[Freesurfer] autorecon1 with skull stripped image

[Rosalia Dacosta Aguayo]

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Dear Free Surfer's team,

I have a doubt. I have a sample of patients in which I already have done
the skull stripping using specific options with bet, so the skull stripping
has been successful. I wonder if I could feed autorecon1 with the skull
stripped image instead of the T1 image with skull.
Thank you very much for your time,
Rosalia
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[Freesurfer] Ask for your help about freesurfer submillimeter reconstruction!

[Nian Rui]

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Dear FreeSurfer Developers,


I am now working on the analysis of MRI images with the voxel resolution less 
than 0.2mm3.
I read your webpage about submillimeter reconstruction, 
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SubmillimeterRecon=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=NtVAAoNRuurWjiGc9gF6zmjCj-yhJX2FiqIQWantaTc=HTIr5eeTbJbG9K4SRzOVI_oGR2mBLs0SJ7kNktw_Jls=G5pESXnip5oTcvgA30e0qjSVsAcnKGo1DekVAyP1VaY=,
 which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 
0.5 mm3 voxels or below will have a brainmask failure (we are working on it!).
So I am writing to ask for your help about the reconstruction with freesurfer.
I would like to know, have you solved the higher resolution problem in the new 
version v6.0?
Could I use it to analyze the cortical thickness of these MRI images now?
If not, is there any other way to help processing these MRI images and we could 
run freesurfer step by step for evaluation?
Look forward to your timely help!
Thanks a lot in advance!
yours sincerely,
Rui
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Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

[Greve, Douglas N.,Ph.D.]

You cannot use QDEC for this. You must use the "command line" stream, 
ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, 
then mri_glmfit-sim. See the tutorial on the wiki.

On 10/17/2018 01:30 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I would like to know how I can run statistical analysis in QDEC on a 
> data set where there are 3 fixed factors each with 2 contrast levels. 
> (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs 
> disease )
>
> Any help would be much appreciated.
> Thank You,
>
>
> -- 
> Azeezat Azeez
> PhD Student
> Department of Biomedical Engineering || New Jersey Institute of 
> Technology
> Graduate School of Biomedical Sciences || Rutgers University
> E: ak...@njit.edu 
>
>
> ___
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[Freesurfer] QDEC analysis with more that 2 fixed factors

[Azeez, Azeezat]

External Email - Use Caution

Hello,

I would like to know how I can run statistical analysis in QDEC on a data
set where there are 3 fixed factors each with 2 contrast levels.
(DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs
disease )

Any help would be much appreciated.
Thank You,


-- 
Azeezat Azeez
PhD Student
Department of Biomedical Engineering || New Jersey Institute of Technology
Graduate School of Biomedical Sciences || Rutgers University
E: ak...@njit.edu
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Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

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  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  > 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
> > > > > combination of LME and Survival Analysis (as for the SA you
> > > > > need to 

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
> > > > combination of LME and Survival Analysis (as for the SA you
> > > > need to have measurements of all subjects at all time points,
> > > > so you estimate that from the LME model). 
> > > 
> > > Thank you for the link, I will take a look at. So if understand,
> > > this analysis has to be done after LME statistical analysis ?
> > > Thereafter since SA need all time points, LME model will allow me
> > > to estimate missing time points ?
> > > 
> > > > > > 3. see above (power analysis)
> > > > > > 4. GIGO means garbage in, garbage out, so the less you QC,
> > > > > > the more likely will your results be junk. The more you QC
> > > > > > the less likely will it be junk, but could still be. The FS
> > > > > > wiki has lots of tutorial information on checking
> > > > > > freesurfer recons. For longitudinal, you should
> > > > > > additionally check the surfaces in the base, the brain 

Re: [Freesurfer] Raw Data for Clusters

[Greve, Douglas N.,Ph.D.]

try
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf 
mc-z.abs.th13.cluster.ocn.dat --excludeid 0


On 10/17/2018 12:57 AM, WON JONG CHWA wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer Experts,
> I am running Qdec 1.4 and I want to extract raw data (in this case, 
> volume) from the significant clusters after Monte-Carlo simulation. In 
> this particular case, the summary file shows 5 significant clusters 
> after correction:
>
> # Cluster Growing Summary (mri_surfcluster)
> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
> # CreationTime 2018/10/16-23:28:21-GMT
> # cmdline mri_surfcluster --in 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh
>  
> --csd 
> /Users/user/MyInstall/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm18/abs/th13/mc-z.csd
>  
> --mask 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/mask.mgh 
> --cwsig 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.mgh
>  
> --vwsig 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.vertex.mgh
>  
> --sum 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.summary
>  
> --ocn 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.mgh
>  
> --oannot 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.annot
>  
> --csdpdf 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.pdf.dat
>  
> --annot aparc --cwpvalthresh 0.05 --o 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.masked.mgh
>  
> --surf white
> # cwd /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only
> # sysname  Darwin
> # hostname N-Volunteer-iMac.local
> # machine  x86_64
> # FixVertexAreaFlag 1
> # FixSurfClusterArea 1
> #
> # Input 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh
> # Frame Number  0
> # srcsubj fsaverage
> # hemi rh
> # surface white
> # annot aparc
> # SUBJECTS_DIR /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only
> # SearchSpace_mm2 64328
> # SearchSpace_vtx 149926
> # Bonferroni 0
> # Minimum Threshold 1.3
> # Maximum Threshold infinity
> # Threshold Sign    abs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold    0 mm^2
> # CSD thresh  1.30
> # CSD nreps    1
> # CSD simtype  null-z
> # CSD contrast NA
> # CSD confint  90.00
> # Overall max 2.06685 at vertex 34785
> # Overall min -4.82491 at vertex 356
> # NClusters  5
> # Total Cortical Surface Area 64328 (mm^2)
> # FixMNI = 1
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY TalZ    CWP    
> CWPLow    CWPHi   NVtxs   Annot
>    1   -4.825 356   2272.51 60.8   -9.4   -1.7 0.00010  
> 0.0  0.00020  3745  superiortemporal
>    2   -4.419  146292   2658.98 19.8   52.0   -5.7 0.00010  
> 0.0  0.00020  3104  rostralmiddlefrontal
>    3   -4.267  138330   1525.99 35.6   35.2    7.0 0.00460  
> 0.00370  0.00550  1936  rostralmiddlefrontal
>    4   -3.304  140353   1712.65 34.9  -30.2   56.6 0.00220  
> 0.00160  0.00280  3540  postcentral
>    5   -3.050   28351   1096.87 19.6  -34.8   -8.7 0.04530  
> 0.04260  0.04800  1687  parahippocampal
>
> --
> However, when I run the command to extract the raw data from these 
> clusters using this line:
> mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf 
> mc-z.abs.th13.cluster.ocn.dat --excludeid 0
>
> The terminal window outputs this:
>
> rh-Diff-SZ-HC-Intercept-volume user$ mri_segstats --i y.mgh --seg 
> mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat 
> --excludeid 0
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>
> cwd
>
> cmdline mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh 
> --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0
>
> sysnameDarwin
>
> hostname N-Volunteer-iMac.local
>
> machinex86_64
>
> useruser
>
> UseRobust0
>
> Loading mc-z.abs.th13.sig.cluster.mgh
>
> Loading y.mgh
>
> Voxel Volume is 1 mm^3
>
> Generating list of segmentation ids
>
> Found4 segmentations
>
> Computing statistics for each segmentation
>
> 0-468496849.000
>
> 1-254765476.000
>
> 2-116871687.000
>
> Reporting on3 segmentations
>
> Computing spatial average of each frame
>
> 012
>
> Writing to mc-z.abs.th13.cluster.ocn.dat
>
> mri_segstats done
>
> -
>
> So I get a .dat file that only has 3 columns, which does not match up 
> to the 5 that I originally observed after the correction. If you could 
> let me know what the problem is that would be greatly 

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Bruce Fischl]

Hi Amanda

what is your command line? And is there any reason you can't convert it 
back to binary and load it that way if ascii fails?


cheers
Bruce
On Wed, 17 Oct 2018, 
Worker, Amanda wrote:




External Email - Use Caution

Hi Bruce,


I have the same issue in freeview. The error is:


ERROR: could not determine type 
of/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
mri_read(): couldn't determine type of 
file/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
ERROR: could not determine type 
of/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
could not read overlay data 
from/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
mri_read(): couldn't determine type of 
file/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc

Thanks,

Amanda


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: 16 October 2018 18:13:18
To: Freesurfer support list
Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer  
Hi Amanda

can you try it in freeview? tksurfer has been deprecated for a while now

cheers
Bruce
On
Tue, 16 Oct 2018, Worker, Amanda wrote:

>
> External Email - Use Caution
>
> Thank you!
>
>
> So the answer to the first question is that yes I can convert it back to a
> curvature file and that curvature file can be loaded as an overlay. So this
> must mean that the problem is with reading the .asc file rather than the
> file being corrupt?
>
>
> Cheers,
>
>
> Amanda
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 October 2018 17:06:26
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
>  
> Hi Amanda
>
> mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
>
> should do the trick
> cheers
> Bruce
> On Mon, 15 Oct
> 2018, Worker, Amanda wrote:
>
> >
> > External Email - Use Caution
> >
> > How would I do that? mris_convert doesn't seem to take .asc as an input?
> >
> >
> >
> >___
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of
> > Greve, Douglas N.,Ph.D. 
> > Sent: 15 October 2018 16:25:51
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Using a .asc file as overlay in
> freeview/tksurfer  
> > Not sure. Can you use mris_convert to convert the asc back to a curv file?
> >
> > On 10/15/2018 11:20 AM, Worker, Amanda wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello,
> > >
> > >
> > > I am trying to overlay a .asc file in either freeview or tksurfer, but
> > > so far having no luck.
> > >
> > >
> > > As practice and to determine the right format, I am simply using
> > > lh.thickness, which I've converted to .asc using the following command:
> > >
> > >
> > > % mris_convert -c lh.thickness lh.white lh.thickness.asc
> > >
> > >
> > > I am trying to overlay this onto lh.pial for one subject, however I
> > > cannot load the file and I get the following error message:
> > >
> > >
> > > % mri_read(): couldn't determine type of file
> >>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
> 62a631d19/surf/lh.thickne
> > ss.asc
> > > surfer: couldn't load
> >>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
> 62a631d19/surf/lh.thickne
> > ss.asc.
> > >  If you were trying to load a functional volume, make sure
> > > you selected the right registration method, and if necessary,
> > > that the registration file exists.
> > > If you were trying to load a volume-encoded value file,
> > > make sure it has the same number of values as this surface
> > > does vertices (128970).
> > > sclv_read_from_volume: error in FunD_New
> > >
> > > Interestingly, I can load the file as a curvature file, but then can't
> > > play around with the threshold.
> > >
> > >
> > > Do you have any idea what I'm doing wrong? Any help would be
> appreciated!
> > >
> > >
> > > Thanks,
> > >
> > >
> > > Amanda
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> >>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm
> r.mgh.harvard.edu%2Fmailm
> >an%2Flistinfo%2Ffreesurferdata=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
> ac3c35e85fb46f47e2c08d63
> >2b28e63%7C8370cf1416f34c16b83c724071654356%7C0sdata=p6poNQ0vBOYwWAjR4U
> jk5lfKTtIcbEDR6icoWCJ2mz
> > 8%3Dreserved=0
> >
> >
> > 

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Worker, Amanda]

External Email - Use Caution

Hi Bruce,


I have the same issue in freeview. The error is:


ERROR: could not determine type of 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
mri_read(): couldn't determine type of file 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
ERROR: could not determine type of 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
could not read overlay data from 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
mri_read(): couldn't determine type of file 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc

Thanks,

Amanda



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 16 October 2018 18:13:18
To: Freesurfer support list
Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Hi Amanda

can you try it in freeview? tksurfer has been deprecated for a while now

cheers
Bruce
On
Tue, 16 Oct 2018, Worker, Amanda wrote:

>
> External Email - Use Caution
>
> Thank you!
>
>
> So the answer to the first question is that yes I can convert it back to a
> curvature file and that curvature file can be loaded as an overlay. So this
> must mean that the problem is with reading the .asc file rather than the
> file being corrupt?
>
>
> Cheers,
>
>
> Amanda
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 October 2018 17:06:26
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
>
> Hi Amanda
>
> mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
>
> should do the trick
> cheers
> Bruce
> On Mon, 15 Oct
> 2018, Worker, Amanda wrote:
>
> >
> > External Email - Use Caution
> >
> > How would I do that? mris_convert doesn't seem to take .asc as an input?
> >
> >
> >
> >___
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of
> > Greve, Douglas N.,Ph.D. 
> > Sent: 15 October 2018 16:25:51
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Using a .asc file as overlay in
> freeview/tksurfer
> > Not sure. Can you use mris_convert to convert the asc back to a curv file?
> >
> > On 10/15/2018 11:20 AM, Worker, Amanda wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello,
> > >
> > >
> > > I am trying to overlay a .asc file in either freeview or tksurfer, but
> > > so far having no luck.
> > >
> > >
> > > As practice and to determine the right format, I am simply using
> > > lh.thickness, which I've converted to .asc using the following command:
> > >
> > >
> > > % mris_convert -c lh.thickness lh.white lh.thickness.asc
> > >
> > >
> > > I am trying to overlay this onto lh.pial for one subject, however I
> > > cannot load the file and I get the following error message:
> > >
> > >
> > > % mri_read(): couldn't determine type of file
> >>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
> 62a631d19/surf/lh.thickne
> > ss.asc
> > > surfer: couldn't load
> >>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
> 62a631d19/surf/lh.thickne
> > ss.asc.
> > >  If you were trying to load a functional volume, make sure
> > > you selected the right registration method, and if necessary,
> > > that the registration file exists.
> > > If you were trying to load a volume-encoded value file,
> > > make sure it has the same number of values as this surface
> > > does vertices (128970).
> > > sclv_read_from_volume: error in FunD_New
> > >
> > > Interestingly, I can load the file as a curvature file, but then can't
> > > play around with the threshold.
> > >
> > >
> > > Do you have any idea what I'm doing wrong? Any help would be
> appreciated!
> > >
> > >
> > > Thanks,
> > >
> > >
> > > Amanda
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> >>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm
> r.mgh.harvard.edu%2Fmailm
> >an%2Flistinfo%2Ffreesurferdata=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
> ac3c35e85fb46f47e2c08d63
> >2b28e63%7C8370cf1416f34c16b83c724071654356%7C0sdata=p6poNQ0vBOYwWAjR4U
> jk5lfKTtIcbEDR6icoWCJ2mz
> > 8%3Dreserved=0
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr
> .mgh.harvard.edu%2Fmailm
> >an%2Flistinfo%2Ffreesurferdata=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
> 

[Freesurfer] license format error

[Georg Schramm]

External Email - Use Caution

Dear FreeSurfer Developers,

I have a installed freesurfer (6.0.0-centos6_x86_64)
on 2 of our linux servers.

One the first server:
platform: ubuntu 16.04
uname -a: Linux fermi 4.4.0-133-generic #159-Ubuntu SMP Fri Aug 10 07:31:43 UTC 
2018 x86_64 x86_64 x86_64 GNU/Linux
It runs fine.

On the second server:
platform: CentOS 7.4.1708
uname -a: Linux r23g36 3.10.0-862.11.6.el7.x86_64 #1 SMP Tue Aug 14 21:49:04 
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
I get the following license format error when running recon-all:
--
GNU libc version: 2.17
ERROR: Systems running GNU glibc version greater than 2.15
...
--

The license files are new (downloaded this week)
and exactly the same on both servers
(I compared the hexdumps).
I also checked that I have read permissions to the license file
in $FREESURFER_HOME on the 2nd server.

Do you have any idea what could go wrong on the 2nd server?

Bests,
Georg

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