[Freesurfer] GPU/supercomputer adaptation of freesurfer?

[John Absher]

External Email - Use Caution

Hi,

I'm planning a freesurfer analysis of a large MRI dataset, and want to use the 
"380 GPU nodes" (and other cores/nodes) on the Palmetto Cluster 
(https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html) to 
speed up the process. Since I am not a programmer, I'm hoping someone can give 
me a quick tutorial:


a)  Is this going to speed up recon-all and the data analysis?

b)  How much programming/expertise is required to enable freesurfer to take 
advantage of a supercomputer's resources?

c)   Has anyone done this already?

d)  The Palmetto Cluster is more or less limited to command-line. As long 
as I visualize the data on another system, I assume this will not be a problem, 
right?

Thanks,

John R. Absher, MD

jabs...@ghs.org
GHS Neuroscience Associates
University of South Carolina School of Medicine Greenville
864-350-6655 (mobile)

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Elena Pozzi]

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to use FIR to get HRF shape

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

Hi Lauri, what is non-ideal about it?
doug

On 12/06/2018 05:30 PM, Lauri Tuominen wrote:
>  External Email - Use Caution
>
> Hi there,
>
> I would like to know if a condition leads to a delayed HRF peaking.
>
> To device an experiment to answer this, I collected finger tapping pilot data 
> with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, 
> TR=1.6.
>
> The trials are not TR locked because I thought I’d sample different portions 
> of the HRF during each trial.
>
> I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine.
>
> My problem is that the resulting ces.nii.gz has only 16 volumes, which 
> correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time 
> resolution for peak detection would be 1.6, which is not what I would like it 
> to be. This is obviously less than ideal for answering my research question.
>
> How could I get the FIR fit to each timepoint so I could reconstruct the HRF 
> myself? Or would there be some other workaround / analysis? Or do I need to 
> collect the data in some other way, i.e somehow sliding the TR-event locking?
>
> Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, 
> iminsig.nii.gz and minsig.nii.gz?
>
> Thanks so much again for the help
>
> Lauri Tuominen
>
>   
>
>
>
>   
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] How to use FIR to get HRF shape

[Lauri Tuominen]

External Email - Use Caution

Hi there, 

I would like to know if a condition leads to a delayed HRF peaking.

To device an experiment to answer this, I collected finger tapping pilot data 
with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, 
TR=1.6.

The trials are not TR locked because I thought I’d sample different portions of 
the HRF during each trial. 

I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. 

My problem is that the resulting ces.nii.gz has only 16 volumes, which 
correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time 
resolution for peak detection would be 1.6, which is not what I would like it 
to be. This is obviously less than ideal for answering my research question.  

How could I get the FIR fit to each timepoint so I could reconstruct the HRF 
myself? Or would there be some other workaround / analysis? Or do I need to 
collect the data in some other way, i.e somehow sliding the TR-event locking?

Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, iminsig.nii.gz 
and minsig.nii.gz? 

Thanks so much again for the help

Lauri Tuominen

 



 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

[Sahil Bajaj]

External Email - Use Caution

Thanks Dr. Greve, actually I was using --bg 2 in my command line. Removing
--bg has now speeded up the process.

Thanks again for your help.

Regards,
Sahil

On Thu, Dec 6, 2018 at 12:04 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I think something is wrong if you only have 45 subjects, it should not
> take that long. Can you send your mri_glmfit command line and the
> terminal output of mri_glmfit-sim?
>
> On 12/06/2018 01:14 PM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Dear Dr. Greve,
> >
> > I have 45 subjects as input. SLURM is also a parallel processing
> > pipeline similar to PBS, Grid Engine, or Condor:
> > https://en.wikipedia.org/wiki/Slurm_Workload_Manager
> > I am not sure how can I speed up the mri_glmfit-sim processing.
> >
> > Thanks !
> >
> > On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I don't know what Slurm is, so I guess the answer is no. If you have
> > multiple processors on your machine, you can use the --bg option. In
> > general, I have not seen it take that long to run. How many input
> > subjects do you have?
> >
> > On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello experts,
> > >
> > > I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm
> > 1000 1.3
> > > abs --cwp 0.05 --2spaces command, but its taking forever even if I
> > > reduce # of permutations from 1000 to 10.
> > >
> > > I was just wondering if there’s a version of FreeSurfer for Slurm
> > > parallel processing clusters.
> > >
> > > Thanks !
> > > Sahil
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fMRI time series extraction

[Zhi Li]

External Email - Use Caution

Thank you very much, Douglas. It works now. How could I know the ROI index
of each column in the .dat file? And if it is available to use pca during
extracting time series as fcseed-config?

Best,

Zhi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fMRI time series extraction

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

On 12/06/2018 02:07 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Thank you very much, Douglas. It works now. How could I know the ROI 
> index of each column in the .dat file?
If you add --sum sum.dat, the sum file will tell you the order
> And if it is available to use pca during extracting time series as 
> fcseed-config?
Not from mri_segstats. If that is the route you really  want to go, then 
you will have to either program it yourself, or transfer the annot to 
each subject (mris_apply_reg), then transfer it to the volume 
(mri_aparc2aseg), then run fcseed-config specifying that output and the 
segmentation number you want
>
> Best,
>
> Zhi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

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

I think something is wrong if you only have 45 subjects, it should not 
take that long. Can you send your mri_glmfit command line and the 
terminal output of mri_glmfit-sim?

On 12/06/2018 01:14 PM, Sahil Bajaj wrote:
>
> External Email - Use Caution
>
> Dear Dr. Greve,
>
> I have 45 subjects as input. SLURM is also a parallel processing 
> pipeline similar to PBS, Grid Engine, or Condor: 
> https://en.wikipedia.org/wiki/Slurm_Workload_Manager
> I am not sure how can I speed up the mri_glmfit-sim processing.
>
> Thanks !
>
> On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I don't know what Slurm is, so I guess the answer is no. If you have
> multiple processors on your machine, you can use the --bg option. In
> general, I have not seen it take that long to run. How many input
> subjects do you have?
>
> On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Hello experts,
> >
> > I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm
> 1000 1.3
> > abs --cwp 0.05 --2spaces command, but its taking forever even if I
> > reduce # of permutations from 1000 to 10.
> >
> > I was just wondering if there’s a version of FreeSurfer for Slurm
> > parallel processing clusters.
> >
> > Thanks !
> > Sahil
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: Overall maxima is high and still no significant cluster

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

did you do this?

First, install a new version of mri_glmfit-sim from 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim 
(copy it to $FREESURFER_HOME/bin and make it executable with chmod a+rx 
mri_glmfit-sim).


On 12/06/2018 01:28 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Thanks Dough for your suggestions. I tried to use permutation method, 
> but its giving me following error:
>
> ERROR: design matrix is not orthogonal, cannot be used with permutation.
>
> If this something you really want to do, run with --perm-force
>
>
> Can you please tell me how can I fix this issue or if I can run with 
> --perm-force?
>
>
> Thanks for the help.
>
>
> On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> For it to show up in the output file, the cluster-wise pvalue must
> be <
> .05 (CWT). To see all the clusters regardless of significance, run it
> with a CWT of 1. If you want to run with a more liberal cluster
> forming
> threshold (CFT), you can try using permutation. See
> http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 12/05/2018 11:44 PM, Martin Juneja wrote:
> >
> > External Email - Use Caution
> >
> >
> > Dear experts,
> >
> > Could you please help me in resolving following issue?
> >
> > Thanks.
> > -- Forwarded message -
> > From: *Martin Juneja*    >>
> > Date: Wed, Nov 28, 2018 at 2:23 PM
> > Subject: Overall maxima is high and still no significant cluster
> > To: Freesurfer support list  
> >  >>
> >
> >
> > Hi FS experts,
> >
> > I am estimating the group-behavioral thickness interaction using
> > contrast 2 FSGD file:
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT <
> 0.01 and
> > CWT < 0.05 at FWHM of 12 mm.
> >
> > I do not find any significant clusters and my output summary
> text file
> > looks like the following. This file shows that overall maxima is
> > 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) =
> 4, so
> > I am just wondering despite the fact that maxima is > 4, why I
> do not
> > see this cluster in the summary/output *.mgh file?
> >
> > I would really appreciate any clarification and tips to modify my
> > input thresholds so that I do not miss any significant findings
> here.
> >
> > Thanks.
> > -
> >
> > # SearchSpace_mm2 76467.1
> > # SearchSpace_vtx 149953
> > # Bonferroni 2
> > # Minimum Threshold 2
> > # Maximum Threshold infinity
> > # Threshold Sign    abs
> > # AdjustThreshWhenOneTail 1
> > # CW PValue Threshold: 0.05
> > # Area Threshold    0 mm^2
> > # CSD thresh  2.00
> > # CSD nreps    1
> > # CSD simtype  null-z
> > # CSD contrast NA
> > # CSD confint  90.00
> > # Overall max 4.58212 at vertex 10608
> > # Overall min -2.84277 at vertex 75476
> > # NClusters          0
> > # FixMNI = 0
> > #
> > # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX  MNIY  MNIZ    CWP
> > CWPLow    CWPHi   NVtxs   WghtVtx   Annot
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fMRI time series extraction

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

The easiest thing would be to run
mri_segstats --annot subject lh  yourannot --excludeid 0 --i 
fmc.odd.sm5.fsaverage.lh.nii.gz --avgwf avgwf.dat

avgwf.dat will have a row for each fmri time point and a column for each 
parcellation


On 12/06/2018 01:45 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Thank you for your kind reply. Sorry for the confusing question. Now I 
> have an annotation file in fsaverage space. And I want to extracted 
> mean time series from each roi in this annotation file from 
> preprocessed fMRI data, e.g. fmc.odd.sm5.fsaverage.lh.nii.gz. I think 
> the fcseed-config and fcseed-sess works when I input the volume data 
> such as fmc.odd.nii.gz, namely in the individual space. I have tried 
> transform this annotation file to the individual segmentation file, 
> however, the segmentation was wrong for each roi. May I ask if it is 
> available to extract time series from the surface data with the custom 
> annotation file in the fsaverage space? I am not clear if I could use 
> mri_segstats to achieve this, I found a example of this command in 
> individual space "mri_segstats --seg aseg-in-func.img --ctab 
> $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --i func.img 
> --mask spmT.img --maskthresh 2.3 --sum bert.aseg-in-func.sum --avgwf 
> bert.avgwf.dat --avgwfvol bert.avgwf.img".  How could I apply it into 
> the surface data? Any suggestions would be appreciated.
>
> Best wishes,
>
> Zhi
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fMRI time series extraction

[Zhi Li]

External Email - Use Caution

Thank you for your kind reply. Sorry for the confusing question. Now I have
an annotation file in fsaverage space. And I want to extracted mean time
series from each roi in this annotation file from preprocessed fMRI data,
e.g. fmc.odd.sm5.fsaverage.lh.nii.gz. I think the fcseed-config and
fcseed-sess works when I input the volume data such as fmc.odd.nii.gz,
namely in the individual space. I have tried transform this annotation file
to the individual segmentation file, however, the segmentation was wrong
for each roi. May I ask if it is available to extract time series from the
surface data with the custom annotation file in the fsaverage space? I am
not clear if I could use mri_segstats to achieve this, I found a example of
this command in individual space "mri_segstats --seg aseg-in-func.img
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --i func.img
--mask spmT.img --maskthresh 2.3 --sum bert.aseg-in-func.sum --avgwf
bert.avgwf.dat --avgwfvol bert.avgwf.img".  How could I apply it into the
surface data? Any suggestions would be appreciated.

Best wishes,

Zhi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: Overall maxima is high and still no significant cluster

[Martin Juneja]

External Email - Use Caution

Thanks Dough for your suggestions. I tried to use permutation method, but
its giving me following error:

ERROR: design matrix is not orthogonal, cannot be used with permutation.

If this something you really want to do, run with --perm-force


Can you please tell me how can I fix this issue or if I can run with
--perm-force?


Thanks for the help.

On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> For it to show up in the output file, the cluster-wise pvalue must be <
> .05 (CWT). To see all the clusters regardless of significance, run it
> with a CWT of 1. If you want to run with a more liberal cluster forming
> threshold (CFT), you can try using permutation. See
> http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 12/05/2018 11:44 PM, Martin Juneja wrote:
> >
> > External Email - Use Caution
> >
> >
> > Dear experts,
> >
> > Could you please help me in resolving following issue?
> >
> > Thanks.
> > -- Forwarded message -
> > From: *Martin Juneja* mailto:mj70...@gmail.com>>
> > Date: Wed, Nov 28, 2018 at 2:23 PM
> > Subject: Overall maxima is high and still no significant cluster
> > To: Freesurfer support list  > >
> >
> >
> > Hi FS experts,
> >
> > I am estimating the group-behavioral thickness interaction using
> > contrast 2 FSGD file:
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT < 0.01 and
> > CWT < 0.05 at FWHM of 12 mm.
> >
> > I do not find any significant clusters and my output summary text file
> > looks like the following. This file shows that overall maxima is
> > 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) = 4, so
> > I am just wondering despite the fact that maxima is > 4, why I do not
> > see this cluster in the summary/output *.mgh file?
> >
> > I would really appreciate any clarification and tips to modify my
> > input thresholds so that I do not miss any significant findings here.
> >
> > Thanks.
> > -
> >
> > # SearchSpace_mm2 76467.1
> > # SearchSpace_vtx 149953
> > # Bonferroni 2
> > # Minimum Threshold 2
> > # Maximum Threshold infinity
> > # Threshold Signabs
> > # AdjustThreshWhenOneTail 1
> > # CW PValue Threshold: 0.05
> > # Area Threshold0 mm^2
> > # CSD thresh  2.00
> > # CSD nreps1
> > # CSD simtype  null-z
> > # CSD contrast NA
> > # CSD confint  90.00
> > # Overall max 4.58212 at vertex 10608
> > # Overall min -2.84277 at vertex 75476
> > # NClusters  0
> > # FixMNI = 0
> > #
> > # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX  MNIY   MNIZCWP
> > CWPLowCWPHi   NVtxs   WghtVtx   Annot
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

[Sahil Bajaj]

External Email - Use Caution

Dear Dr. Greve,

I have 45 subjects as input. SLURM is also a parallel processing pipeline
similar to PBS, Grid Engine, or Condor:
https://en.wikipedia.org/wiki/Slurm_Workload_Manager
I am not sure how can I speed up the mri_glmfit-sim processing.

Thanks !

On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't know what Slurm is, so I guess the answer is no. If you have
> multiple processors on your machine, you can use the --bg option. In
> general, I have not seen it take that long to run. How many input
> subjects do you have?
>
> On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Hello experts,
> >
> > I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3
> > abs --cwp 0.05 --2spaces command, but its taking forever even if I
> > reduce # of permutations from 1000 to 10.
> >
> > I was just wondering if there’s a version of FreeSurfer for Slurm
> > parallel processing clusters.
> >
> > Thanks !
> > Sahil
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

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

I don't know what Slurm is, so I guess the answer is no. If you have 
multiple processors on your machine, you can use the --bg option. In 
general, I have not seen it take that long to run. How many input 
subjects do you have?

On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
>
> External Email - Use Caution
>
> Hello experts,
>
> I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 
> abs --cwp 0.05 --2spaces command, but its taking forever even if I 
> reduce # of permutations from 1000 to 10.
>
> I was just wondering if there’s a version of FreeSurfer for Slurm 
> parallel processing clusters.
>
> Thanks !
> Sahil
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal Stream - LONG step

[Figueiro Longo, Maria Gabriela]

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 
 on behalf of Greve, Douglas N.,Ph.D. 

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
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fw: Surface based paired t test

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

Right, you can't use --fsgd. The FSGD file is used to get a list of 
subjects, but you have already specified the list with the --iv options. 
Does it run properly if you remove --fsgd (but keep --paired-diff)?

On 12/06/2018 12:45 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve, yes exactly this is what I did. i user mri_corg and I got 
> the reg.lta file. Then I used mris_preproc with the flag --iv but this 
> output an error message that the flags --fsgd, paired-diff and --iv 
> doesn't work together. This is the reason for my question.
>
> I appreciate any suggestion.
>
>
> If you have not sampled the PET data onto the surface, you will need 
> to run mri_coreg to create a registration to the anatomical. Then use 
> can use mris_preproc with the --iv option (listing each subject with a 
> different --iv). Run mris_preproc with --help to get examples
>
>
> On 12/06/2018 12:31 PM, john Anderson wrote:
>
> >
>
> > External Email - Use Caution
>
> >
>
> > Hi Dr Greve,
>
> >> I tried to follow this web page
>
> >> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
>
> >> This tutorial seems to be for cortical thickness data. After sampling
>
> >> each individual's surface onto the average surface, how can I modify
>
> >> this command to fit PET data mris_preproc --target fsaverage --hemi
>
> >> lh \
>
> >>--meas thickness --out lh.paired-diff.thickness.mgh \
>
> >>--fsgd pairs.fsgd --paired-diff
>
> >>
>
> >>
>
> >> Thanks for any help!
>
> >> John
>
> >>
>
> >>
>
> >> ‐‐‐ Original Message ‐‐‐
>
> >> On Tuesday, November 20, 2018 6:34 PM, john Anderson
>
> >> mailto:john.ande...@protonmail.com>> 
> wrote:
>
> >>
>
> >>> Dear Freesurfer experts,
>
> >>> I would like to run surface based paired  t test of PET data on
>
> >>> surface. For every subject I have visit pre treatment and post
>
> >>> treatment. I tried to follow the instructions here
>
> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the
>
> >>> toturial seems to be for cortical thickness data.
>
> >>> How can i modify the command mris_preproc to do paired test of PEt
>
> >>> data on brain surface
>
> >>>mris_preproc --target fsaverage --hemi lh \
>
> >>>--meas thickness --out lh.paired-diff.thickness.mgh \
>
> >>>--fsgd pairs.fsgd --paired-diff
>
> >>> thanks for any suggestion
>
> >>> John
>
> >>
>
> >
>
> >
>
> >
>
> > ___
>
> > Freesurfer mailing list
>
> > Freesurfer@nmr.mgh.harvard.edu 
>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu 
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Pial sueface error

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

Is that a subcortical GM structure (eg, amygdala)? The path of the 
surface in subcort GM structures is unimportant

On 11/29/2018 03:17 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer devs,
>
>
>  I´m doing a visual quality control of my pial and white matter 
> segmentation using freeview and I noticed that several subjects could 
> present an error in pial surface segmentation. I have attached two 
> images.
>
> Is this an pial surface error? in that case, How can I fix it? maybe 
> adding control points in order to extend the pial surface limit?
>
>
> Thanks
>
> Cheers,
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Question regarding mri_label2label and mris_anatomicalstats

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

Your command looks right. Sometimes there can be some stretching or 
compression of the labels as it is transformed back to an individual, 
especially if it is very small. Can you send pics of what you are seeing?

On 11/27/2018 05:19 PM, Wang, Xiaoyu wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
>
> I am currently doing a Longitudinal LME comparison between early and 
> late onset Parkinson's Patients.
>
> After the Matlab analysis, I view the resulting sig.mgh file in 
> tksurfer and create a label based on regions that pass FDR 0.05.
>
>
> I then use the mri_label2label on the label I created to resample it 
> back onto my subject pool using the following loop.
>
>
> for i in `less ./list`
> do
> echo $i
>
> mri_label2label \
>   --srcsubject fsaverage \
>   --srclabel fsaverage/label/ReFront.label \
>   --trgsubject $i \
>   --trglabel $i/label/ReFront.label \
>   --hemi lh \
>   --regmethod surface \
>
>
> done
>
>
> However, the resulting labels have a different shape and surface area 
> from the one I first created, and the data I obtained from 
> mris_anatomical_stats conflicts with the results from LME.
>
> What am I doing wrong?
>
>
> Sincerely,
>
> Xiaoyu Wang
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] CerebralWhiteMatterVol {Disarmed}

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

On 11/27/2018 02:16 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I had a follow up question regarding the CerebralWhiteMatter variable 
> from aseg.stats.
>
> 1.Does this include the white matter underlying the cortex?
>
It includes the all the WM in each hemisphere (excludes cerebellum WM 
and brainstem)
>
> 2.How about the subcortical white matter? (For example, I noticed  
> that there was a separate value for gray matter –SubCortGray- but not 
> for white matter. Is it because this is already included in the 
> CerebralWhiteMatter?)
>
What do you mean by subcortical WM? Technically, there is no WM in 
cortex, so all WM is sub-cortical whereas GM can be cortical or subcortical
>
> Thank you so much in advance for your help!
>
> Best regards,
>
> Da-Yea
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Greve, 
> Douglas N.,Ph.D.
> *Sent:* Tuesday, November 20, 2018 6:22 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] CerebralWhiteMatterVol
>
> No, it does not.
>
> On 11/20/18 3:54 PM, Song, Da-Yea wrote:
>
> *External Email - Use Caution *
>
> Hello,
>
> Does the CerebralWhiteMatterVol (from the aseg.stats) include the
> cerebellum?
>
> Thank you so much in advance for your help!
>
> Best,
>
> Da-yea
>
> 
>
> Disclaimer:
>
>
> The materials in this e-mail are private and may contain Protected
> Information. Please note that e-mail communication is not
> encrypted by default. You have the right to request further emails
> be encrypted by notifying the sender. Your continued use of e-mail
> constitutes your acknowledgment of these confidentiality and
> security limitations. If you are not the intended recipient, be
> advised that any unauthorized use, disclosure, copying,
> distribution, or the taking of any action in reliance on the
> contents of this information is strictly prohibited. If you have
> received this e-mail in error, please immediately notify the
> sender via telephone or return e-mail.
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu 
>
> *MailScanner has detected a possible fraud attempt from
> "urldefense.proofpoint.com" claiming to be*
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mean LGI per hemisphere

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

The 2nd row. The value you want is 3.3455



On 11/27/2018 08:19 AM, C.P.E. Rollins wrote:
>  External Email - Use Caution
>
> Dear Freesurfer developers,
> I have a quick question regarding calculating mean LGI (Marie Schaer's
> measure) per hemisphere.
> I believe that I can get the mean LGI per hemisphere with a command
> like:
>
> mri_segstats --slabel subject_ID lh
> $SUBJECTS_DIR/subject_ID/label/lh.cortex --i
> $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum
> lh.aparc.pial_lgi_lh.stats
>
> which gives me a file like this:
> # SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
> # subjectname Sub_010
> # Label Sub_010 lh
> /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/Sub_010/label/lh.cortex
> # InVolFile
> /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/Sub_010/surf/lh.pial_lgi
> # InVolFileTimeStamp  2018/11/13 16:38:05
> # InVolFrame 0
> # ExcludeSegId
> # Only reporting non-empty segmentations
> # VertexArea_mm2 0.678865
> # TableCol  1 ColHeader Index
> # TableCol  1 FieldName Index
> # TableCol  1 Units NA
> # TableCol  2 ColHeader SegId
> # TableCol  2 FieldName Segmentation Id
> # TableCol  2 Units NA
> # TableCol  3 ColHeader NVertices
> # TableCol  3 FieldName Number of Vertices
> # TableCol  3 Units unitless
> # TableCol  4 ColHeader Area_mm2
> # TableCol  4 FieldName Area
> # TableCol  4 Units mm^2
> # TableCol  5 ColHeader StructName
> # TableCol  5 FieldName Structure Name
> # TableCol  5 Units NA
> # TableCol  6 ColHeader Mean
> # TableCol  6 FieldName Intensity Mean
> # TableCol  6 Units unknown
> # TableCol  7 ColHeader StdDev
> # TableCol  7 FieldName Itensity StdDev
> # TableCol  7 Units unknown
> # TableCol  8 ColHeader Min
> # TableCol  8 FieldName Intensity Min
> # TableCol  8 Units unknown
> # TableCol  9 ColHeader Max
> # TableCol  9 FieldName Intensity Max
> # TableCol  9 Units unknown
> # TableCol 10 ColHeader Range
> # TableCol 10 FieldName Intensity Range
> # TableCol 10 Units unknown
> # NRows 2
> # NTableCols 10
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range
> 1   0  7509 5068.1  Seg 2.6260 0.3824 1.8121
> 3.0658 1.2537
> 2   113478791531.4  Seg0001 3.3455 0.8431 1.9459
> 5.7739 3.8280
>
> I was wondering which row corresponds to the mean LGI for the left
> hemisphere (and what the other row corresponds to?
>
> Many thanks,
> Colleen
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

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

On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Hi Douglas,
>
> Thanks a lot for your answers.
>
> 1) For the permutations, would you recommend using this for 
> controlling for MC in cortical thickness analyses too? 
Yes
> Why is it recommended to use permutation simulation as opposed to Z 
> Monte Carlo simulation for an LGI analysis?
Because the spatial correlations are very high (which makes MCZ less 
accurate)
>
> 2) I've attached here the output from ls -Rl 
> $FREESURFER_HOME/subjects/fsaverage.
It looks like there is a difference in where you think FREESURFER_HOME 
is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the 
attached file says it is in /applications/freesurfer/freesurfer_6.0.0. 
Which one is it?


>
> Thanks again,
> Colleen
>
> On 2018-11-23 16:26, C.P.E. Rollins wrote:
>> Dear Freesurfer Developers,
>> I have a 2-part question:
>> 1) I was advised to use permutation to control for multiple
>> comparisons in an LGI analysis, would you mind elaborating how to do
>> this in command line (in terms of command and parameters)?
>> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
>> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
>> (attached). I was wondering if you might have any advice? The file
>> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
>> view it in freeview.
>>
>> Many thanks,
>> Colleen
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] How to run GLM FIT simulation in parallel?

[Sahil Bajaj]

External Email - Use Caution

Hello experts,

I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 abs
--cwp 0.05 --2spaces command, but its taking forever even if I reduce # of
permutations from 1000 to 10.

I was just wondering if there’s a version of FreeSurfer for Slurm parallel
processing clusters.

Thanks !
Sahil
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FSGD File

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

If you want to use the --cache-in option, you need to have run recon-all 
with the -qcache option. If you take away the -cache-in option, then 
mris_preproc should run correctly

On 11/28/2018 12:45 PM, Larissa Bechtle wrote:
>
> External Email - Use Caution
>
> Hi everyone,
> thank you very much for answering!
> Originally I created the FSGD File with excel, saved it as a tab 
> delimited text file and used the tr-command afterwards (tr ’\r’ ’\n’ < 
> FSGD_2.fsgd.txt > FSGD_2.fsgd).
> After having read your message I recreated the FSGD-File with TextEdit 
> instead. Now it is
> [kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% mris_preproc 
> --fsgd FSGD.fsgd --cache-in thickness.fwhm10.fsaverage --target 
> fsaverage --hemi lh --out lh.gewalt.10.mgh
> nsubjects = 46
> ERROR: cannot find 
> /Users/Forschung/Desktop/Larissa/Gewalt//xp09/surf/lh.thickness.fwhm10.fsaverage.mgh
> I send you the actual fsgd-File an an attachement and would be very 
> thankful for some advice
> Best,
> Larissa
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mkcontrast-sess and mkcontrast2 matlab errors

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

what is your $MATLAB variable set to? It should be set to the matlab 
executable

On 11/30/2018 01:30 PM, Emily Levin wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer experts,
>
> I'm trying to run mkcontrast-sess using the newest development version 
> of freesufer from Nov 30th, 2018, and I am getting a matlab permission 
> denied error (see mkcontrast-sess_error text file).
>
> It seems to be happening around line 150-160 of mkcontrast2. However, 
> when I copy the old mkcontrast-sess and mkcontrast2 scripts from 
> freesurfer 6.0.0 (non-development version), it works fine in the 
> development version.
>
> The two versions in question are the stable release 6.0.0 and the 
> development release for centos7 Nov 30th, 2018.
>
> Any insight into why I'm getting permission denied would be really 
> helpful. There don't seem to be any changes between the two scripts so 
> I'm a little confused.
>
>
> Thanks,
> Emily
>
>
>
> -- 
> Emily J. Levin
> Lab Manager
> Attention & Perception Neuroimaging Lab
> Boston University
> Lab: 617-358-1737
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal Stream - LONG step

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

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
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Fw: Surface based paired t test

[john Anderson]

External Email - Use Caution

Hi Dr Greve, yes exactly this is what I did. i user mri_corg and I got the 
reg.lta file. Then I used mris_preproc with the flag --iv but this output an 
error message that the flags --fsgd, paired-diff and --iv doesn't work 
together. This is the reason for my question.

I appreciate any suggestion.

If you have not sampled the PET data onto the surface, you will need to run 
mri_coreg to create a registration to the anatomical. Then use can use 
mris_preproc with the --iv option (listing each subject with a different --iv). 
Run mris_preproc with --help to get examples

On 12/06/2018 12:31 PM, john Anderson wrote:

>

> External Email - Use Caution

>

> Hi Dr Greve,

>> I tried to follow this web page

>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

>> This tutorial seems to be for cortical thickness data. After sampling

>> each individual's surface onto the average surface, how can I modify

>> this command to fit PET data mris_preproc --target fsaverage --hemi

>> lh \

>> --meas thickness --out lh.paired-diff.thickness.mgh \

>> --fsgd pairs.fsgd --paired-diff

>>

>>

>> Thanks for any help!

>> John

>>

>>

>> ‐‐‐ Original Message ‐‐‐

>> On Tuesday, November 20, 2018 6:34 PM, john Anderson

>>  wrote:

>>

>>> Dear Freesurfer experts,

>>> I would like to run surface based paired  t test of PET data on

>>> surface. For every subject I have visit pre treatment and post

>>> treatment. I tried to follow the instructions here

>>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the

>>> toturial seems to be for cortical thickness data.

>>> How can i modify the command mris_preproc to do paired test of PEt

>>> data on brain surface

>>>   mris_preproc --target fsaverage --hemi lh \

>>> --meas thickness --out lh.paired-diff.thickness.mgh \

>>> --fsgd pairs.fsgd --paired-diff

>>> thanks for any suggestion

>>> John

>>

>

>

>

> ___

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] volume and mean intensity values from single nii file with multiple ROIs

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

Use mri_segstats. Run with --help to get more info

On 12/03/2018 06:12 AM, Anik Dar wrote:
>
> External Email - Use Caution
>
> Dear All,
>
> I have segmented the midbrain of each subjects into different 
> subregions (peduncle, substantia nigra, red nucleus etc) using an 
> atlas. I am trying to extract the volume of each region (the regions 
> are labeled 101, 102, 103 etc) and also trying to extract the mean 
> intensity from MPRAGE from each of these regions.
>
> Is there a way to do this in freesurfer tools ? I realize that there 
> is no color lut / index file associated with this atlas in freesurfer.
>
> Please let me know.
>
> Thank you,
>
> Ani
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fMRI time series extraction

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

On 12/03/2018 03:14 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Experts,
>
> Now I have a custom annotation file (only the cortical surface). May I 
> ask how could I use it to extract the mean time series from the 
> fsfast-preprocessed fMRI data? I have tried to transform this 
> annotation file into anatomical volume first:
>
> mri_aparc2aseg --s fsaverage --annot test --o test.mgz
>
> It seems I cannot do it to the left and right surface respectively, 
> right?
I'm not sure what you mean. It should do both left and right to create a 
single output file with both hemis.
> How should use this .mgz file next? Any suggestions would be appreciated.
When running fcseed-config, specify --seg test.mgz and then select the 
segmentation id (--segid) that you want to use
>
> Best wishes,
>
> Zhi Li
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Surface based paired t test

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

If you have not sampled the PET data onto the surface, you will need to 
run mri_coreg to create a registration to the anatomical. Then use can 
use mris_preproc with the --iv option (listing each subject with a 
different --iv). Run mris_preproc with --help to get examples

On 12/06/2018 12:31 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>> I tried to follow this web page 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
>> This tutorial seems to be for cortical thickness data. After sampling 
>> each individual's surface onto the average surface, how can I modify 
>> this command to fit PET data
>> mris_preproc --target fsaverage --hemi lh \
>> --meas thickness --out lh.paired-diff.thickness.mgh \
>> --fsgd pairs.fsgd --paired-diff
>>
>>
>> Thanks for any help!
>> John
>>
>>
>> ‐‐‐ Original Message ‐‐‐
>> On Tuesday, November 20, 2018 6:34 PM, john Anderson 
>>  wrote:
>>
>>> Dear Freesurfer experts,
>>> I would like to run surface based paired  t test of PET data on 
>>> surface. For every subject I have visit pre treatment and post 
>>> treatment. I tried to follow the instructions here 
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the 
>>> toturial seems to be for cortical thickness data.
>>> How can i modify the command mris_preproc to do paired test of PEt 
>>> data on brain surface
>>>   mris_preproc --target fsaverage --hemi lh \
>>> --meas thickness --out lh.paired-diff.thickness.mgh \
>>> --fsgd pairs.fsgd --paired-diff
>>> thanks for any suggestion
>>> John
>>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fsaverage6 FS6

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

Try using mris_apply_reg. The command line is simpler (but otherwise 
gives the same result).

On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote:
>
> External Email - Use Caution
>
> ​Dear FreeSurfer experts,
>
>
> I am encountering a problem when trying to downsample to fsaverage6 
> with FreeSurfer v.6.(see below):
>
>
> mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s 
> --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject 
> fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval 
> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh 
> --sval 
> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi 
> --sfmt curv --noreshape --cortex
>
> srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s
> srcval  =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi
> srctype    = curv
> trgsubject = fsaverage6
> trgval     = 
> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh
> trgtype    =
> srcsurfreg = fsaverage6.sphere.reg
> trgsurfreg = sphere.reg
> srchemi    = lh
> trghemi    = lh
> frame      = 0
> fwhm-in    = 0
> fwhm-out   = 0
> label-src  = lh.cortex.label
> label-trg  = lh.cortex.label
> OKToRevFaceOrder  = 1
> UseDualHemi = 0
> Reading source surface reg 
> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg
> No such file or directory
>
> I guess it's because the naming of the sphere file is now different 
> compared to v.5.3 (it was sufficient to run recon-all with the 
> additional -qcache -target fsaverage6 flag), so it can't be found by 
> mri_surf2surf. I tried to run mris_preproc instead of recon-all but I 
> still get the same error. Could you please help me with the right command?
>
> Thank you very much in advance!
>
> Best
> Rachele​
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Surface based paired t test

[john Anderson]

External Email - Use Caution

Hi Dr Greve,

> I tried to follow this web page 
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> This tutorial seems to be for cortical thickness data. After sampling each 
> individual's surface onto the average surface, how can I modify this command 
> to fit PET data
>
> mris_preproc --target fsaverage --hemi lh \
>--meas thickness --out lh.paired-diff.thickness.mgh \
>--fsgd pairs.fsgd --paired-diff
>
> Thanks for any help!
> John
>
> ‐‐‐ Original Message ‐‐‐
> On Tuesday, November 20, 2018 6:34 PM, john Anderson 
>  wrote:
>
>> Dear Freesurfer experts,
>> I would like to run surface based paired  t test of PET data on surface. For 
>> every subject I have visit pre treatment and post treatment. I tried to 
>> follow the instructions here 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the toturial 
>> seems to be for cortical thickness data.
>> How can i modify the command mris_preproc to do paired test of PEt data on 
>> brain surface
>>
>> mris_preproc --target fsaverage --hemi lh \
>>--meas thickness --out lh.paired-diff.thickness.mgh \
>>--fsgd pairs.fsgd --paired-diff
>>
>> thanks for any suggestion
>> John___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] hippocampus cortex surface

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

sorry, we don't have a hippo cortex analysis method

On 12/05/2018 10:26 AM, Yixin Ma wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer experts,
>
> After running the segmentation of hippocampus subfields, I'm wondering 
> if I can get the surface of the gray matter and white matter of 
> hippocampus in addition to subfields.
>
> My goal is to divide the hippocampus cortex into multiple layers.
>
> Thanks for your help in advance.
>
> Yixin
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Necessity of Matlab for Using FsFast

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

It is possible to use octave instead with
export FS_USE_OCTAVE=1
You must have octave installed of course

On 12/05/2018 02:38 AM, Maedeh Khalilian wrote:
>
> External Email - Use Caution
>
> Dear experts,
> Is it necessary to install Matlab to use FsFast for functional 
> connectivity?
> Thanks in advance
> Best
> Maedeh,
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem with mri_label2vol

[Mareike Grotheer]

External Email - Use Caution

Hi Greve,

It is a volume label that is supposed to be on the cortical ribbon. I want
to perform surface-based dilation.

Thank you,
Mareike

On Thu, Dec 6, 2018 at 9:11 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
> Is this a volume label that is supposed to be on the cortical ribbon? An
> you wan to do a surface-based dilation? Or do you just want to dilate it
> in 3D?
>
>
> On 12/04/2018 08:28 PM, Mareike Grotheer wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I am trying to bring functional ROIs defined in a different program
> > into FreeSurfer, so that I can dilate them into the white matter with
> > –proj abs, but I am running into a problem I was hoping you could help
> > me with. Here are the steps I am taking:
> >
> > 1)I am converting my ROIs, which are in nifti format, to FreeSurfer
> > labels using:
> >
> > cmd = ['mri_vol2label --c ' outFile{1} ' --id ' num2str(roiVal(roi)) '
> > --l ' saveLabel{1} ' --surf ' subject ' ' hemi ];
> > unix(cmd);
> >
> > 2)Next, I want to dilate the labels using this:
> >
> > cmd = sprintf('!mri_label2vol --subject %s --label %s --o %s.nii.gz
> > --hemi %s --reg %s.dat --temp %s --proj abs -7 0 .1 --fillthresh
> > .001', fs_subject,labelFileName,niftiRoiName,hemisphere, tmpRegFile,
> > regMgzFile);
> > eval(cmd);
> >
> > This does not work, I get the following Error Message: ERROR: label
> > my_label.label is not a surface label.
> >
> > I can circumvent this error by manually opening the label in tksurfer
> > and saving it again. After that mri_label2vol runs without error. I
> > assume that tksurfer automatically converts the label to a surface
> > label. While this solves my problem in principle, I have many labels
> > and am hoping that there may be a better way. Do you have any ideas
> > how one could do this automatically? I am running the above code in
> > Matlab R2015a. I am using FreeSurfer version 6.0.0 on Ubuntu 12.04 LTS.
> >
> > Thank you very much,
> >
> > Mareike
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registering Anatomical Parcellation to DWI

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

Can you be more specific about which files you want to map into your DWI 
space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You 
will need a registration file which you can obtain with bbregister


On 12/05/2018 02:34 AM, Maedeh Khalilian wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
> I have a parcellation  and a whole brain white matter files which are 
> the outputs of FreeSurfer.
> I want to register them to my DWI. I mean I want my parcellation and 
> white matter to be in the physical space of my DWI.
> Can FreeSurfer do it for me?
> If not , can you suggest me a toolbox that can do it fast?
> I would be grateful if u could help me.
> Cheers,
> Maedeh,
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: fcseedcor output

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

Can  you send the full terminal output?

On 12/05/2018 01:25 AM, Sara Jafakesh wrote:
>
> External Email - Use Caution
>
>
>
>
>
>
> Dear freesurfer experts,
> I want to calculate corrolation between two seeds with
> freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using
> fcseed-config and fseed-sess , I used fcseedcor. the command
> that I trying to run is as follow:
> fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed
> lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg
> 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat
> but the output of fcseedcor is not  .dat file ( the
> connectivity matrix for my result 2*2 matrix)  as it has been
> explained in the fcssedcor help. the output is just the .log
> file named  seedcor2.dat.log. although it has been done
> without error.
> I really dont know what is the problem.
> I would be grateful if you could help me.
> best regards,
> sara
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem with mri_label2vol

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

Is this a volume label that is supposed to be on the cortical ribbon? An 
you wan to do a surface-based dilation? Or do you just want to dilate it 
in 3D?


On 12/04/2018 08:28 PM, Mareike Grotheer wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I am trying to bring functional ROIs defined in a different program 
> into FreeSurfer, so that I can dilate them into the white matter with 
> –proj abs, but I am running into a problem I was hoping you could help 
> me with. Here are the steps I am taking:
>
> 1)I am converting my ROIs, which are in nifti format, to FreeSurfer 
> labels using:
>
> cmd = ['mri_vol2label --c ' outFile{1} ' --id ' num2str(roiVal(roi)) ' 
> --l ' saveLabel{1} ' --surf ' subject ' ' hemi ];
> unix(cmd);
>
> 2)Next, I want to dilate the labels using this:
>
> cmd = sprintf('!mri_label2vol --subject %s --label %s --o %s.nii.gz 
> --hemi %s --reg %s.dat --temp %s --proj abs -7 0 .1 --fillthresh 
> .001', fs_subject,labelFileName,niftiRoiName,hemisphere, tmpRegFile,  
> regMgzFile);
> eval(cmd);
>
> This does not work, I get the following Error Message: ERROR: label 
> my_label.label is not a surface label.
>
> I can circumvent this error by manually opening the label in tksurfer 
> and saving it again. After that mri_label2vol runs without error. I 
> assume that tksurfer automatically converts the label to a surface 
> label. While this solves my problem in principle, I have many labels 
> and am hoping that there may be a better way. Do you have any ideas 
> how one could do this automatically? I am running the above code in 
> Matlab R2015a. I am using FreeSurfer version 6.0.0 on Ubuntu 12.04 LTS.
>
> Thank you very much,
>
> Mareike
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Help with Data

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

On 12/04/2018 02:17 PM, T and LS wrote:
>
> External Email - Use Caution
>
>
> Dear Help Desk - I have a few basic questions about freesurfer.  I am 
> retired military bomb technician working on a blast TBI initiative and 
> not a research so please bear with me.  We are looking at a long term 
> study of bomb technicians and I am curious about the following before 
> moving forward.
>
>  1. Total number of images processed by freesurver?  Is this in the
> thousands or millions?
>
Do you mean since FS was created? Probably around 100,000 by now.
>
>  1. Cohart group data is this from each organization or is there a
> central pool.  e.g. I had a 3D volumetric MRI done with DTI at
> Washington University in St Louis and am 49yrs old is this only
> from their pool or larger data base? Any idea number of images in
> that data base?
>
I'm not sure what you mean. Can you elaborate? You cannot use DTI as 
input to freesurfer. Are you talking about the Human Connectome Project 
(HCP) data from Wash U?
>
>  1. Standard Deviations, Patient Annual Volume Change and Group Annual
> Volume change; are these organizations specific or a larger data base.
>
I'mnot sure what you mean. Are you asking if we have such a data base?
>
>  1. How accurate are the volumes from a 3T MRI and is there a huge
> fluctuation if scans are done on the same exact MRI system?  e.g.
> in my scan some of the thicknesses were down to .0013mm and
> volumes down to .9mm3 = is there a lot of error in those numbers.
>
The actual values are not accurate downto that level. It is hard to say 
what the accuracy really is but probably worse than 3%.
> Thanks for any information you can provide!  It seems there will be a 
> DVBIC site open soon where our school is and I would like to be able 
> to provide some input on this.
>
> Thanks,
> Todd Sheckley
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Extracting ROI from atlases

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

You can use
mri_binarize --i aparc+aseg.mgz --match 1028 --o 
ctx-lh-superiorfrontal.nii.gz
See  $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use


On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> Is there a command to extract ROIs from atlases (ex. desikan) in nifti 
> file formats?
>
> Thank you so much in advance for your time.
>
> Best,
>
> Da-Yea
>
> 
> Disclaimer:
>
>
> The materials in this e-mail are private and may contain Protected 
> Information. Please note that e-mail communication is not encrypted by 
> default. You have the right to request further emails be encrypted by 
> notifying the sender. Your continued use of e-mail constitutes your 
> acknowledgment of these confidentiality and security limitations. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying, distribution, or the taking of any action in 
> reliance on the contents of this information is strictly prohibited. 
> If you have received this e-mail in error, please immediately notify 
> the sender via telephone or return e-mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Direction of significant group comparison

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

You can tell from the sign of the "VtxMax" column that indicates the 
maximum in the cluster. If you used a signed test (pos or neg), then 
they will all have the given sign. If  you used an unsigned test (abs), 
then they may have different signs.


On 12/04/2018 11:54 AM, Backhausen, Lea wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I am running whole-brain based group comparisons of cortical measures 
> between a patient group and a control group using glm-fit and 
> Monte-Carlo correction for multiple comparisons.
>
> It works fine but I am not sure where to find information on which 
> group has more or less volume, for example, in a significant cluster.
>
> I use the xxx.sig.cluster.summary files which give me something like 
> this:
>
> ClusterNo
>
>   
>
> Max
>
>   
>
> VtxMax
>
>   
>
> Size(mm^2)
>
>   
>
> MNIX
>
>   
>
> MNIY
>
>   
>
> MNIZ
>
>   
>
> CWP
>
>   
>
> CWPLow
>
>   
>
> CWPHi
>
>   
>
> NVtxs
>
>   
>
> WghtVtx
>
>   
>
> Annot
>
> 1
>
>   
>
> 3.806
>
>   
>
> 82573
>
>   
>
> 3279.56
>
>   
>
> 44.3
>
>   
>
> 22.8
>
>   
>
> 29.5
>
>   
>
> 0.00020
>
>   
>
> 0.0
>
>   
>
> 0.00040
>
>   
>
> 5510
>
>   
>
> 11256.20
>
>   
>
> rostralmiddlefrontal
>
> 2
>
>   
>
> 2.099
>
>   
>
> 122283
>
>   
>
> 806.53
>
>   
>
> 38.4
>
>   
>
> -69.6
>
>   
>
> 44.6
>
>   
>
> 0.68055
>
>   
>
> 0.67327
>
>   
>
> 0.68774
>
>   
>
> 1654
>
>   
>
> 2759.09
>
>   
>
> inferiorparietal
>
> Is the direction hidden somewhere or in another file? Do I have to run 
> additional commands to get to the information?
>
> Thank you so much for any advice!
>
> Best
>
> Lea
>
> --
>
> Lea Backhausen
>
> Research Assistant
>
> Department of Child and Adolescent Psychiatry, Faculty of Medicine of 
> the TU Dresden, Germany
> http://www.uniklinikum-dresden.de 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] fsaverage6 FS6

[Sanfelici, Rachele]

External Email - Use Caution
​Dear FreeSurfer experts,



I am encountering a problem when trying to downsample to fsaverage6 with FreeSurfer v.6.(see below):




mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh
 --sval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi --sfmt curv --noreshape --cortex 




srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s

srcval     =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi

srctype    = curv

trgsubject = fsaverage6

trgval     = ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh

trgtype    = 

srcsurfreg = fsaverage6.sphere.reg

trgsurfreg = sphere.reg

srchemi    = lh

trghemi    = lh

frame      = 0

fwhm-in    = 0

fwhm-out   = 0

label-src  = lh.cortex.label

label-trg  = lh.cortex.label


OKToRevFaceOrder  = 1


UseDualHemi = 0

Reading source surface reg /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg

No such file or directory




I guess it's because the naming of the sphere file is now different compared to v.5.3 (it was sufficient to run recon-all with the additional -qcache -target fsaverage6 flag), so it can't be found by
 mri_surf2surf. I tried to run mris_preproc instead of recon-all but I still get the same error. Could you please help me with the right command?





Thank you very much in advance!





Best


Rachele​






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mris_preproc paired diff outputs 0 values

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

If you just want to look at the difference maps, you can load the 
mris_preproc output stack as an overlay, then scroll through each one of 
them. You're still looking at each one of them, but you don't have to 
open them up one-by-one.

On 12/05/2018 02:21 PM, Sims, Sara A wrote:
>
> External Email - Use Caution
>
> I have now gotten this to run on 3 subjects. However I have 786 
> subjects and need to find the bad apple. Is there a way I can do 
> quality checks on each subject’s difference map in fsaverage space 
> that mris_preproc has made? Basically I want to cycle through the 
> concatenated file in a systematic way that hopefully doesn’t involve 
> me opening them one at a time in freeview. How could I do this?
>
> Sara Sims
>
> *From: * on behalf of Sara 
> Sims 
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, December 3, 2018 at 10:56 AM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] mris_preproc paired diff outputs 0 values
>
> *External Email - Use Caution *
>
> Hello,
>
> I am trying to do a paired difference analysis of two runs of 
> probtrackx (I have already put them on the surface). The two 
> conditions are “central” and “far” for each subject. I have already 
> checked the individual subjects data and it does indeed have values.
>
> *Here is a sample of my subject list:*
>
> 100206.central
>
> 100206.far
>
> 100307.central
>
> 100307.far
>
> 100408.central
>
> 100408.far
>
> …etc.
>
> *Here is my mris_preproc script:*
>
> mris_preproc --target fsaverage --hemi lh --isp 
> $in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh 
> --isp $in/FP/100307.central/lhsurf.mgh --isp 
> $in/FP/100307.far/lhsurf.mgh --isp $in/FP/100408.central/lhsurf.mgh 
> --isp $in/FP/100408.far/lhsurf.mgh … --out 
> $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff
>
> *The output log shows no errors, the number of inputs equals the 
> number in the subject list and it creates a file but it’s all zeros. I 
> just have no idea as to why this would happen?*
>
> **
>
> Thanks,
>
> Sara Sims
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: Overall maxima is high and still no significant cluster

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

For it to show up in the output file, the cluster-wise pvalue must be < 
.05 (CWT). To see all the clusters regardless of significance, run it 
with a CWT of 1. If you want to run with a more liberal cluster forming 
threshold (CFT), you can try using permutation. See 
http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 12/05/2018 11:44 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
>
> Dear experts,
>
> Could you please help me in resolving following issue?
>
> Thanks.
> -- Forwarded message -
> From: *Martin Juneja* mailto:mj70...@gmail.com>>
> Date: Wed, Nov 28, 2018 at 2:23 PM
> Subject: Overall maxima is high and still no significant cluster
> To: Freesurfer support list  >
>
>
> Hi FS experts,
>
> I am estimating the group-behavioral thickness interaction using 
> contrast 2 FSGD file: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT < 0.01 and 
> CWT < 0.05 at FWHM of 12 mm.
>
> I do not find any significant clusters and my output summary text file 
> looks like the following. This file shows that overall maxima is 
> 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) = 4, so 
> I am just wondering despite the fact that maxima is > 4, why I do not 
> see this cluster in the summary/output *.mgh file?
>
> I would really appreciate any clarification and tips to modify my 
> input thresholds so that I do not miss any significant findings here.
>
> Thanks.
> -
>
> # SearchSpace_mm2 76467.1
> # SearchSpace_vtx 149953
> # Bonferroni 2
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Sign    abs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold    0 mm^2
> # CSD thresh  2.00
> # CSD nreps    1
> # CSD simtype  null-z
> # CSD contrast NA
> # CSD confint  90.00
> # Overall max 4.58212 at vertex 10608
> # Overall min -2.84277 at vertex 75476
> # NClusters          0
> # FixMNI = 0
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX  MNIY   MNIZ    CWP    
> CWPLow    CWPHi   NVtxs   WghtVtx   Annot
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

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

On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Thank you for answering. Please find below new questions.
> Bien cordialement,
>
>
> Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> a écrit :
>
> Hi Matthieu, sorry for the delay
>
> On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
> >          External Email - Use Caution
> >
> > Dear Freesurfer's experts,
> >
> > I tried to use PETSurfer to correct partial volume effect on my
> FDG PET images, testing both Muller-Gartner and RBV corrections.
> >
> > I ran the commands specified in PETSurfer website and used the
> two following commands for both MGX and RBV corrections respectively:
> >
> > mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
> --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output
> >
> > mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
> --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig
> >
> > 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX
> correction encompass more than just GM and values at the
> boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant.
> This is expected. The MG method gives you a value every place that
> there
> is GM signal *in the PET volume after partial volume effects*. So
> basically, if you were to take the cortical ribbon and smooth it
> by your
> PSF, every non-zero voxel has some GM in it (which is why the
> edges are
> so high). When you run it with --mgx .01, it will exclude voxels that
> have less than 1% GM after smoothing. If you you are disturbed by the
> wide ribbon, just make the threshold higher. In theory, every point
> along the surface normal gives you a valid answer, but the further
> from
> the center of the ribbon, the noisier it is going to be, so we
> generally
> only sample it at the center (--projfrac 0.5 to mri_vol2surf).
>
>
> Basically, please find below the mgx.ctxgm with threshold set at 0.01:
> image.png
>
> Then threshold set at 0.1:
> image.png
>
> Values at some parts of the cortex (olfactory, visual) are not the 
> same between the two thresholds. In the first one in these parts of 
> the brain, values are higher than the second and seem kind of 
> aberrant. Is there no reason to prefer a threshold at 0.1 than 0.01 ? 
> For example, in (Douglas et al., 2016, NeuroImage) a threshold of 0.3 
> has been found to be optimal: how determine visually or quantitatively 
> this optimal threshold ?
So when you click on the same voxel in both images, you get different 
values? Or is it just that the color scale is changing? The threshold 
should not change the values, just what is in or out of the final mask. 
The threshold of 0.3 was chosen mainly because it worked for the ROI 
analysis. In general, you should use GTM instead of MG for ROI analysis. 
For surface-based analysis, the threshold is not critical because the GM 
PVF is generally pretty high in cortex. It will make more of a 
difference in subcortical analysis.
>
>
> >
> > 2) Concerning RBV correction, output rbv.nii.gz seems to me
> following more precisely the GM ribbon. However contrary to what
> is said in PETSurfer website, rbv.nii.gz seems to be in the
> anatomical space (not in native PET) at the resolution of
> gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when
> mapping the volume to the surface ?
> Where does it say this? It should be in the anatomical space in the
> sense that it shares an RAS space with the conformed volume (aseg
> does
> gtmseg.mgz). This means that you can use --regheader with
> mri_vol2surf
> or mri_vol2vol when mapping into another space.
>
>
>  In https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer it says that 
> "mgx.ctxgm is in same resolution of the input PET", which is the case 
> since resolution and orientation are identical to native PET. The 
> PETsurfer tutorial then explains that "bbpet2anat.lta. is a 
> registration file that can be used to map the output PET volume (in 
> the mask bounding box) to the anatomical space".
>
> However, when I open rbv.nii file it is not in native PET resolution 
> and orientation but those of gtmseg.mgz (anatomical space but with 
> resolution of 0.5x0.5x05 mm). Why these differences between these two 
> methods of PVC and which registration file then to use when mapping 
> rbv.nii to the surface (rbv2anat.lta ?) ? I think I can't use directly 
> --regheader since resolution of rbv.nii is 0.5 mm3 whereas anatomical 
> space is of 1 mm3.
Yes, the rbv is in a higher resolution because the rbv does not have 
separate maps for each tissue type, so you need 

Re: [Freesurfer] visual cortex {Disarmed}

[Bruce Fischl]

Hi Zheng

if you mean primary visual cortex, then you can use our estimate of BA17 
which is stored in the subject's label subdirectory (as are BA18 and MT). 
If you mean all of visually-responsive cortex I don't think we have 
anything (nor is that a terribly well-defined concept, since some of it 
will be multimodal cortex)


cheers
Bruce


 On Thu, 6 Dec 2018, 郑凤莲 wrote:



External Email - Use Caution

Hi experts,

I want to do some research on the cortical thickness of visual cortex using FS 
6.0. Is there
specified or associated cortex model for the segmentation of visual cortex?
Thanks for your reply in advance. I need your help.

Sincerely,
Zheng

MailScanner has detected a possible fraud attempt from "maas.mail.163.com" 
claiming to be
MailScanner has detected a possible fraud attempt from "maas.mail.163.com" 
claiming to be
[7ab82759fd2726fb1920b652c2487756.jpg]
郑凤莲
邮箱：zhengfenglian0...@163.com

签名由 网易邮箱大师 定制


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Longitudinal processing and paralllel flag

[Erik O'Hanlon]

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

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

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


[cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png]

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] visual cortex {Disarmed}

[郑凤莲]

External Email - Use Caution

Hi experts,

I want to do some research on the cortical thickness of visual cortex using FS 
6.0. Is there specified or associated cortex model for the segmentation of 
visual cortex?
Thanks for your reply in advance. I need your help.

Sincerely,
Zheng


| |
郑凤莲
|
|
邮箱：zhengfenglian0...@163.com
|

签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer