 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). 
You suggested we calculate the difference between 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.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote:


Hi Paul,

for the statistical analysis take a look at the available options
here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
<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 the script to look for the stats in the
*.long.basename directories.

Best, Martin


Am 26.09.2017 um 17:50 schrieb miracle ozzoude:

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help
suggested that I calculate the different on the results from the
longitudinal command (e.g. tp2.long.longbase -
tp1.long.longbase). Let say, my timepoints were named
1001_Baseline.long.longbase and 1001_Followup.long.longbase; is
there a command i can use to preform this?

Second question, i want to extract the output of the longitudinal
pipeline using asegstats2table and aparcstats2table commands.
what flag/s should i include in  the original command to perform
this?

Thanks.
Paul


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Re: [Freesurfer] freesurfer longitudinal pipeline

[Martin Reuter]

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 
the script to look for the stats in the *.long.basename directories.


Best, Martin


Am 26.09.2017 um 17:50 schrieb miracle ozzoude:

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested 
that I calculate the different on the results from the longitudinal 
command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my 
timepoints were named 1001_Baseline.long.longbase and 
1001_Followup.long.longbase; is there a command i can use to preform 
this?


Second question, i want to extract the output of the longitudinal 
pipeline using asegstats2table and aparcstats2table commands. what 
flag/s should i include in  the original command to perform this?


Thanks.
Paul


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Re: [Freesurfer] Longitudinal increase in thickness/volume

[Martin Reuter]

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 the precentral region. I've run the subjects 
through the longitudinal stream. Because of time constraints, I've 
mostly focused on editing the precentral regions as well as any 
significant errors outside of the region. I've observed increases in 
thickness of up to 0.1mm in the precentral region. In some cases 
there's an increase in volume as well. Upon inspection though, the 
precentral wm/pial surfaces look fine. Is this a normal range of error?



Thank you,

-Caleb



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Re: [Freesurfer] longitudinal freesurfer- different scanners

[Martin Reuter]

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 are slight differences in WM/GM contrast. Probably 
better to use the scans from the same scanner and not use the third.


*Van:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *Namens *Michelle 
VanTieghem

*Verzonden:* zondag 17 september 2017 19:18
*Aan:* Freesurfer support list
*Onderwerp:* Re: [Freesurfer] longitudinal freesurfer- different scanners

Hi all,

I just wanted to follow up on my question:

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal pipeline 
help to account for different scanners, since it creates the average 
base image for all 3 time points? or is this not recommended to use 
different scanners in longitudinal pipeline?


Thanks!

- M

On Mon, Sep 4, 2017 at 5:27 PM, Michelle VanTieghem 
> 
wrote:


Hello,

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal pipeline 
help to account for different scanners, since it creates the average 
base image for all 3 time points? or is this not recommended?


Thank you,

Michelle

--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University

mrv2...@columbia.edu 



--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University

mrv2...@columbia.edu 



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Re: [Freesurfer] Longitudinal processing -qcache ERROR

[Martin Reuter]

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 
longitudinal processing. It is not the baseline (=first time point).


Best, Martin



Am 15.09.2017 um 16:00 schrieb Lisa Delalande:

Hi everyone,

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

"Error : cannot find /.../template_1-02/surf/_*lh.w-g.pct.mgh*_"_*
*_
I would like to kown if you know where the problem comes ? And what 
can I do to fix it ?


Thank you,
Best regards,

Lisa


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Re: [Freesurfer] longitudinal freesurfer- different scanners

[Martin Reuter]

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 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 or not). Often these changes are regional, not 
linear and not just offsets. Often the seem to interact with disease, 
age etc (meaning they affect older or more diseased subjects 
differently from young or healthy subjects). Therefore even including 
a co-variate to correct for scanner upgrade in the statistics may not 
be sufficient.


In your case you can either run the analysis only with the first three 
time points. Or run it with all three and include a scanner covariate 
in the statistic with interaction terms. In both cases you would 
profit from using the longitudinal stream in Freesurfer.


Best, Martin




Am 05.09.2017 um 02:27 schrieb Michelle VanTieghem:

Hello,

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal 
pipeline help to account for different scanners, since it creates the 
average base image for all 3 time points? or is this not recommended?


Thank you,
Michelle

--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu <mailto:mrv2...@columbia.edu>


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] longitudinal freesurfer- different scanners

[Martin Reuter]

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 or 
not). Often these changes are regional, not linear and not just offsets. 
Often the seem to interact with disease, age etc (meaning they affect 
older or more diseased subjects differently from young or healthy 
subjects). Therefore even including a co-variate to correct for scanner 
upgrade in the statistics may not be sufficient.


In your case you can either run the analysis only with the first three 
time points. Or run it with all three and include a scanner covariate in 
the statistic with interaction terms. In both cases you would profit 
from using the longitudinal stream in Freesurfer.


Best, Martin




Am 05.09.2017 um 02:27 schrieb Michelle VanTieghem:

Hello,

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal pipeline 
help to account for different scanners, since it creates the average 
base image for all 3 time points? or is this not recommended?


Thank you,
Michelle

--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu 


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.