[Freesurfer] repost: more on comparing runs on the same scan

[Krieger, Donald N.]

Hi everyone,

I'm reposting this from 2 days ago.
Please excuse if someone responded and I missed it.

We have been able to establish that we are getting identical results when 
running recon-all -all on the same scan on different machine for the following:
All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing 
using mri_diff ...
All of the .label and .annot files in directory label with md5sum ...
Many of the files in directory surf with mris_diff.

We continue to see differences in the label/BA*.annot files and in about 20 of 
the files in surf including [lr]h.inflated|orig|pial .
We do see identity for lh.area.pial but not for lh.pial for instance.
I've attached the output of our test routine.

Your thoughts would be welcome on this pesky question.

Best - Don

MRN_1_comet_diamond =?= MRN_1_mwt2_2_diamond ...
... directory mri ...
aparc.a2009s+aseg.mgz ok
aparc+aseg.mgz ok
aseg.auto.mgz ok
aseg.auto_noCCseg.mgz ok
aseg.mgz ok
brain.finalsurfs.mgz ok
brainmask.auto.mgz ok
brainmask.mgz ok
brain.mgz ok
ctrl_pts.mgz ok
filled.mgz ok
lh.ribbon.mgz ok
norm.mgz ok
nu.mgz ok
nu_noneck.mgz ok
orig.mgz ok
orig_nu.mgz ok
rawavg.mgz ok
rh.ribbon.mgz ok
ribbon.mgz ok
T1.mgz ok
wm.asegedit.mgz ok
wm.mgz ok
wmparc.mgz ok
wm.seg.mgz ok
... directory mri/orig ...
001.mgz ok
... directory mri/transforms ...
talairach.m3z.inv.x.mgz ok
talairach.m3z.inv.y.mgz ok
talairach.m3z.inv.z.mgz ok
... directory surf ...
lh.area ok
lh.area.mid ok
lh.area.pial ok
lh.avg_curv ok
lh.curv ok
lh.curv.pial ok
lh.defect_borders ok
lh.defect_chull ok
lh.defect_labels ok
lh.inflated Surfaces are not the same
lh.inflated.H ok
lh.inflated.K ok
lh.inflated.nofix Surfaces are not the same
lh.jacobian_white ok
lh.orig Surfaces are not the same
lh.orig.nofix Surfaces are not the same
lh.pial Surfaces are not the same
lh.qsphere.nofix Surfaces are not the same
lh.smoothwm Surfaces are not the same
lh.smoothwm.BE.crv ok
lh.smoothwm.C.crv ok
lh.smoothwm.FI.crv ok
lh.smoothwm.H.crv ok
lh.smoothwm.K1.crv ok
lh.smoothwm.K2.crv ok
lh.smoothwm.K.crv ok
lh.smoothwm.nofix Surfaces are not the same
lh.smoothwm.S.crv ok
lh.sphere Surfaces are not the same
lh.sphere.reg Surfaces are not the same
lh.sulc ok
lh.thickness ok
lh.volume ok
lh.w-g.pct.mgh ok
lh.white Surfaces are not the same
rh.area ok
rh.area.mid ok
rh.area.pial ok
rh.avg_curv ok
rh.curv ok
rh.curv.pial ok
rh.defect_borders ok
rh.defect_chull ok
rh.defect_labels ok
rh.inflated Surfaces are not the same
rh.inflated.H ok
rh.inflated.K ok
rh.inflated.nofix Surfaces are not the same
rh.jacobian_white ok
rh.orig Surfaces are not the same
rh.orig.nofix Surfaces are not the same
rh.pial Surfaces are not the same
rh.qsphere.nofix Surfaces are not the same
rh.smoothwm Surfaces are not the same
rh.smoothwm.BE.crv ok
rh.smoothwm.C.crv ok
rh.smoothwm.FI.crv ok
rh.smoothwm.H.crv ok
rh.smoothwm.K1.crv ok
rh.smoothwm.K2.crv ok
rh.smoothwm.K.crv ok
rh.smoothwm.nofix Surfaces are not the same
rh.smoothwm.S.crv ok
rh.sphere Surfaces are not the same
rh.sphere.reg Surfaces are not the same
rh.sulc ok
rh.thickness ok
rh.volume ok
rh.w-g.pct.mgh ok
rh.white Surfaces are not the same
label files ok
... directory label/*.annot ...
lh.aparc.a2009s.annot ok
lh.aparc.annot ok
lh.aparc.DKTatlas40.annot ok
lh.BA.annot not ok ... 29d66ea8614488a56cb74e5cc5fe9470 != 
bc9507b6e0c7051b7e89554beb5d875f
lh.BA.thresh.annot not ok ... 3b51e59d298014da180ee266d29805b8 != 
576a09cfa118ed245b4103ca7f5f6753
rh.aparc.a2009s.annot ok
rh.aparc.annot ok
rh.aparc.DKTatlas40.annot ok
rh.BA.annot not ok ... 7b1b4e8ea47f9fa366d8bff5079fe0c1 != 
a062a4b0494d64ac958894621161499d
rh.BA.thresh.annot not ok ... af3a74b7f59a9924857d65678ca57fde != 
7de02e148e7000f51ca9ef0d7816e834
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Re: [Freesurfer] -qcache of v5.0 data with newer versions

[Douglas N Greve]

Yes, but use one or the other but not both

On 02/17/2016 08:47 AM, Daniel Ferreira wrote:
> Dear experts,
>
> Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been 
> recon-all -all with FS 5.0.0?
>
> Thanks
>
> Dani
>
>
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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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear Zeke,

Great, thanks for the clarification!
All the best,
Barbara

On 17/02/2016 16:53, Z K wrote:
> hello Barbara,
>
> A freesurfer v6.0-beta was released some months ago. But after various
> rounds of QA testing it was decided that additional significant
> development was required. So the beta version was withdrawn and active
> development remains ongoing in the dev version. You can download the
> latest dev version using the following link:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> Anyone claiming to use "version 6.0" is using the 6.0-beta version
> released several months ago, which has been significantly modified since
> its beta release.
>
> -Zeke
>
> On 02/17/2016 11:45 AM, Barbara Kreilkamp wrote:
>> Dear all,
>>
>> Sorry to bother you again. I am a bit confused as others seem to use a
>> 'version 6.0' but I cannot find reference inthe nightly development (
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev ) of it being
>> called a version 6.0.
>>
>> Am I missing something?
>> I don't know where I got this link from
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/
>> but it does not seem to point anywhere anymore.
>>
>> Thank you very much,
>> Barbara
>>
>>
>>
>>
>> On 17/02/2016 14:30, Barbara Kreilkamp wrote:
>>> Dear Douglas,
>>>
>>> Thanks a lot, I found the version.
>>> Best wishes,
>>> Barbara
>>>
>>> On 16/02/2016 20:44, Douglas N Greve wrote:
 We don't have a v6 ready. You can get a development version, you just
 have to keep in mind that it is a snapshot and that the software will
 change without notice.

 On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
> Dear Freesurfer experts,
>
> How may I get Freesurfer v 6 ?
>
> Thank you very much,
> Best wishes,
> Barbara
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>
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>>
>>
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> at
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Re: [Freesurfer] Freesurfer version 6.0

[Z K]

hello Barbara,

A freesurfer v6.0-beta was released some months ago. But after various 
rounds of QA testing it was decided that additional significant 
development was required. So the beta version was withdrawn and active 
development remains ongoing in the dev version. You can download the 
latest dev version using the following link:

   https://surfer.nmr.mgh.harvard.edu/fswiki/Download

Anyone claiming to use "version 6.0" is using the 6.0-beta version 
released several months ago, which has been significantly modified since 
its beta release.

-Zeke

On 02/17/2016 11:45 AM, Barbara Kreilkamp wrote:
> Dear all,
>
> Sorry to bother you again. I am a bit confused as others seem to use a
> 'version 6.0' but I cannot find reference inthe nightly development (
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev ) of it being
> called a version 6.0.
>
> Am I missing something?
> I don't know where I got this link from
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/
> but it does not seem to point anywhere anymore.
>
> Thank you very much,
> Barbara
>
>
>
>
> On 17/02/2016 14:30, Barbara Kreilkamp wrote:
>> Dear Douglas,
>>
>> Thanks a lot, I found the version.
>> Best wishes,
>> Barbara
>>
>> On 16/02/2016 20:44, Douglas N Greve wrote:
>>> We don't have a v6 ready. You can get a development version, you just
>>> have to keep in mind that it is a snapshot and that the software will
>>> change without notice.
>>>
>>> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
 Dear Freesurfer experts,

 How may I get Freesurfer v 6 ?

 Thank you very much,
 Best wishes,
 Barbara
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>
>
> ___
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>
>
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Re: [Freesurfer] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear all,

Sorry to bother you again. I am a bit confused as others seem to use a 
'version 6.0' but I cannot find reference inthe nightly development ( 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev ) of it being 
called a version 6.0.

Am I missing something?
I don't know where I got this link from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/
but it does not seem to point anywhere anymore.

Thank you very much,
Barbara




On 17/02/2016 14:30, Barbara Kreilkamp wrote:
> Dear Douglas,
>
> Thanks a lot, I found the version.
> Best wishes,
> Barbara
>
> On 16/02/2016 20:44, Douglas N Greve wrote:
>> We don't have a v6 ready. You can get a development version, you just
>> have to keep in mind that it is a snapshot and that the software will
>> change without notice.
>>
>> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
>>> Dear Freesurfer experts,
>>>
>>> How may I get Freesurfer v 6 ?
>>>
>>> Thank you very much,
>>> Best wishes,
>>> Barbara
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>

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Re: [Freesurfer] Hippocampal subfield segmentation in FS 6.0

[Eugenio Iglesias]

Hi Sarah, 
It's perfectly fine. Ideally, one would process everything with the same 
version so results are more easily reproducible but, since there's no FS 6.0 
available yet, this is probably your best option for now, actually. 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Sarah Lancaster"  
To: "Freesurfer support list"  
Sent: Wednesday, February 17, 2016 3:39:16 PM 
Subject: [Freesurfer] Hippocampal subfield segmentation in FS 6.0 

Hi all, 

We are running hippocampal subfield segmentations on about 300 subjects. We 
initially ran recon-all using FreeSurfer 5.3, but we used the new FreeSurfer 
6.0 method for the hippocampal subfields. Will this cause problems in our 
analysis? Should we run them through recon-all again with 6.0? 

Thanks, 
Sarah 

Sarah Lancaster 
Research Assistant 

Duke-UNC Brain Imaging and Analysis Center 
Mental Illness Research, Education and Clinical Center 
Durham VA Medical Center 
sarah.lancas...@dm.duke.edu 
919-286-0411 x7660 

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Re: [Freesurfer] R: Re: v.6.0 Permissions Error

[Z K]

Hello Brendan,

Sorry about that, we created a new atlas and the initial install didnt 
work properly. It should be all set now.

-Zeke

On 02/17/2016 09:44 AM, Grafe,Brendan P. (BIDMC - Neurology) wrote:
> Hello Doug,
>
> I tried rerunning the -base creation step without any luck. It appears
> that this process is reliant on the removed file:
>
> ERROR: cannot find
> /usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca
>
> -Brendan
>
> --
>
> Message: 21
>
> Date: Tue, 16 Feb 2016 16:40:43 -0500
>
> From: Douglas N Greve 
>
> Subject: Re: [Freesurfer] v.6.0 Permissions Error
>
> To: freesurfer@nmr.mgh.harvard.edu
>
> Message-ID: <56c3975b.60...@nmr.mgh.harvard.edu>
>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> ok, try now
>
> On 02/16/2016 04:38 PM, Grafe,Brendan P. (BIDMC - Neurology) wrote:
>
>  >
>
>  > Hello all,
>
>  >
>
>  > I am in the middle of a FreeSurfer v.6.0 longitudinal analysis,
>
>  > running on the Martinos cluster, and I received an error today during
>
>  > the (-base) template creation step regarding a file
>
>  > that the pipeline calls upon:
>
>  >
>
>  > GCAread(/usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca):
>
>  > could not open file
>
>  >
>
>  > I noticed that permissions access to this file are limited at present
>
>  > to the greve group and that the file was last modified earlier today.
>
>  > I’m unfamiliar with this component’s functionality, but am assuming
>
>  > access to it is necessary for template creation. Would this simply be
>
>  > the issue?
>
> -
>
> Brendan P. Grafe MSc
>
> Clinical Research Assistant
>
> Berenson-Allen Center for Noninvasive Brain Stimulation
>
> Beth Israel Deaconess Medical Center
>
> 330 Brookline Avenue
>
> Boston, MA 02215
>
> Tel: 617-667-0256
>
> Fax: 617-975-5322
>
>
> 
>
> This message is intended for the use of the person(s) to whom it may be
> addressed. It may contain information that is privileged, confidential,
> or otherwise protected from disclosure under applicable law. If you are
> not the intended recipient, any dissemination, distribution, copying, or
> use of this information is prohibited. If you have received this message
> in error, please permanently delete it and immediately notify the
> sender. Thank you.
>
>
> ___
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[Freesurfer] R: Re: v.6.0 Permissions Error

[Grafe,Brendan P. (BIDMC - Neurology)]

Hello Doug,

I tried rerunning the -base creation step without any luck. It appears that 
this process is reliant on the removed file:

ERROR: cannot find /usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca

-Brendan
--
Message: 21
Date: Tue, 16 Feb 2016 16:40:43 -0500
From: Douglas N Greve 
Subject: Re: [Freesurfer] v.6.0 Permissions Error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <56c3975b.60...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

ok, try now

On 02/16/2016 04:38 PM, Grafe,Brendan P. (BIDMC - Neurology) wrote:
>
> Hello all,
>
> I am in the middle of a FreeSurfer v.6.0 longitudinal analysis,
> running on the Martinos cluster, and I received an error today during
> the (-base) template creation step regarding a file
> that the pipeline calls upon:
>
> GCAread(/usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca):
> could not open file
>
> I noticed that permissions access to this file are limited at present
> to the greve group and that the file was last modified earlier today.
> I'm unfamiliar with this component's functionality, but am assuming
> access to it is necessary for template creation. Would this simply be
> the issue?

-
Brendan P. Grafe MSc
Clinical Research Assistant
Berenson-Allen Center for Noninvasive Brain Stimulation
Beth Israel Deaconess Medical Center
330 Brookline Avenue
Boston, MA 02215
Tel: 617-667-0256
Fax: 617-975-5322




This message is intended for the use of the person(s) to whom it may be 
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[Freesurfer] Hippocampal subfield segmentation in FS 6.0

[Sarah Lancaster]

Hi all,

We are running hippocampal subfield segmentations on about 300 subjects. We 
initially ran recon-all using FreeSurfer 5.3, but we used the new FreeSurfer 
6.0 method for the hippocampal subfields. Will this cause problems in our 
analysis? Should we run them through recon-all again with 6.0?

Thanks,
Sarah

Sarah Lancaster
Research Assistant

Duke-UNC Brain Imaging and Analysis Center
Mental Illness Research, Education and Clinical Center
Durham VA Medical Center
sarah.lancas...@dm.duke.edu
919-286-0411 x7660
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Re: [Freesurfer] Reading values from overlays with PETcoreg

[Benjamin Spurny]

Hi Doug,

Yes kind of,
I am just looking for a way to read out PET data from a surface.
I want to do an ROI-based analysis just on brainsurfaces of PET data.

What I did so far is that I coregistered the PET with the MR and used to 
vol2surf function to project my surface on the fsaverage with each 
subject.

Is there now a method to read the .mgh files of the surfaces ROI-based 
using the Desikan atlas?

Currently I am reading them out in Matlab using the .mgh file of my 
subjects surface and the .annot file from the fsaverage.
I just wondered if there is a way to do this in Freesurfer as well?

Best,
Benjamin


Am 16.02.2016 20:56, schrieb Douglas N Greve:
> Hi Benjamin, do you still have a question about this? I lost the thread
> so please summarize the problem again.
> thanks
> doug
> 
> On 02/09/2016 05:01 AM, Benjamin Spurny wrote:
>> Hello Doug,
>> 
>> Thanks for your answer!
>> I already tried this workflow but basically I am interested in a
>> surface-based analysis. Is it possible by using this workflow to get 
>> the
>> any stats.dat just for surface-ROIs?
>> 
>> Best,
>> Benjamin Spurny
>> 
>> 
>> On Fr, 29.01.2016, 01:34, Douglas N Greve wrote:
>>> 
>>> On 01/28/2016 06:50 PM, Pradeep wrote:
 Hello Doug,
 
 I have used the gtmseg with --keep-cc  flag and the corresponding 
 ctab
 files showed the labels but the mri_gtmpvc step failed.
 
 Loading seg for gtm gtmseg.mgz
 Loading seg ctab gtmseg.ctab
 Reading gtmseg.lta
 Replacing 18
 ERROR: CheckSegTissueType() no entry for seg 192
 Failed tissue type check
 
>>> What is your mri_gtmpvc command line? What is the rest of the 
>>> terminal
>>> output?
 My objective is to use the combination of all CC's as a reference
 region and obtain the PVC results, which would be listed in
 gtm.stats.dat
>>> It will be best to combine them when running mri_gtmpvc using 
>>> --replace,
>>> eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 
>>> 255
>>> 251
>>> this will cause all segments of the CC to appear to be a single 
>>> segment
>>> (251).
 Also, I read in the previous email discussions that the default
 ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with
 another ROI as a reference region,
 would it be OK take a ratio of the ROI's in gtm.stats.dat table.
>>> Yes, or you can spec the new region, eg --rescale 251
 Thanks,
 Pradeep
 
 On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve
 > 
 wrote:
 
 
  If you want to use partial volume correction, then you are 
 better
 off
  using mri_gtmpvc with the bbr registration, something like
 
  1. To start, run
 
  gtmseg --s subject
 
  This will take a couple of hours and produces some files needed
  for GTM
  PVC (which is used for GTM, MG, RBV).
 
  2. You'd then register the PET to the anatomical with 
 bbregister
  (probably with --t2 weighting). Make sure to save the output as 
 an
 LTA
  (--lta). I usually use the mean TAC as the input. You can do 
 this in
  parallel with #1.
 
  3. You'd then run mri_gtmpvc, something like
 
  mri_gtmpvc --i pet.nii.gz --psf PSF  --auto-mask PSF+2 .01 
 --seg
  gtmseg.mgz
  --reg reg.lta --default-seg-merge  --o gtmpvc.output
 
  PSF is the point-spread FWHM of the scanner; reg.lta is the
  registration from #2. By default, this will scale by pons. The
 output
  will be gtm.stats.dat and gtm.nii.gz. They both basically have 
 the
  same information. gtm.stats.dat is an easy to read text file. 
 Where
  each row is an ROI, something like:
 
  9   17 Left-Hippocampussubcort_gm   473
  174.0831.406   0.1216
 
  9 = nineth row
  17 = index for RO
  Left-Hippocampus = name of ROI
  subcort_gm = tissue class
  473 = number of PET voxels in the ROI
  174 = variance reduction factor for ROI (based on GLM/SGTM)
  1.406 = PVC uptake of ROI relative to Pons
  0.1216 = resdiual varaince across voxels in the ROI
 
  gtm.nii.gz is a nifti file with each "voxel" being an ROI. The 
 value
  is the PVC uptake of ROI relative to Pons. These can easily be
  concatenated together (mri_concat) and used as input to 
 mri_glmfit
  for group analysis.
 
 
 
 
  On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
  > Dear Freesurfer experts!
  >
  > I am currently working on PET analysis using FS
  >
  > I coregistered my PET with the processed MR using bbregister,
  > transfered it to a surface using mri_vol2surf
  > and now 

Re: [Freesurfer] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear Douglas,

Thanks a lot, I found the version.
Best wishes,
Barbara

On 16/02/2016 20:44, Douglas N Greve wrote:
> We don't have a v6 ready. You can get a development version, you just
> have to keep in mind that it is a snapshot and that the software will
> change without notice.
>
> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
>> Dear Freesurfer experts,
>>
>> How may I get Freesurfer v 6 ?
>>
>> Thank you very much,
>> Best wishes,
>> Barbara
>> ___
>> Freesurfer mailing list
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>>
>>

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[Freesurfer] -qcache of v5.0 data with newer versions

[Daniel Ferreira]

Dear experts,

Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been
recon-all -all with FS 5.0.0?

Thanks

Dani
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