Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

[Heidi Foo]

Thanks Douglas, it works now!

On Thu, Aug 25, 2016 at 6:45 AM, Douglas N Greve 
wrote:

> It actually looks like it might be a problem with your covariates.mat
> file (MatrixReadTxT error). Can you send that file?
>
>
> On 08/22/2016 10:06 PM, Heidi Foo wrote:
> > Dear FreeSurfer team,
> >
> > I am currently running mri_glmfir --eres-save using FreeSurfer 6.0.
> > However, there is an error saying "not enough memory to buffer." I
> > have attached the error log for your reference. Do you have any idea
> > how I can solve this problem?
> >
> > Thank you.
> >
> > Regards,
> > Heidi
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] Fwd: Cannot allocate memory mri_glmfit to remove covariates

[Douglas Greve]

This looks like it is a binary matlab file. This should be a simple text 
ascii file.



On 8/24/16 9:01 PM, Heidi Foo wrote:

Hi Douglas,

Attached the covariates.mat file.

Thanks.

Regards,
Heidi Foo

-- Forwarded message --
From: *Douglas N Greve* >

Date: Thu, Aug 25, 2016 at 6:45 AM
Subject: Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove 
covariates

To: freesurfer@nmr.mgh.harvard.edu 


It actually looks like it might be a problem with your covariates.mat
file (MatrixReadTxT error). Can you send that file?


On 08/22/2016 10:06 PM, Heidi Foo wrote:
> Dear FreeSurfer team,
>
> I am currently running mri_glmfir --eres-save using FreeSurfer 6.0.
> However, there is an error saying "not enough memory to buffer." I
> have attached the error log for your reference. Do you have any idea
> how I can solve this problem?
>
> Thank you.
>
> Regards,
> Heidi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 



--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 

www.nmr.mgh.harvard.edu/facility/filedrop/index.html 

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[Freesurfer] overlapping area question

[Arkadiy Maksimovskiy]

Hello Freesurfers,

I was wondering if someone might have information for how I can measure
overlapping areas between a cluster that was generated as a results of a
cortical thickness analysis, with a portion of a Yeo Network atlas.
Specifically, I would like to calculate the percentage that the cortical
thickness significant cluster (cache.th13.abs.sig.ocn.annot) overlaps with
one region of the "lh.Yeo2011_7Networks_N1000.annot" overlay.

I am not sure if there is a way to trace the two in tksurfer, and measure
their overlapping area in that manner.

Any help would be greatly appreciated.

Thank you,

Arkadiy
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[Freesurfer] Fwd: Cannot allocate memory mri_glmfit to remove covariates

[Heidi Foo]

Hi Douglas,

Attached the covariates.mat file.

Thanks.

Regards,
Heidi Foo

-- Forwarded message --
From: Douglas N Greve 
Date: Thu, Aug 25, 2016 at 6:45 AM
Subject: Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove
covariates
To: freesurfer@nmr.mgh.harvard.edu


It actually looks like it might be a problem with your covariates.mat
file (MatrixReadTxT error). Can you send that file?


On 08/22/2016 10:06 PM, Heidi Foo wrote:
> Dear FreeSurfer team,
>
> I am currently running mri_glmfir --eres-save using FreeSurfer 6.0.
> However, there is an error saying "not enough memory to buffer." I
> have attached the error log for your reference. Do you have any idea
> how I can solve this problem?
>
> Thank you.
>
> Regards,
> Heidi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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covariates.mat
Description: application/matlab-workspace
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Re: [Freesurfer] Recon-all error using Freesurfer 6.0

[Elpiniki Andrew]

Thankyou! It worked when I removed the trailing " / ". However after it 
finished running, I received this error:

ERROR reading 
/usr/local/DTI_processed_data/freesurfer_data_dir/fsaverage/label/lh.BA1_exvivo.label

Because the  "lh.BA1_exvivo.label"  file for some reason, when I checked, was 
not in my subjects_dir.

What should I do?

Thankyou very much!

Elpiniki


Douglas N 
Greve
 Mon, 22 Aug 2016 13:12:24 
-0700
Nothing looks suspicious. Try setting

setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir

ie, removing the trailing "/"

On 08/22/2016 02:12 AM, Elpiniki Andrew wrote:
> Hello Freesurfer experts,
>
> I'm having a bit of difficulty running the recon-all command. I
> recently downloaded Freesurfer version 6.0.
>
> The command that I'm running is:
>
>  recon-all -all -s $name -hippocampal-subfields-T1
>
> However I keep receiving this error:
>
> If: Expression Syntax
>
> I've attached the output using the -debug flag.
>
> I'm using Linux ( centos6.3). Not sure if this is related but I
> initially had an issue with recon-all stopped with an error when I
> first ran the same dataset. There was an error in the log file " too
> many levels of symbolic links".
> So, I created a new subjects directory and created a symlink to the
> fsaverage dir as per the instructions on the freesurfer wiki page.
>
>
> Thankyou very much in advance for your time and efforts!
>
> Kind regards,
> Elpiniki
>
>
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Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

[Douglas N Greve]

Yes, that is possible, but you should see some sort of trend, eg, most 
the ROI should have a certain sign


On 08/24/2016 06:47 PM, miracoo...@gmail.com wrote:
> Thanks doug. Also, let's say I extract the aparcstat table and perform t 
> -test using spss and a ROI become significant, is it possible the significant 
> effect will be lost using GLM surface based?
> Best,
> Paul
>
> Sent from my BlackBerry 10 smartphone.
>Original Message
> From: Douglas N Greve
> Sent: Wednesday, August 24, 2016 5:39 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] GLM surface based cortical thickness analysis vs 
> aparcstat table cortical thickness
>
> One is a map-based/voxel-wise analysis, each voxel is treated
> separately. The aparc stats table is an average over all vertices in the
> ROI. If you have an effect that does goes across the ROI boundary, it
> could be lost in the ROI analysis. On the other hand, the ROI analysis
> may be more powerful because of the averaging across space and fewer
> issues with registration across subject
>
>
> On 08/23/2016 04:59 PM, miracoo...@gmail.com wrote:
>> Hello freesurfer experts,
>> What's the difference between GLM surface based cortical thickness
>> analysis and the cortical thickness analysis performed when using
>> regions extracted from aparcstat table?
>> Best,
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>>
>>
>> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

[miracooloz]

Thanks doug. Also, let's say I extract the aparcstat table and perform t -test 
using spss and a ROI become significant, is it possible the significant effect 
will be lost using GLM surface based? 
Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Douglas N Greve
Sent: Wednesday, August 24, 2016 5:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] GLM surface based cortical thickness analysis vs 
aparcstat table cortical thickness

One is a map-based/voxel-wise analysis, each voxel is treated 
separately. The aparc stats table is an average over all vertices in the 
ROI. If you have an effect that does goes across the ROI boundary, it 
could be lost in the ROI analysis. On the other hand, the ROI analysis 
may be more powerful because of the averaging across space and fewer 
issues with registration across subject


On 08/23/2016 04:59 PM, miracoo...@gmail.com wrote:
> Hello freesurfer experts,
> What's the difference between GLM surface based cortical thickness 
> analysis and the cortical thickness analysis performed when using 
> regions extracted from aparcstat table?
> Best,
> Paul
>
> Sent from my BlackBerry 10 smartphone.
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

[Douglas N Greve]

It actually looks like it might be a problem with your covariates.mat 
file (MatrixReadTxT error). Can you send that file?


On 08/22/2016 10:06 PM, Heidi Foo wrote:
> Dear FreeSurfer team,
>
> I am currently running mri_glmfir --eres-save using FreeSurfer 6.0. 
> However, there is an error saying "not enough memory to buffer." I 
> have attached the error log for your reference. Do you have any idea 
> how I can solve this problem?
>
> Thank you.
>
> Regards,
> Heidi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] freeview error:

[Alison Boos]

Hi FreeSurfer Team,
 
I am trying to edit longitudinal data using FreeView. The original timepoints 
were processed and edited using FreeSurfer 5.1. The longitudinal data was also 
ran using FreeSurfer 5.1. I am currently trying to edit the longitudinal data 
using FreeView, however FreeView seems to have updated with the OS X and is 
incompatible with FreeSurfer 5.1. When I try to view the longitudinal base 
using FreeView errors pop up that say "failed to load". I don't want to update 
to FreeSurfer 5.3 for this project because it has all been run in 5.1 thus far. 
Does anyone have any insight about this?
 
I'm using a MAC PRO (2009) with OS X 10.9.5
FreeSurfer Version: freesurfer-Darwin-leopard-i868-stable-pub-v5.1.0
FreeView Information:
Process: freeview.bin [29818]
Path:
/Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview.bin
Identifier:  freeview.bin
Version: ???
OS Version:  Mac OS X 10.9.5 (13F1911)
Report Version:  11___
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[Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

[Silas]

Dear FreeSurfer team,


I'm doing a structural analysis with 50 MS patients and 50 healthy controls 
(T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white 
matter. My co-worker did manual editing (bullet points) in the FLAIR images, 
and i would like to use these edits when running recon-all in order to avoid 
further manual editing.


Steps in analysis:


1) First steps of recon-all:

recon-all -autorecon1 -autorecon2


2) Reslicing the FLAIR images:

The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR 
(resliced to 1mm, co-registered in MNI-space and with manually drawn binary 
lesion masks (218x182x182)). I overcome this problem by reslicing the FLAIR 
images using aseg.auto.nii as the image defining space. This was done in SPM8, 
and prior to this the aseg.auto.mgz was converted to a .nii using mri_convert.


3) Insert lesions from the resliced FLAIR images to aseg.mgz:

aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg

manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever format, but 
should be binary

ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol ~= 0);

newaseg = aseg;

newaseg.vol(ind) = 77;

MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so make a 
backup


4) The last steps of recon-all:

recon- all -autorecon2-cp -autorecon3

When running the following command i get this error:

/depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS -autorecon2-cp 
-autorecon3 subjid 01MS





'#@# Intensity Normalization2 Mon Aug  DATE
/.../subjects_FLAIR/01MS/mri

 mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz

using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
5361 control points removed
Building bias image
mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
building Voronoi diagram...
Numerical argument out of domain
Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC 2015 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 01MS exited with ERRORS at Mon Aug  8 15:31:32 CEST 2016


The lesions looks alright (as if they are in the right place). Do you have any 
suggestions what to do if they are not? And what could be the problem if they 
are placed correctly?

What is the advantage of starting by running autorecon-1 and 2 and then 
inserting the lesions from the FLAIR?


Thanks a lot for all your help!


Best, Silas

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Re: [Freesurfer] FW: Correcting for both hemispheres in thickness analysis using a PFC mask

[Douglas N Greve]

I've been pushing people to use this method when running monte carlo sims

http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

To correct for two hemis, just add --2spaces to the command line. All 
this does is to bonferroni correct the final clusterwise p-values across 
two measurements


On 08/24/2016 10:25 AM, Gold, Andrea (NIH/NIMH) [F] wrote:
> Hi,
>
> I have a question about correcting for 2 hemispheres in a thickness
> analysis using a PFC mask. Here are the steps I ran:
>
> 1) I ran the analysis in qdec without a mask.
>
> 2) I found the mri_glmfit.log file from step 1 and cut out the  mri_glmfit
> command that runs the analysis and
>   replaced ³label² option with path to our mask:
> cmdline mri_glmfit --y
> /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
> _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/y.mgh --fsgd
> /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
> _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/qdec.fsgd
>   dods --glmdir
> /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
> _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151 --surf fsaverage lh
> --label
> /gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/lab
> el/labels/PFC_mask_8ROIs_LH --C
> /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
> _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Avg-Intercept-
> thickness.mat --C
> /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
> _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Diff-anxiousyo
> uth-healthyyouth-Intercept-thickness.mat
>
>
> 3) I then ran mri_glmfit-sim:
>   mri_glmfit-sim  --glmdir ./Thickness_LH_sm10_Dichtomous_n151 --sim mc-z
> 1 1.3 mc-z.1p3.abs --sim-sign abs
>
> Question: I am 99% the mri_glmfit-sim command does not correct for both
> hemispheres.
> Is it possible to figure out if the cluster survives correction for 2
> hemis based on the cluster summary file (attached) from steps 1-3 above?:
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP
> CWPLowCWPHi   NVtxs   Annot
> 12.480  124922479.68 -7.2   29.0  -16.8  0.00440
> 0.00360  0.00530   887  medialorbitofrontal
>
> Thanks!
> Andrea
>
>
>
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Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

[Douglas N Greve]

One is a map-based/voxel-wise analysis, each voxel is treated 
separately. The aparc stats table is an average over all vertices in the 
ROI. If you have an effect that does goes across the ROI boundary, it 
could be lost in the ROI analysis. On the other hand, the ROI analysis 
may be more powerful because of the averaging across space and fewer 
issues with registration across subject


On 08/23/2016 04:59 PM, miracoo...@gmail.com wrote:
> Hello freesurfer experts,
> What's the difference between GLM surface based cortical thickness 
> analysis and the cortical thickness analysis performed when using 
> regions extracted from aparcstat table?
> Best,
> Paul
>
> Sent from my BlackBerry 10 smartphone.
>
>
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Re: [Freesurfer] PET surface sampling

[Douglas N Greve]

Sample the raw TAC data onto the surface (and not the BPs), then smooth 
on the surface, then run the mrtm2 with all the same arguments except 
use the surface data as the input (--y) instead of the ROI data.

On 08/23/2016 05:13 PM, Jonathan DuBois wrote:
> Hi,
>
> I’m trying to use the PETsurfer Pipeline to perform BP analysis, but 
> I’m not sure at which point in the pipeline to sample the data to the 
> surface and what registration to use?
>
> I tried running the pipeline using dynamic kinetic modeling as 
> described here: http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, 
> and then used the following command to try and sample the BP map the 
> surface:
> mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov 
> mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o lh.bp_pf5.mgh
>
> But got the following error:
> ERROR: source volume is neither source nor target of the registration
>
> I also tried sampling the mrtm2/bp.nii.gz to the orig.mgz volume space 
> and then to the surface using:
> mri_vol2vol --mov mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o 
> mrtm2/bp_2anat.nii.gz --targ $SUBJECTS_DIR/subject1/mri/orig.mgz; 
> mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov 
> mrtm2/bp_2anat.nii.gz --regheader subject1 --o lh.bp_pf5.mgh
>
> This worked, although the surface file did not have any values…
>
> Could you please let me know what is the best way to sample the data 
> to the surface, and if it should be down prior to mri_glmfit or after.
>
> Thanks
> Jonathan
>
>
>
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Re: [Freesurfer] which CUDA version driver to use

[R Edgar]

On 24 August 2016 at 03:57, Карамфил бахчеванов  wrote:
> Compiling is something new for me, but will try it.

Well, install the binaries, and try that first

Richard

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Re: [Freesurfer] version 6 NOT released yet

[pedrogomesrosa]

Many thanks!

Pedro Rosa.

> On Aug 24, 2016, at 13:48, Iglesias, Eugenio  wrote:
> 
> You can! It just makes your results harder to reproduce (running recon-all 
> with one version, and the subfields with the other).
>  
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
> 
> 
>> On 24 Aug 2016, at 17:01, Douglas Greve  wrote:
>> 
>> I don't know. This is a question for Eugenio
>> 
>>> On 8/24/16 11:53 AM, pedrogomesr...@gmail.com wrote:
>>> Hi, Doug.
>>> Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 5.3 
>>> recons, or this also should not be done?
>>> Best,
>>> Pedro Rosa.
>>> 
>>> On Aug 24, 2016, at 11:58, Douglas Greve  wrote:
>>> 
 
 PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN 
 TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT.
 
 Thanks
 
 The FreeSurfer Team
 
 
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 is
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Re: [Freesurfer] version 6 NOT released yet

[Iglesias, Eugenio]

You can! It just makes your results harder to reproduce (running recon-all with 
one version, and the subfields with the other).

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Aug 2016, at 17:01, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I don't know. This is a question for Eugenio

On 8/24/16 11:53 AM, pedrogomesr...@gmail.com 
wrote:
Hi, Doug.
Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 5.3 
recons, or this also should not be done?
Best,
Pedro Rosa.

On Aug 24, 2016, at 11:58, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN
TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT.

Thanks

The FreeSurfer Team


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Re: [Freesurfer] version 6 NOT released yet

[Douglas Greve]

I don't know. This is a question for Eugenio


On 8/24/16 11:53 AM, pedrogomesr...@gmail.com wrote:

Hi, Doug.
Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 
5.3 recons, or this also should not be done?

Best,
Pedro Rosa.

On Aug 24, 2016, at 11:58, Douglas Greve > wrote:




PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN
TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT.

Thanks

The FreeSurfer Team


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Re: [Freesurfer] version 6 NOT released yet

[pedrogomesrosa]

Hi, Doug.
Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 5.3 
recons, or this also should not be done?
Best,
Pedro Rosa.

> On Aug 24, 2016, at 11:58, Douglas Greve  wrote:
> 
> 
> PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN 
> TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT.
> 
> Thanks
> 
> The FreeSurfer Team
> 
> 
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Re: [Freesurfer] Fs 6.0 dev version update

[Z K]

Hello Renata,

As far as I know, the only change between those two versions was a bug 
fix that related to the number of arguments based to the longitudinal 
component of the HippoSF code. If you didnt encounter this error before 
than I dont think anything would change for you.

HOWEVER, I must reiterate that you are using developmental code and that 
this code is possibly updated at any time. We do not advertise it as 
stable or version6. On the same token, I have discussed this issue with 
Eugenio Iglesias (primary developer of Hippocampus Subfields code) and 
he indicates that their is *likely* to be very little if any difference 
between the current dev version and the version in the upcoming v6 release.

Hope this helps.

-Zeke

On 08/24/2016 11:42 AM, Vaz pandolfo, Renata wrote:
> Hi Douglas,
>
> Thank you for the quick response.
> Maybe I didn't explain it well enough, I am downloading it from here:
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>
> I know it is the developmental version, but we are looking at the
> subregions and that's the only way we can.
>
> My question was about the change between the different developmental
> versions 11.08.16 and 14.08.16, I was wondering if whatever had been
> changed between them would affect the Hippocampus Subfields.
>
> Thanks!
>
> Renata
>
> On Wed, Aug 24, 2016 at 5:28 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Renata, version 6 is not ready and should not be used.  As far as
> we know, there is not a link to 6.0 anywhere on our web pages. Where
> did you find it?
>
> doug
>
>
> On 8/24/16 5:48 AM, Vaz pandolfo, Renata wrote:
>> Dear FS experts,
>>
>> I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and
>> now I see that there is a new version since the 14th of August.
>>
>> I ran about 20 recon-alls with the 11.08 version and now I am
>> wondering if there were any major changes between that and the new
>> one, and if so, whether I should rerun anything.
>>
>> I am assuming that having the newest version is always better, but
>> I would rather check if it is necessary before downloading the new
>> one and rerunning all the recon-alls.
>>
>>
>> Thanks!
>>
>> Renata
>>
>> Ps.: I am using the hippocampal subfields flag and checking the
>> volumes of the subregions of the hippocampus.
>>
>>
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Re: [Freesurfer] Fs 6.0 dev version update

[Vaz pandolfo, Renata]

Hi Douglas,

Thank you for the quick response.
Maybe I didn't explain it well enough, I am downloading it from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

I know it is the developmental version, but we are looking at the
subregions and that's the only way we can.

My question was about the change between the different developmental
versions 11.08.16 and 14.08.16, I was wondering if whatever had been
changed between them would affect the Hippocampus Subfields.

Thanks!

Renata

On Wed, Aug 24, 2016 at 5:28 PM, Douglas Greve 
wrote:

> Hi Renata, version 6 is not ready and should not be used.  As far as we
> know, there is not a link to 6.0 anywhere on our web pages. Where did you
> find it?
>
> doug
>
> On 8/24/16 5:48 AM, Vaz pandolfo, Renata wrote:
>
> Dear FS experts,
>
> I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and now I see
> that there is a new version since the 14th of August.
>
> I ran about 20 recon-alls with the 11.08 version and now I am wondering if
> there were any major changes between that and the new one, and if so,
> whether I should rerun anything.
>
> I am assuming that having the newest version is always better, but I would
> rather check if it is necessary before downloading the new one and
> rerunning all the recon-alls.
>
>
> Thanks!
>
> Renata
>
> Ps.: I am using the hippocampal subfields flag and checking the volumes of
> the subregions of the hippocampus.
>
>
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Re: [Freesurfer] Fs 6.0 dev version update

[Douglas Greve]

Hi Renata, version 6 is not ready and should not be used.  As far as we 
know, there is not a link to 6.0 anywhere on our web pages. Where did 
you find it?


doug


On 8/24/16 5:48 AM, Vaz pandolfo, Renata wrote:

Dear FS experts,

I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and now I 
see that there is a new version since the 14th of August.


I ran about 20 recon-alls with the 11.08 version and now I am 
wondering if there were any major changes between that and the new 
one, and if so, whether I should rerun anything.


I am assuming that having the newest version is always better, but I 
would rather check if it is necessary before downloading the new one 
and rerunning all the recon-alls.



Thanks!

Renata

Ps.: I am using the hippocampal subfields flag and checking the 
volumes of the subregions of the hippocampus.



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[Freesurfer] ROI-based laminar BOLD analysis

[James Wilks]

Dear FreeSurfer team,
My name is Alex Wilks, an undergrad in the fMRI lab at the University of 
Michigan. We are trying to learn the ropes of FreeSurfer so that we may be able 
to perform high resolution fMRI analysis across multiple cortical layers. 

So far, I have understood how to generate intermediate layers between the pial 
and white surfaces of the cortex, however, I’ve hit a roadblock in performing 
ROI analysis on specific regions of the brain to analyze the amplitude of the 
BOLD signal across the layers. I was going through your published article 
titled “Laminar analysis of 7 T BOLD using an imposed spatial activation 
pattern in human V1” and I believe that the steps you used to collect the data 
in the “ROI analysis” subsection of your article are what we would like to 
repeat. Could you walk me through the steps you took to study the BOLD response 
as a function of cortical depth?

Respectfully,
Alex Wilks
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Re: [Freesurfer] dmri_poistats

[Anastasia Yendiki]

Hi Mohamad - This tool hasn't been worked on for over a decade, and there 
is nobody here who can support it. There are tools out there that do 
tractography without anatomical priors (in fact that's approximately all 
the tools out there), but none in freesurfer at the moment.


Best,
a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:


Hi Anastasia,
This tool is available in (FS 5.3 and FS v6.0) as version 1.0 Beta. But in the 
paper that I have pointed to, the folks used the version 1.4 of this tool. 
That's why I am a bit confused.

Kindly, are there any tools that can help to do tractography for the 
corticospinal tract  when T1 images are not available?


Thank you for any advice
Mohamad



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Wednesday, August 24, 2016 10:36 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] dmri_poistats


Hi Mohamad - This tool is *way* deprecated. It should not have been included in 
beta releases. Thanks for bringing this to our attention.

a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:



Dear Freesurfer experts,

I would like to inquire about the tool “dmri_poistats”
https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is 
included as a beta release ( in FS5.3 and FS 6.0).

 

In literature review I found colleagues used the version 1.4  of this
tool. e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/

 

Kindly, I have the following two questions:

1.   What is the final release of this tool?

2.   I have DWI images and no T1 images are available. Is it reliable to do 
tractography for the corticospinal tract using this tool?

 

Thank you for any advice!

Mohamad

 





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[Freesurfer] version 6 NOT released yet

[Douglas Greve]

PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN 
TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT.

Thanks

The FreeSurfer Team


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Re: [Freesurfer] dmri_poistats

[Alshikho, Mohamad J.]

Hi Anastasia,
This tool is available in (FS 5.3 and FS v6.0) as version 1.0 Beta. But in the 
paper that I have pointed to, the folks used the version 1.4 of this tool. 
That's why I am a bit confused.

Kindly, are there any tools that can help to do tractography for the 
corticospinal tract  when T1 images are not available?


Thank you for any advice
Mohamad



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Wednesday, August 24, 2016 10:36 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] dmri_poistats


Hi Mohamad - This tool is *way* deprecated. It should not have been included in 
beta releases. Thanks for bringing this to our attention.

a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:

> 
> Dear Freesurfer experts,
> 
> I would like to inquire about the tool “dmri_poistats” 
> https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is 
> included as a beta release ( in FS5.3 and FS 6.0).
> 
>  
> 
> In literature review I found colleagues used the version 1.4  of this 
> tool. e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/
> 
>  
> 
> Kindly, I have the following two questions:
> 
> 1.   What is the final release of this tool?
> 
> 2.   I have DWI images and no T1 images are available. Is it reliable to 
> do tractography for the corticospinal tract using this tool?
> 
>  
> 
> Thank you for any advice!
> 
> Mohamad
> 
>  
> 
> 
>

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Re: [Freesurfer] dmri_poistats

[Anastasia Yendiki]

Hi Mohamad - This tool is *way* deprecated. It should not have been 
included in beta releases. Thanks for bringing this to our attention.


a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:



Dear Freesurfer experts,

I would like to inquire about the tool “dmri_poistats” 
https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is 
included
as a beta release ( in FS5.3 and FS 6.0).

 

In literature review I found colleagues used the version 1.4  of this tool. 
e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/

 

Kindly, I have the following two questions:

1.   What is the final release of this tool?

2.   I have DWI images and no T1 images are available. Is it reliable to do 
tractography for the corticospinal tract using this tool?

 

Thank you for any advice!

Mohamad

 


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[Freesurfer] FW: Correcting for both hemispheres in thickness analysis using a PFC mask

[Gold, Andrea (NIH/NIMH) [F]]

Hi,

I have a question about correcting for 2 hemispheres in a thickness
analysis using a PFC mask. Here are the steps I ran:

1) I ran the analysis in qdec without a mask.

2) I found the mri_glmfit.log file from step 1 and cut out the  mri_glmfit
command that runs the analysis and
 replaced ³label² option with path to our mask:
cmdline mri_glmfit --y
/gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
_anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/y.mgh --fsgd
/gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
_anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/qdec.fsgd
 dods --glmdir 
/gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
_anxious/qdec/Thickness_LH_sm10_Dichtomous_n151 --surf fsaverage lh
--label 
/gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/lab
el/labels/PFC_mask_8ROIs_LH --C
/gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
_anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Avg-Intercept-
thickness.mat --C 
/gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs
_anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Diff-anxiousyo
uth-healthyyouth-Intercept-thickness.mat


3) I then ran mri_glmfit-sim:
 mri_glmfit-sim  --glmdir ./Thickness_LH_sm10_Dichtomous_n151 --sim mc-z
1 1.3 mc-z.1p3.abs --sim-sign abs

Question: I am 99% the mri_glmfit-sim command does not correct for both
hemispheres.
Is it possible to figure out if the cluster survives correction for 2
hemis based on the cluster summary file (attached) from steps 1-3 above?:
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP
CWPLowCWPHi   NVtxs   Annot
   12.480  124922479.68 -7.2   29.0  -16.8  0.00440
0.00360  0.00530   887  medialorbitofrontal

Thanks!
Andrea

-- 
Andrea Gold, Ph.D.

Section on Development and Affective Neuroscience
National Institute of Mental Health
Room 201, Bldg. 15K, MSC 2670
Bethesda, MD 20892-2670
Phone: 301-827-9804
Fax: 301-402-2010

Email: andrea.g...@nih.gov








mc-z.1p3.abs.sig.cluster.summary
Description: mc-z.1p3.abs.sig.cluster.summary
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[Freesurfer] output description

[Vaz pandolfo, Renata]

Dear FS experts,

Is there a complete list of all output files followed by their description?
The one I can find online seems to be incomplete (and/or out of date):

https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles#A-allOutputFiles

For example, the volumes brain.mgz and brainmask.mgz.If I would like to
quickly check what the difference between them is, where should I look?

Thank you!

Renata
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[Freesurfer] Fs 6.0 dev version update

[Vaz pandolfo, Renata]

Dear FS experts,

I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and now I see
that there is a new version since the 14th of August.

I ran about 20 recon-alls with the 11.08 version and now I am wondering if
there were any major changes between that and the new one, and if so,
whether I should rerun anything.

I am assuming that having the newest version is always better, but I would
rather check if it is necessary before downloading the new one and
rerunning all the recon-alls.


Thanks!

Renata

Ps.: I am using the hippocampal subfields flag and checking the volumes of
the subregions of the hippocampus.
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Re: [Freesurfer] which CUDA version driver to use

[Карамфил бахчеванов]

Compiling is something new for me, but will try it.

-Original Message-
From: "R Edgar" 
Sent: ‎16.‎8.‎2016 ‎г. 21:25
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] which CUDA version driver to use

On 15 August 2016 at 19:21, Karamfil Bahchevanov  wrote:

> I'd like to experiment with faster proceesing, in fact I'd like to try CUDA.
> However there are several possible drivers for my quadro K2000. I'm not sure
> which one to choose. Should I install the latest 7.5. version, or use the
> older version 6, or even older? I'm not sure if the latest will run with
> freesurfer smoothly.
> Here is my system: Xeon e5-1620, QUADRO K2000
> I'm running Freesurfer v5.3 on CentOS 6.8, kernel 2.6.32-642.1.1.el6.x86_64.

I've had success getting Freesurfer to compile with the CUDA 7.5
toolkit. You just have to make sure that the configure script is
really picking up your CUDA installation.

Regards,

Richard
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