[Freesurfer] Freesurfer from source library dependencies dead link

[King, Maximilian]

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Hi Freesurfer folks!

I am attempting to build freesurfer from source for our HPC center here at
Brown University, but are running into a snag. Looks like the documentation
points to a dead link for Step 3 of the freesurfer_linux_developers_page

where
we are required to get the prebuilt bundle of 3rd party dependancies using:

wget 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz


However, the command fails as the directory does not exist.

$ wget
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz

--2018-12-21 11:07:49--
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz

   => ‘centos6-x86_64-packages.tar.gz’

Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)...
132.183.240.105

Connecting to surfer.nmr.mgh.harvard.edu
(surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...
connected.

Logging in as anonymous ... Logged in!

==> SYST ... done.==> PWD ... done.

==> TYPE I ... done.  ==> CWD (1)
/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64 ...

No such directory ‘pub/dist/fs_supportlibs/prebuilt/centos6_x86_64’.

Any chance I could get the updated path for these dependencies? Happy
holidays!

Cheers,
Max

-- 


*Maximilian King, MSc*
HPC Application Scientist
Center for Computation and Visualization

Brown University Computing and Information Systems
180 George St, Providence, RI 02906, USA
Tel: +1 (401) 863-7448
*maximilian_k...@brown.edu* 
*http://ccv.brown.edu* 
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[Freesurfer] mris_fwhm problem

[shahin]

Dear Surfers,
   I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel
size 1 mm iso)using the below command:

mris_fwhm --s --hemi rh --smooth-only --i
fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o
fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask
/masks/brain.self.rh.nii.gz

When I apply this command, it works without any error. The message on
screen is as below:

 rh white
Number of vertices 160391
Number of faces320778
Total area 102725.085938
GroupSurface 0
AvgVtxArea   0.640467
AvgVtxDist   0.875515
StdVtxDist   0.253406
Loading mask masks/brain.self.rh.nii.gz
Found 36045 voxels in mask
Not Polynomial detrending
Smoothing input by fwhm=0.66, gstd=0.280276, niters=0
Only smoothing, so saving and exiting now

   But the outcome is the same as input. I think it is expected based on
(niters=0).  When I use the same command with fwhm =1, then i see the
difference and niters=1.

My question is, why is fwhm = 0.66 not acceptable? How can i solve this
issue.

Regards

_

Shahin Nasr

Assistant Prof. in Radiology
Harvard Medical School
Martinos Imaging Center, MGH
Bldg 149, 13th street,
Charlestown, MA 02129

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[Freesurfer] Postdoctoral position at UCL

[Arman Eshaghi]

External Email - Use Caution

Apologies for the cross-posting and wide distribution.

Postdoc advertisement
==

The NMR Research Unit is  a multidisciplinary research team focusing on
multiple sclerosis (MS).   A Research Fellow is sought to work primarily on
the development and optimisation of a high-dimensional model to predict
individual treatment responses in MS, as part of an NIHR Research
Professorship awarded to Professor Olga Ciccarelli.  This is a
collaborative project with Dr Parashkev Nachev's team, who are working on
the creation of individually predictive models of clinical outcome from
high-dimensional analysis of large-scale clinical datasets

The project aims to create a prototype software that predicts whether an
individual patient with MS will respond to  a medication by using machine
learning techniques (a crucial step towards "personalized medicine").  All
the elements constituting an individual MS profile will be collected
prospectively in a large-scale registry.  The post holder will be
responsible for organising the project database on XNAT, developing
probabilistic, high-dimensional models that can achieve high individual
predictive value, assisting with the day-to-day running of the project, and
co-ordinating public and patient engagement (PPE) and involvment (PPI)
activities.

The post is available immediately and is funded by a grant from the NIHR
for three years in the first instance.

Apply here:

https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTc4NDY5OSZ2dF90ZW1wbGF0ZT05NjUmb3duZXI9NTA0MTE3OCZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJmpvYl9yZWZfY29kZT0xNzg0Njk5JnBvc3RpbmdfY29kZT0yMjQ


You can get in touch with me (a.esha...@ucl.ac.uk) for more information.

Best wishes,
Arman Eshaghi, MD, PhD
Research Associate
Queen Square Multiple Sclerosis Center
Queen Square UCL Institute of Neurology
University College London
United Kingdom
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Re: [Freesurfer] surfreg cannot allocate memory

[Hoopes, Andrew]

That’s odd – seems like somehow the file got corrupted. I suggest just 
regenerating the brain.mgz by running:

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

from your subject’s mri directory. That should fix things.

best
Andrew


From:  on behalf of Haoran Xu 

Reply-To: FS Help 
Date: Thursday, December 20, 2018 at 5:47 PM
To: FS Help 
Subject: Re: [Freesurfer] surfreg cannot allocate memory


External Email - Use Caution
WOW I cannot. Freeview showed “failed to load MRI .../mri/brain.mgz”. I had 
permission to read and write though...
Haoran

On Dec 20, 2018, at 3:50 PM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Haoran, are you able to load the subject’s mri/brain.mgz in freeview without 
getting this error?
Andrew


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Haoran Xu mailto:haora...@gmail.com>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, December 20, 2018 at 2:33 PM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surfreg cannot allocate memory


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Thank you Andrew!
The log is copied here below.
Haoran

$ surfreg --s subj001 --t fsaverage_sym --lh --xhemi
Thu Dec 20 13:01:31 EST 2018

setenv SUBJECTS_DIR /home/haoran/FP/data/NBMLdata/anatomicals/
cd /home/haoran/FP/data/NBMLdata/anatomicals/subj001
/usr/local/freesurfer/bin/surfreg --s subj001 --t fsaverage_sym --lh --xhemi

Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 
2018 x86_64 x86_64 x86_64 GNU/Linux
xhemi does not exist for subj001, running now
xhemireg --s subj001
outdir is /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi
Logfile is 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/xhemireg.lh.log
/usr/local/freesurfer/bin/xhemireg
--s subj001
$Id: xhemireg,v 1.26.2.1 2016/08/02 21:16:35 greve Exp $
Thu Dec 20 13:01:31 EST 2018
Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 
2018 x86_64 x86_64 x86_64 GNU/Linux
/home/haoran/FP/data/NBMLdata/anatomicals/subj001
setenv SUBJECTS_DIR /home/haoran/FP/data/NBMLdata/anatomicals/
Thu Dec 20 13:01:31 EST 2018
Thu Dec 20 13:01:31 EST 2018
vol orig --
mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat --o 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/orig.mgz 
--keep-precision --no-save-reg

Matrix from regfile:
-1.0   0.0   0.0   1.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

movvol mri/orig.mgz
targvol mri/orig.mgz
outvol /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/orig.mgz
regfile 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth  0
SynthSeed  1546000118

Final tkRAS-to-tkRAS Matrix is:
-1.0   0.0   0.0   1.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;


Vox2Vox Matrix is:
-1.0   0.0   0.0   255.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Resampling
Output registration matrix is identity

mri_vol2vol done
vol T1 --
mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat --o 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/T1.mgz 
--keep-precision --no-save-reg

Matrix from regfile:
-1.0   0.0   0.0   1.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

movvol mri/T1.mgz
targvol mri/T1.mgz
outvol /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/T1.mgz
regfile 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth  0
SynthSeed  1545834350

Final tkRAS-to-tkRAS Matrix is:
-1.0   0.0   0.0   1.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;


Vox2Vox Matrix is:
-1.0   0.0   0.0   255.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Resampling
Output registration matrix is identity

mri_vol2vol done
vol brain --
mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat --o 
/home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/brain.mgz 
--keep-precision --no-save-reg

Matrix from regfile:

Re: [Freesurfer] mris_fwhm problem

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

The smoothing works through iterative nearest neighbor smoothing, so the 
fwhm is essentially discretized because you can't have fractions of an 
iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 
iteration, so it chooses 0.

On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu wrote:
> Dear Surfers,
> I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel
> size 1 mm iso)using the below command:
>
> mris_fwhm --s --hemi rh --smooth-only --i
> fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o
> fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask
> /masks/brain.self.rh.nii.gz
>
> When I apply this command, it works without any error. The message on
> screen is as below:
>
>  rh white
> Number of vertices 160391
> Number of faces320778
> Total area 102725.085938
> GroupSurface 0
> AvgVtxArea   0.640467
> AvgVtxDist   0.875515
> StdVtxDist   0.253406
> Loading mask masks/brain.self.rh.nii.gz
> Found 36045 voxels in mask
> Not Polynomial detrending
> Smoothing input by fwhm=0.66, gstd=0.280276, niters=0
> Only smoothing, so saving and exiting now
>
> But the outcome is the same as input. I think it is expected based on
> (niters=0).  When I use the same command with fwhm =1, then i see the
> difference and niters=1.
>
> My question is, why is fwhm = 0.66 not acceptable? How can i solve this
> issue.
>
> Regards
>
> _
>
> Shahin Nasr
>
> Assistant Prof. in Radiology
> Harvard Medical School
> Martinos Imaging Center, MGH
> Bldg 149, 13th street,
> Charlestown, MA 02129
>
> ___
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Re: [Freesurfer] mris_fwhm problem

[shahin]

So, is there anyway around this issue?


>
> The smoothing works through iterative nearest neighbor smoothing, so the
> fwhm is essentially discretized because you can't have fractions of an
> iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1
> iteration, so it chooses 0.
>
> On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu wrote:
>> Dear Surfers,
>> I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data
>> (voxel
>> size 1 mm iso)using the below command:
>>
>> mris_fwhm --s --hemi rh --smooth-only --i
>> fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o
>> fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask
>> /masks/brain.self.rh.nii.gz
>>
>> When I apply this command, it works without any error. The message on
>> screen is as below:
>>
>>  rh white
>> Number of vertices 160391
>> Number of faces320778
>> Total area 102725.085938
>> GroupSurface 0
>> AvgVtxArea   0.640467
>> AvgVtxDist   0.875515
>> StdVtxDist   0.253406
>> Loading mask masks/brain.self.rh.nii.gz
>> Found 36045 voxels in mask
>> Not Polynomial detrending
>> Smoothing input by fwhm=0.66, gstd=0.280276, niters=0
>> Only smoothing, so saving and exiting now
>>
>> But the outcome is the same as input. I think it is expected based
>> on
>> (niters=0).  When I use the same command with fwhm =1, then i see the
>> difference and niters=1.
>>
>> My question is, why is fwhm = 0.66 not acceptable? How can i solve this
>> issue.
>>
>> Regards
>>
>> _
>>
>> Shahin Nasr
>>
>> Assistant Prof. in Radiology
>> Harvard Medical School
>> Martinos Imaging Center, MGH
>> Bldg 149, 13th street,
>> Charlestown, MA 02129
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
>
>


_

Shahin Nasr

Assistant Prof. in Radiology
Harvard Medical School
Martinos Imaging Center, MGH
Bldg 149, 13th street,
Charlestown, MA 02129

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Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047

[Bruce Fischl]

did you try to load it as a surface? If you want to upload the entire 
subject dir (tarred and gzipped) to our ftp site we will take a look. In 
the meantime you can also just post an image of the volume in 3 planes, 
that might help


cheers
Bruce
On Fri, 21 Dec 2018, 허정선 wrote:

   External Email - Use Caution 


Thank you for your reply.

Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. 
And, there was a problem like the photo below, and only the recon-all.log could be attached to you. 



Thanks,
Jeongson 
--


Message: 1
Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST)
From: Bruce Fischl 
Subject: Re: [Freesurfer] recon-all error : Too many intersected faces
   for face 120047 (60827, 60826, 59444)
To: Freesurfer support list 
Message-ID:
   
Content-Type: text/plain; charset="utf-8"

Hi Jeongson

it certainly looks like something went badly wrong. 2mm may be too thick
- we typically recommend <=1.5mm for any voxel direction. Can you send us
the recon-all.log? And maybe a snapshot of the volume with the
lh.orig.nofix and rh.orig.nofix overlaid?

cheers
Bruce


On Thu, 20 Dec
2018, ??? wrote:


   External Email - Use Caution

Hello Freesurfer developers
I'm starting using FS and I have a problem running recon-all.
#recon-all -s /usr/local/freesurfer/subjects/20180108 -all
I've attached the output to a ERROR image file.

We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice 
thickness of 2.0mm.
freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118

Any help is greatly appreciated.

Thanks.

Jeongson


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Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

[Bruce Fischl]

Hi Lindsay

it might be easiest to do what you want in matlab. We do supply m-files 
for i/o of our various formats

cheers
Bruce
On Thu, 20 Dec 2018, lindsay hanford wrote:



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Hello Freesurfer Community, 
I am wondering if it is possible to recalculate cortical thickness metrics 
(perhaps using
mri_segstats or aparcstats2table) while including either a SD threshold or an 
exclusion mask. 

Using mri_surf2surf to register scans to the same space and then 
mri_surface_stats to create the std
maps I have been comparing the variability of cortical thickness across the 
cortex for multiple
scans across the same subject. From this I can determine a SD threshold point 
(0.5 say) or create a
mask that includes all regions above that threshold. 

I would like to use this to threshold the regions showing the highest 
variability out of my
calculations for mean hemispheric thickness and also regional thickness. 
Is there a way to use an SD threshold within mri_segstats or aparcstats2table? 
Otherwise apply a
mask image to exclude specific vertices? 

Thank you in advance,

Lindsay




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Re: [Freesurfer] mris_fwhm problem

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

No, not in the current framework. Even if there were, fwhm=.66 would not 
give you much smoothing. The intervertex distance is about 1mm, at 
fwhm=.66mm, the nearest vertex would be about 3 standard deviations 
away, meaning that the smoothing would be minimal.

On 12/21/18 12:12 PM, sha...@nmr.mgh.harvard.edu wrote:
> So, is there anyway around this issue?
>
>
>> The smoothing works through iterative nearest neighbor smoothing, so the
>> fwhm is essentially discretized because you can't have fractions of an
>> iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1
>> iteration, so it chooses 0.
>>
>> On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu wrote:
>>> Dear Surfers,
>>>  I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data
>>> (voxel
>>> size 1 mm iso)using the below command:
>>>
>>> mris_fwhm --s --hemi rh --smooth-only --i
>>> fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o
>>> fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask
>>> /masks/brain.self.rh.nii.gz
>>>
>>> When I apply this command, it works without any error. The message on
>>> screen is as below:
>>>
>>>  rh white
>>> Number of vertices 160391
>>> Number of faces320778
>>> Total area 102725.085938
>>> GroupSurface 0
>>> AvgVtxArea   0.640467
>>> AvgVtxDist   0.875515
>>> StdVtxDist   0.253406
>>> Loading mask masks/brain.self.rh.nii.gz
>>> Found 36045 voxels in mask
>>> Not Polynomial detrending
>>> Smoothing input by fwhm=0.66, gstd=0.280276, niters=0
>>> Only smoothing, so saving and exiting now
>>>
>>>  But the outcome is the same as input. I think it is expected based
>>> on
>>> (niters=0).  When I use the same command with fwhm =1, then i see the
>>> difference and niters=1.
>>>
>>> My question is, why is fwhm = 0.66 not acceptable? How can i solve this
>>> issue.
>>>
>>> Regards
>>>
>>> _
>>>
>>> Shahin Nasr
>>>
>>> Assistant Prof. in Radiology
>>> Harvard Medical School
>>> Martinos Imaging Center, MGH
>>> Bldg 149, 13th street,
>>> Charlestown, MA 02129
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> _
>
> Shahin Nasr
>
> Assistant Prof. in Radiology
> Harvard Medical School
> Martinos Imaging Center, MGH
> Bldg 149, 13th street,
> Charlestown, MA 02129
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Error while saving NPC results

[Daniel Leopold]

External Email - Use Caution

Dear Drs. Winkler, Greve, Fischl, et al.

Could you help me understand which palm options are needed in order to
produce tfce and clustere NPC results that are fwe-corrected across
contrasts (i.e., _cfwep_)?

I'm analyzing area and thickness and have four one-tailed contrasts of
interest (e.g., C1+, C1-, C2+, C2-). Currently, I am only able to get the
"output'_dpv_npc_fisher_cfwep_c[1234]" results, but the palm log ends
abruptly after saving these files and does not save the _tfce_ or
_clustere_ versions:

Saving p-values for NPC between modalities (uncorrected and corrected
within contrasts).

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c1

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c1

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c1

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c1

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c1

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c2

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c2

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c2

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c2

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c2

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c3

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c3

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c3

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c3

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c3

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c4

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c4

 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c4

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c4

 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c4

Saving p-values for NPC between modalities (corrected across contrasts).

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c1

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c2

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c3

 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c4

>>


The error log contains the following text, and my efforts to read through
these source files have been in vain:
{^HCell contents reference from a non-cell array object.

 Error in palm_saveall (line 1043)
distmax(:,j) = plm.Tclumax{m}{c};

Error in palm_core (line 2489)
palm_saveall(plm,opts);

Error in palm (line 81)
palm_core(varargin{:});
}^H
^G

I have essentially permuted the various -corr(con/mod) and -npc(con/mod)
options, as well as various combinations of -T & -C {z}, -Tuni & -Cuni {z},
and -Tnpc & -Cnpc {z}, using a small number of permutations to assess the
number of output maps and whether jobs finish appropriately.

Here's an example of one of the palm commands that resulted in these output
and error logs (with line-breaks for legibility):

fsl_sub -l $logdir palm -designperinput

-i {area_dir}/292_${hemi}.area_stack.mgh

-d {design_dir}/wordadhd_npc_areatotal.mat

-t {design_dir}/wordadhd_npc_areatotal.con

-i {thickness_dir}/292_${hemi}.thickness_stack.mgh

-d {design_dir}/wordadhd_npc_thickmean.mat

-t {design_dir}/wordadhd_npc_thickmean.con

-m {base_dir}/palm/input/${hemi}mask.mgz

-s ${surf_dir}/${hemi}.white ${surf_dir}/${hemi}.white.avg.area.mgh

-o wordadhd_npc_${hemi}

-eb ${EB} -corrcon -corrmod

 -logp -ise -npc -T -C 1.64485 -n 5

If knowing versions helps at all:
PALM alpha109
MATLAB 8.3.0.532 (R2014a)
FreeSurfer 5.3.0
FSL 5.0.8

Any advice you could provide on this particular error, why my input doesn't
produce the tfce_cfwep or clustere_cfwep results, or other problem-solving
suggestions would be greatly appreciated!


With gratitude,
Dan
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work
only when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> You will need to set --psf 0 and --no-tfe to fully turn off PVC.
>
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Could you help me on this point ?
>
> Best,
> Matthieu
>
>
> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> a écrit :
>
>> Dear Douglas,
>>
>> Is it possible to use mri_gtmpvc command in order to intensity normalize
>> PET images without applying PVE correction by setting --psf to 0 ?
>>
>> Best,
>> Matthieu
>>
>
>
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Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Thanks for these clarifications. I have however one misunderstanding.

When sampling PVC corrected PET image onto surface:
- I use bbpet2anat.lta when MGX was used as specified un tutorial
- I use rbv2anat.lta when RBV was used

But why not to use template.reg.lta computed by mri_coreg ? What are the
differences between those different files ?

Best,
Matthieu

Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

>
>
> On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
> >  External Email - Use Caution
> >
> > Hi Douglas,
> >
> > Thanks for these clarifications. I added some others questions inline
> below.
> >
> > Best,
> > Matthieu
> >
> >> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. 
> a écrit :
> >>
> >>
> >>
> >> 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.
> > Yes, thresholding at 0.01 and 0.1 gave me different values in the same
> voxel in both images. Whereas when thresholding between 0.1 and 0.3 gave me
> same values. What could it be due to ?
> I don't know. Are the differences widespread or just a voxel near the edge?
> >
> > GTM is always computed in the *.stat file whatever the method specified
> in mri_gtmpvc command ?
> Yes, the GTM is the basis for all the methods.
> >
> > If threshold is not critical for cortical surface, how to determine the
> best threshold for subcortical analysis ? Is it better to have more in the
> final mask ?
> In general, I don't think it is c

Re: [Freesurfer] Robust PET signal projection

[Matthieu Vanhoutte]

External Email - Use Caution

Thanks Douglas.

Is there a way to compute a weighted average in one command with fscalc ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 18:03, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> you can use mri_vol2surf to sample at different depths. If you want a
> simple average across cortex, then you can use --projfrac-avg .35 .65 .05
> If you want to do more sophisticated weighting, then you will have to
> sample at each layer and then combine the files (eg, fscalc). Unless you
> have very small voxels, it probably will not make a difference.
>
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Dear experts,
>
> Is there any advice on this point ?
>
> Best,
> Matthieu
>
>
> Le mer. 12 déc. 2018 à 10:47, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> a écrit :
>
>> Dear Freesurfer's experts,
>>
>> In order to have a robust PET signal projection, is it possible compute
>> the projected PET signal as a weighted average of the PET signal
>> intersecting with the surfaces ranging from 35 to 65% of the cortical
>> tickness with a step t=5% ?
>>
>> More weight would be given to the surfaces located near the mid distance
>> between the pial and white surfaces as they have a higher probability to be
>> well located within the cortex (using a normal distribution for example).
>>
>> Thank you for helping.
>>
>> Best,
>> Matthieu
>>
>
>
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