Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

[Meena M. Makary]

External Email - Use Caution

Thank you Bruce for your reply and the helpful information. Our data never
went through Analyze format (we converted the data from dcm > NIFTI using
mricron). FreeView reads the data appropriately (confirmed by attaching a
Vitamin D pill to one of our subject's right side).

Thanks again;
--Meena

On Fri, Dec 14, 2018 at 5:59 PM Bruce Fischl 
wrote:

> when you bring it up in freeview does it properly show left and right? If
> it ever went through analyze as a format you will have lost the
> information that lets us distinguish left from right
>
> cheers
> Bruce
> On Fri, 14 Dec 2018,
> Geha, Paul wrote:
>
> > It is NIFTI format.
> > ——
> > Paul Geha, MD
> > Assistant Professor of Psychiatry
> > Yale School of Medicine
> > Assistant Fellow, The John B. Pierce Laboratory
> > Email: paul.g...@yale.edu
> > Tel:(203)903-4334
> >
> >
> >
> >   On Dec 14, 2018, at 10:53 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >
> > what is your input data format?
> > On Fri, 14 Dec 2018, Geha, Paul wrote:
> >
> >   Dear Bruce,
> >
> >   Thank you for your reply.
> >
> >   However, we are obtaining an odd result with FreeSurfer when we
> examine the volume
> >   of the left and right accumbens.  In the UK  BioBank data >20K
> subjects freesurfer
> >   segmentations the left accumbens is clearly significantly larger
> than the right
> >   accumbens (
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fla
> > bel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu
> %7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c
> >
> bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN
> >   MMSLiAGyXq734%3Dreserved=0<
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fl
> > abel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu
> %7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8
> >
> cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM
> >   NMMSLiAGyXq734%3Dreserved=0>). Also, the attached paper used
> freesurfer and
> >   found left accumbens > right.  In our hands, and in  2 different
> data sets
> >   collected in two different sites,  we obtain the opposite with
> FreeSurfer (right
> >   accumbens > left accumbens).
> >
> >   Furthermore, when we segment these same data sets with FIRST from
> FSL we do obtain
> >   Left accumbens > right Accumbens in both data sets in agreement
> with the
> >   literature.
> >
> >   Any help in solving this discrepancy is much appreciated.
> >
> >   Regards,
> >   Paul
> >   ——
> >   Paul Geha, MD
> >   Assistant Professor of Psychiatry
> >   Yale School of Medicine
> >   Assistant Fellow, The John B. Pierce Laboratory
> >   Email: paul.g...@yale.edu
> >   Tel:(203)903-4334
> >
> >
> >
> > On Dec 13, 2018, at 3:49 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >
> > Hi Meena
> >
> > it shouldn't. We reorient everything to radiological
> >
> > cheers
> > Bruce
> > On Thu, 13 Dec 2018, Meena M. Makary wrote:
> >
> >  External Email - Use Caution
> >   Hi;
> >   I am wondering if the orientation of the input data to
> >   recon-all (i.e. Neurological Vs. Radiological)
> >   produces different results in terms of laterality
> (right
> >   vs. left)?
> >   Thanks;
> >   --Meena
> >   —
> >   Meena M. Makary, Ph.D.
> >   Assistant Professor | Cairo University
> >   Postdoctoral Fellow | Yale University School of
> Medicine
> >   Postdoctoral Associate |  The John B. Pierce Laboratory
> >   Postdoc Committee Chair | The John B. Pierce Laboratory
> >   Career Development and Mentoring Manager Elect | OHBM
> >   Student and Postdoc SIG
> >   290 Congress Avenue, New Haven, CT 06519
> >   +1 (475) 731-5592
> >
> >
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
—
*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University 
Postdoctoral Fellow | Yale University School of Medicine

Postdoctoral Associate |  The John B. Pierce Laboratory

Postdoc Committee Chair | The John B. Pierce Laboratory

Career Development and Mentoring Manager Elect | OHBM Student and 

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed} {Disarmed}

[Winkelbeiner, Stephanie A]

External Email - Use Caution

My bad, I found that the output file from label2vol, vol250-?h.nii.gz, is not 
oriented correctly when I view it in fsleyes...
Trying fslorient2std left vol250-?h.nii.gz totally un-impressed with the same 
orientation as before.
Fslswapdim also doesn't seem to do the trick.

Would it make more sense to reorient the DTI images to freesurfer space since 
I'm using a freesurfer command to extract values anyway?

Or which command would be appropriate to get vol250-?h.nii.gz into fsl space? 
This I should probably ask in the fsl mailing list, I guess.

Would you have some advice nonetheless?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, 
Stephanie A
Sent: Friday, December 14, 2018 4:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices {Disarmed} {Disarmed}


External Email. Use Caution.

External Email - Use Caution
Hi Doug & Bruce,

Thanks again to both of your for your help!

I ended up using label2vol to extend the parcels into the wm and register them 
to DTI space.
Using mri_segstats with an FA_skeletonised mask and the dti_FA.nii.gz image, I 
get reasonable WM values.
However, for some of the subjects I get more 0 values in the left than the 
right hemisphere.

I would have expected to get values for all the parcels or at least zero values 
consistently for some parcels as I registered all parcels to the individual 
subjects dti_FA.nii.gz image.

Am I missing something?

Thanks,
Steph

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, December 11, 2018 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices {Disarmed}


External Email. Use Caution.
It might be that the mri_aparc2aseg route requires two transformations (one to 
1mm, then one to your DTI).
On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:

External Email - Use Caution
Hi Doug,

Thanks a lot for getting back to me and your helpful comments!
Good that you mention the mri_aparc2aseg option. I had tried that and 
registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister 
and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% 
of parcels having zero values (with the label2vol approach I get values in 
almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to 
be perfectly coregistered.
Could you think of any reason why that is?

Thanks,
Steph

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, December 11, 2018 10:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices


External Email. Use Caution.
That all looks like it would work to me. Another thing you can try is the way 
we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in 
the recon-all.log file (make sure to set the output name so that you don't 
overwrite wmparc.mgz). You can specify the max distance away from cortex that 
the label can grow.
On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:

External Email - Use Caution
Hi Douglas,

I was wondering if I can use an annot file in surf2vol to project those parcels 
into the FA image space? Or would label2vol be more appropriate?
Bruce was so kind to give me his advice already and we discussed my challenges 
a bit (see below).

Besides surf2vol with lh.white, I tried the following:

for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_label2vol \
  --annot label/lh.250.aparc.annot \
  --temp $dtipath/$subj/dti_FA.nii.gz \
  --reg mri/register.dat \
  --proj abs -3 -2 .1 \
  --subject $subj --hemi lh \
  --o mri/vol250-lh.nii.gz
cd ../
fi
done

Then, I used the vol250-lh image with mri_segstats to get the FA values (see 
below). This gives reasonable FA values.

Would you consider this a valid approach?

I’d greatly appreciate your input.
Cheers,
Steph


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, 
Stephanie A
Sent: Sunday, December 09, 2018 8:58 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices


External Email. Use Caution.

External Email - Use Caution

Hi Bruce,



you are exactly right. We are interested in projecting the parcellations into 
the WM to extract 

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed} {Disarmed}

[Winkelbeiner, Stephanie A]

External Email - Use Caution

Hi Doug & Bruce,

Thanks again to both of your for your help!

I ended up using label2vol to extend the parcels into the wm and register them 
to DTI space.
Using mri_segstats with an FA_skeletonised mask and the dti_FA.nii.gz image, I 
get reasonable WM values.
However, for some of the subjects I get more 0 values in the left than the 
right hemisphere.

I would have expected to get values for all the parcels or at least zero values 
consistently for some parcels as I registered all parcels to the individual 
subjects dti_FA.nii.gz image.

Am I missing something?

Thanks,
Steph

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, December 11, 2018 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices {Disarmed}


External Email. Use Caution.
It might be that the mri_aparc2aseg route requires two transformations (one to 
1mm, then one to your DTI).
On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:

External Email - Use Caution
Hi Doug,

Thanks a lot for getting back to me and your helpful comments!
Good that you mention the mri_aparc2aseg option. I had tried that and 
registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister 
and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% 
of parcels having zero values (with the label2vol approach I get values in 
almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to 
be perfectly coregistered.
Could you think of any reason why that is?

Thanks,
Steph

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, December 11, 2018 10:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices


External Email. Use Caution.
That all looks like it would work to me. Another thing you can try is the way 
we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in 
the recon-all.log file (make sure to set the output name so that you don't 
overwrite wmparc.mgz). You can specify the max distance away from cortex that 
the label can grow.
On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:

External Email - Use Caution
Hi Douglas,

I was wondering if I can use an annot file in surf2vol to project those parcels 
into the FA image space? Or would label2vol be more appropriate?
Bruce was so kind to give me his advice already and we discussed my challenges 
a bit (see below).

Besides surf2vol with lh.white, I tried the following:

for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_label2vol \
  --annot label/lh.250.aparc.annot \
  --temp $dtipath/$subj/dti_FA.nii.gz \
  --reg mri/register.dat \
  --proj abs -3 -2 .1 \
  --subject $subj --hemi lh \
  --o mri/vol250-lh.nii.gz
cd ../
fi
done

Then, I used the vol250-lh image with mri_segstats to get the FA values (see 
below). This gives reasonable FA values.

Would you consider this a valid approach?

I’d greatly appreciate your input.
Cheers,
Steph


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, 
Stephanie A
Sent: Sunday, December 09, 2018 8:58 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 
vertices


External Email. Use Caution.

External Email - Use Caution

Hi Bruce,



you are exactly right. We are interested in projecting the parcellations into 
the WM to extract the corresponding FA values.



I had tried



for subj in SPN01*; do

if [ -d "${subj}" ];

then

cd $subj/

# extract FA

mri_segstats \

 --seg mri/parc2502dwi.nii.gz \  # parcellation extended & 
registered to dti_FA.nii.gz

 --ctab colortable.txt \

 --i $dtipath/$subj/dti_FA.nii.gz \

 --excludeid 0 \

 --sum ../FA/${subj}_fa.stats

cd ../

fi

done

but had so many zero values that I wanted to check first if I get values for 
all the parcels if I use the non-extended annot-file.

Thanks a lot for helping me with this problem!
Cheers,
Steph



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>>
Sent: Sunday, 9 December 2018 5:24 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than 

[Freesurfer] mri_segstats reporting more decimals

[Winkelbeiner, Stephanie A]

External Email - Use Caution

Hi Freesurfers,

Is there an option to write out more decimals when using the mri_segstats 
command?
I'm extracting mean diffusivity values and would need at least 5 decimals to 
make sense of them.

Thanks for your help!
Cheers
Stephanie



The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
confidential and exempt from disclosure under applicable law. If the reader of 
this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
telephone and electronic mail, and delete the original communication and any 
attachment from any computer, server or other electronic recording or storage 
device or medium. Receipt by anyone other than the intended recipient is not a 
waiver of any attorney-client, physician-patient or other privilege.___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Program installation - fmriprep

[Alshelh, Zeynab]

Hi,


Please see below my issue with a freesurfer license when I try to run fmriprep.


Kind regards,




Zeynab Alshelh, PhD | Postdoctoral Research Fellow

Neuroinflammation and Pain Imaging Laboratory


A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 
149 Thirteenth Street, Room 1101 | Charlestown, MA 02129

+1 (617) 794 6838

zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu



From: Help Desk -- Domenic Minicucci 
Sent: Friday, December 14, 2018 3:40 PM
To: Alshelh, Zeynab
Subject: Re: Program installation - fmriprep

I recommend you ask freesurfer@nmr.mgh.harvard.edu about the license issue. My
understanding is that you need to use the --fs-license-file flag and point it
to a file that contains just these lines:

d...@nmr.mgh.harvard.edu
001-4567-634
*Cler0.zkanMc
FSAe6u/4WBa.E

--
Domenic Minicucci (http://help.nmr.mgh.harvard.edu)

On Fri, 14 Dec 2018 8:30pm, Alshelh, Zeynab wrote:

> Is it returning an error : 'ERROR: a valid license file is required for 
> FreeSurfer to run. '
>
>
> Also, the link you sent is broken.
>
>
> Kind regards,
>
>
> 
>
> Zeynab Alshelh, PhD | Postdoctoral Research Fellow
>
> Neuroinflammation and Pain Imaging Laboratory
>
>
> A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital 
> | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
>
> +1 (617) 794 6838
>
> zalsh...@mgh.harvard.edu | 
> www.nmr.mgh.harvard.edu
>
> 
> From: Help Desk -- Domenic Minicucci 
> Sent: Friday, December 14, 2018 2:48:31 PM
> To: Alshelh, Zeynab
> Subject: Re: Program installation - fmriprep
>
> What happens if you use the Singularity container we have built at
>
> /usr/pubsw/packages/fmriprep/1.1.8/fmriprep-1.1.8.simg
>
> Here's their example snippet from
> https://fmriprep.readthedocs.io/en/stable/installation.html:
>
> $ singularity run --cleanenv /my_images/fmriprep-1.1.2.simg \
> path/to/data/dir path/to/output/dir \
> participant \
> --participant-label label
>
> so you'd need to replace /my_images/fmriprep-1.1.2.simg with
> /usr/pubsw/packages/fmriprep/1.1.8/fmriprep-1.1.8.simg
>
> --
> Domenic Minicucci (http://help.nmr.mgh.harvard.edu)
>
> On Fri, 14 Dec 2018 7:32pm, Alshelh, Zeynab wrote:
>
>> Hi Domenic,
>>
>>
>> Thanks for your response.
>>
>>
>> Can I update my singularity? The current version on my machine in 2.4.4 and 
>> any version <2.5 requires a docker installed.
>>
>>
>>
>> "
>>
>> Preparing a Singularity image (Singularity version < 
>> 2.5)
>>
>> In this case, start with a machine (e.g., your personal computer) with 
>> Docker installed. Use 
>> docker2singularity to 
>> create a singularity image. You will need an active internet connection and 
>> some time.
>>
>> "
>>
>> Kind regards
>>
>> 
>>
>> Zeynab Alshelh, PhD | Postdoctoral Research Fellow
>>
>> Neuroinflammation and Pain Imaging Laboratory
>>
>>
>> A. A. Martinos Center for Biomedical Imaging | Massachusetts General 
>> Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
>>
>> +1 (617) 794 6838
>>
>> zalsh...@mgh.harvard.edu | 
>> www.nmr.mgh.harvard.edu>
>>
>> 
>> From: Help Desk -- Domenic Minicucci 
>> Sent: Friday, December 14, 2018 2:13:15 PM
>> To: Alshelh, Zeynab
>> Subject: Re: Program installation - fmriprep
>>
>> Hi Zeynab,
>>
>> Docker is a container that requires elevated root privileges and so we do not
>> support it. Please use the singularity container option instead. We have
>> singularity installed on all CentOS computers at the center already.
>>
>> Best,
>> --
>> Domenic Minicucci (http://help.nmr.mgh.harvard.edu)
>>
>> On Fri, 14 Dec 2018 6:23pm, Alshelh, Zeynab wrote:
>>
>>> Hi,
>>>
>>>
>>> I'm having trouble installing fmriprep on my machine
>>>
>>> The link to the instructions:
>>>
>>> https://fmriprep.readthedocs.io/en/stable/installation.html#singularity-container
>>>
>>>
>>> When I follow the instructions to download the program as a docker 
>>> container, it requires docker to be installed. However, when I attempt to 
>>> install docker, I am denied access.
>>>
>>>
>>> Is this something you can assist with?
>>>
>>>
>>> Kind regards
>>>
>>>
>>> 
>>>
>>> Zeynab Alshelh, PhD | Postdoctoral Research Fellow
>>>
>>> Neuroinflammation and Pain Imaging Laboratory
>>>
>>>
>>> A. A. Martinos Center for Biomedical Imaging | Massachusetts General 
>>> Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129
>>>
>>> +1 (617) 794 6838
>>>
>>> zalsh...@mgh.harvard.edu | 
>>> 

[Freesurfer] FreeSurfer Stats files: format of 'Measure' lines

[ts+ml]

External Email - Use Caution

Dear FreeSurfer experts,


I'm parsing data from FreeSurfer stats files, e.g., 
/stats/lh.aparc.stats and aseg.stats.

My question: when parsing measure lines, which combination of fields are 
guaranteed to uniquely identify a measure? Here are two example lines (from 
aparc.stats):

# Measure Cortex, NumVert, Number of Vertices, 140843, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 94426.8, mm^2

If you ignore the line header part '# Measure ', each line consists of 5 
fields. Is it, for example, safe to assume that the combination of the first 2 
fields ("Cortex" + "NumVert" for the first example line) is unique?


Thanks in advance,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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

Re: [Freesurfer] NormMean information

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

It could be anything related to the T1-weighting, so T1 itself or PD. It is 
possible for the T2* to affect it, but usually the echo time is too short for 
it to make much of a difference. I could imagine some other indirect effects 
because of the normalization itself. The normMean was not added for anything 
specific, I just thought it might be useful at some point.

On 12/13/18 10:40 AM, Keith Harenski wrote:

External Email - Use Caution

Hello,

What would local, individual differences in normMean voxel intensities signify? 
Is this related to any physical properties of the brain, or is the more of a QA 
measure for the white matter segmentation?

Thank you,
Keith

--
Keith Harenski
Mobile MRI Manager
Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory

The Mind Research Network
1101 Yale Blvd NE Albuquerque, NM 87106-4188
Office (Cell): 505.504.1338 | Fax: 505.272.8002
kharen...@mrn.org | www.mrn.org | 
www.lrri.org



___
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 both the GM and WM ROIs

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

No, but each individual subject does.

On 12/14/18 11:04 AM, Song, Da-Yea wrote:
>  External Email - Use Caution
>
> Hello,
>
> Does the fsaverage subject have a wmparc.mgz file?
>
> Thank you,
> Da-Yea
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
> N.,Ph.D.
> Sent: Tuesday, December 11, 2018 5:42 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Extracting both the GM and WM ROIs
>
> what do you mean by the white matter region? The aparc only labels cortex, 
> which is, of course, GM. If you mean the WM adjacent to the aparc, have you 
> looked at the wmparc.mgz file?
>
> On 12/11/2018 05:16 PM, Song, Da-Yea wrote:
>>  External Email - Use Caution
>>
>> Hello,
>>
>> I've been trying to extract ROIs directly from the Desikan atlas by
>> using the mri_annotation2label and the aparc.annot files from the
>> fsaverage folder.
>>
>> I noticed that this pulls out the grey matter portion for these
>> regions but was wondering if there was a command or file that I could
>> use to do the same for both the grey and white matter. For example, is
>> it possible to extract the grey and white matter region of the
>> posteriorcingulate (in one file)?
>>
>> Thank you so much in advance for your help!
>>
>> Best regards,
>>
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv
>> ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLD
>> GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=W
>> G_88ScamnRxidGvqosdhzeRZCdZQnuX2xLbYo_XwPY=k9Hs5g6IDuazjyIsUC1lbrxPb
>> 1WjybRLvFdC-zozuSs=
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=WG_88ScamnRxidGvqosdhzeRZCdZQnuX2xLbYo_XwPY=k9Hs5g6IDuazjyIsUC1lbrxPb1WjybRLvFdC-zozuSs=
>
>
> ___
> 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 both the GM and WM ROIs

[Song, Da-Yea]

External Email - Use Caution

Hello, 

Does the fsaverage subject have a wmparc.mgz file? 

Thank you,
Da-Yea 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, December 11, 2018 5:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Extracting both the GM and WM ROIs

what do you mean by the white matter region? The aparc only labels cortex, 
which is, of course, GM. If you mean the WM adjacent to the aparc, have you 
looked at the wmparc.mgz file?

On 12/11/2018 05:16 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I've been trying to extract ROIs directly from the Desikan atlas by 
> using the mri_annotation2label and the aparc.annot files from the 
> fsaverage folder.
>
> I noticed that this pulls out the grey matter portion for these 
> regions but was wondering if there was a command or file that I could 
> use to do the same for both the grey and white matter. For example, is 
> it possible to extract the grey and white matter region of the 
> posteriorcingulate (in one file)?
>
> Thank you so much in advance for your help!
>
> Best regards,
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv
> ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLD
> GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=W
> G_88ScamnRxidGvqosdhzeRZCdZQnuX2xLbYo_XwPY=k9Hs5g6IDuazjyIsUC1lbrxPb
> 1WjybRLvFdC-zozuSs=


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=WG_88ScamnRxidGvqosdhzeRZCdZQnuX2xLbYo_XwPY=k9Hs5g6IDuazjyIsUC1lbrxPb1WjybRLvFdC-zozuSs=


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

Re: [Freesurfer] Error in running make_average_subject

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

 can you include the full terminal output?

On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:

External Email - Use Caution

Hello Bruce, thanks for your anwer. Sure. The command is

make_average_subject --out avgsubjectPRUEBAESTASI! --subjects  Bartley_Recon 
Baez_Recon Bonilla_Recon

The output is in the attached file

Thanks!

Emanuel


On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Emanuel,

can you include the full command line and output?

cheers
Bruce
On Wed, 12 Dec 2018,
Emanuel Alvaredo wrote:

>
> External Email - Use Caution
>
> Thanks for your answer Douglas. I replaced the make_average_surface  file 
> with the new one but  I
> have the same message error.
> ASeg Vox2RAS: ---
> -1.0   0.0   0.0   128.0;
>  0.0   0.0   1.0  -128.0;
>  0.0  -1.0   0.0   128.0;
>  0.0   0.0   0.0   1.0;
> mghRead(mri/norm.mgz, -1): could not open file
> -
>
> Labeling Slice
> relabeling unlikely voxels in interior of white matter
> mri/norm.mgz: could not load norm volume from (null)
>
> Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 
> UTC 2018 x86_64 x86_64
> x86_64 GNU/Linux
>
> Thanks
>
> Emanuel
>
>
> On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>   Sorry, the disk that held that patch failed and we did not have a 
> backup so not
>   everything was restored. I just put this file there:
>
>   
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>
>   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>
>
>   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>
>   External Email - Use Caution
>
>   Thanks Bruce. The following is the command.
>
>  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects  subject1
> subject2 subject3
>
>
> And I made a mistake in may last mail. I use the word path instead of patch
>
> I have found this page with a patch for de issue
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>
> But I dont know how to apply the patch. Can you give some information about 
> this?
>
>
> Emanuel
>
>
> On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>   Hi Emanuel
>
>   you need to send us the full command you ran and output of it if you 
> want
>   us to be able to help you
>
>   cheers
>   Bruce
>   On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>
>   >
>   > External Email - Use Caution
>   >
>   > Hello!, I am getting the following error using the
>   command make_average_subject
>   >
>   > mri/norm.mgz: could not load norm volume from (null)
>   >
>   > I have found this page with a path for de issue
>   >
>   >
>   
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>   >
>   > But I dont know how to apply the path. Can you give some information 
> about
>   this?
>   >
>   > Thanks!
>   >
>   >
>   >
>   > Emanuel
>   >
>   >___
>   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



___
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] Does data orientation (Neurological Vs. Radiological) produces different results

[Bruce Fischl]

when you bring it up in freeview does it properly show left and right? If 
it ever went through analyze as a format you will have lost the 
information that lets us distinguish left from right


cheers
Bruce
On Fri, 14 Dec 2018, 
Geha, Paul wrote:



It is NIFTI format.  
——
Paul Geha, MD
Assistant Professor of Psychiatry
Yale School of Medicine
Assistant Fellow, The John B. Pierce Laboratory
Email: paul.g...@yale.edu
Tel:(203)903-4334



  On Dec 14, 2018, at 10:53 AM, Bruce Fischl  
wrote:

what is your input data format?
On Fri, 14 Dec 2018, Geha, Paul wrote:

  Dear Bruce,

  Thank you for your reply.

  However, we are obtaining an odd result with FreeSurfer when we examine 
the volume
  of the left and right accumbens.  In the UK  BioBank data >20K subjects 
freesurfer
  segmentations the left accumbens is clearly significantly larger than the 
right
  accumbens 
(https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fla
bel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c
bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN
  
MMSLiAGyXq734%3Dreserved=0). Also, the attached paper used 
freesurfer and
  found left accumbens > right.  In our hands, and in  2 different data sets
  collected in two different sites,  we obtain the opposite with FreeSurfer 
(right
  accumbens > left accumbens).

  Furthermore, when we segment these same data sets with FIRST from FSL we 
do obtain
  Left accumbens > right Accumbens in both data sets in agreement with the
  literature.

  Any help in solving this discrepancy is much appreciated.

  Regards,
  Paul
  ——
  Paul Geha, MD
  Assistant Professor of Psychiatry
  Yale School of Medicine
  Assistant Fellow, The John B. Pierce Laboratory
  Email: paul.g...@yale.edu
  Tel:(203)903-4334



On Dec 13, 2018, at 3:49 PM, Bruce Fischl 

wrote:

Hi Meena

it shouldn't. We reorient everything to radiological

cheers
Bruce
On Thu, 13 Dec 2018, Meena M. Makary wrote:

     External Email - Use Caution
  Hi;
  I am wondering if the orientation of the input data to
  recon-all (i.e. Neurological Vs. Radiological)
  produces different results in terms of laterality (right
  vs. left)?
  Thanks;
  --Meena
  —
  Meena M. Makary, Ph.D.
  Assistant Professor | Cairo University
  Postdoctoral Fellow | Yale University School of Medicine
  Postdoctoral Associate |  The John B. Pierce Laboratory
  Postdoc Committee Chair | The John B. Pierce Laboratory
  Career Development and Mentoring Manager Elect | OHBM
  Student and Postdoc SIG
  290 Congress Avenue, New Haven, CT 06519
  +1 (475) 731-5592




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

Re: [Freesurfer] Inferior colliculus and Brainstem-cochlear-nucleus

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

We don't have ways to automatically segment those (yet). They were 
optimistically added to the LUT a few years ago:)

On 12/14/18 10:49 AM, Chama Belkhiria wrote:

External Email - Use Caution

Dear comittee,
I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can 
freesurfer distinguish it from other brainstem structures in segmentation?
I have found these references in the LUT "7100  Brainstem-inferior-colliculus  
and 7101  Brainstem-cochlear-nucleus", but idid not find them in the aseg or 
aparac files.
How to measure the volume and thickness of these regions?
Thank you in advance
Chama


*
Post Doctoral Researcher
Audition and Cognition Center
Neurosciences Department
Faculty of Medicine, University of Chile



___
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] Inferior colliculus and Brainstem-cochlear-nucleus

[Bruce Fischl]

Hi Chama
sorry, not yet

cheers
Bruce
On Fri, 14 Dec 2018, Chama Belkhiria wrote:



External Email - Use Caution

Dear comittee, I need ROIs of Inferior Colliculus and 
Brainstem-cochlear-nucleus. Can freesurfer
distinguish it from other brainstem structures in segmentation?
I have found these references in the LUT "7100  Brainstem-inferior-colliculus  
and 7101 
Brainstem-cochlear-nucleus", but idid not find them in the aseg or aparac 
files. 
How to measure the volume and thickness of these regions? 
Thank you in advance
Chama 

*
Post Doctoral Researcher
Audition and Cognition Center
Neurosciences Department
Faculty of Medicine, University of Chile


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

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

[Bruce Fischl]

what is your input data format?
On Fri, 14 Dec 2018, Geha, Paul wrote:


Dear Bruce,

Thank you for your reply.

However, we are obtaining an odd result with FreeSurfer when we examine the volume of the left 
and right accumbens.  In the UK  BioBank data >20K subjects freesurfer segmentations the 
left accumbens is clearly significantly larger than the right accumbens ( 
http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=110 
). Also, the attached paper used 
freesurfer and found left accumbens > right.  In our hands, and in  2 different data sets 
collected in two different sites,  we obtain the opposite with FreeSurfer (right accumbens 
> left accumbens).

Furthermore, when we segment these same data sets with FIRST from FSL we do obtain 
Left accumbens > right Accumbens in both data sets in agreement with the 
literature.

Any help in solving this discrepancy is much appreciated.

Regards,
Paul
——
Paul Geha, MD
Assistant Professor of Psychiatry
Yale School of Medicine
Assistant Fellow, The John B. Pierce Laboratory
Email: paul.g...@yale.edu
Tel:(203)903-4334




On Dec 13, 2018, at 3:49 PM, Bruce Fischl  wrote:

Hi Meena

it shouldn't. We reorient everything to radiological

cheers
Bruce
On Thu, 13 Dec 2018, Meena M. Makary wrote:


External Email - Use Caution
Hi;
I am wondering if the orientation of the input data to recon-all (i.e. 
Neurological Vs. Radiological)
produces different results in terms of laterality (right vs. left)?
Thanks;
--Meena
—
Meena M. Makary, Ph.D.
Assistant Professor | Cairo University
Postdoctoral Fellow | Yale University School of Medicine
Postdoctoral Associate |  The John B. Pierce Laboratory
Postdoc Committee Chair | The John B. Pierce Laboratory
Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG
290 Congress Avenue, New Haven, CT 06519
+1 (475) 731-5592


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

[Freesurfer] Inferior colliculus and Brainstem-cochlear-nucleus

[Chama Belkhiria]

External Email - Use Caution

Dear comittee,
I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can
freesurfer distinguish it from other brainstem structures in segmentation?
I have found these references in the LUT "7100
Brainstem-inferior-colliculus  and 7101  Brainstem-cochlear-nucleus", but
idid not find them in the aseg or aparac files.
How to measure the volume and thickness of these regions?
Thank you in advance
Chama

*
Post Doctoral Researcher
Audition and Cognition Center
Neurosciences Department
Faculty of Medicine, University of Chile
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Segmentation Query

[Bruce Fischl]

Hi Fariha

The number of regions is based on the anatomy. You can combine them if 
you like. The volume to use is probably the aparc+aseg.mgz, which is 
easily convertible to .nii with mri_convert.


Also, you should use freeview not tkmedit (tkmedit has been deprecated 
for many years)


cheers
Bruce
On Fri, 14 Dec 2018, Fariha 
Muazzam wrote:




External Email - Use Caution

Hi Bruce
I am working on segmentation of brain regions. I wanted to know:
1. If it is possible that I could get brain segmented into 8 regions or maybe 
20, because when I
segmented using recon-all command, I got segmentation of 45 regions ?
2. I was looking at the capability of generating my own atlas using tkmedit, 
but I was stuck at that
as well.
3. Plus I don't understand which is the label image. I use the command tkmedit 
subject_name image
-aseg command to view the segmentations. The aseg.mgz alone volume does not 
show all the segmented
regions. If I want a single volume that has the labels, how would I get that. I 
eventually want a
.nii label volume and .nii original volume

Thank You


On Thu, Dec 13, 2018 at 8:13 PM Bruce Fischl  wrote:
  Hi Fariha

  can give us more details? How would you like to customize them? I think 
the
  answer is probably no, but I'm not sure I understand what you are trying 
to
  do
  cheers
  Bruce


  On Wed,
  12 Dec 2018, Fariha Muazzam wrote:

  >
  > External Email - Use Caution
  >
  > Hi
  >
  > I am working in Freesurfer for subcortical segmentation of brain, I did 
segmentation of
  a volume and
  > I got around 45 regions. Is it possible that I could customize the 
regions I want or
  number of
  > segments that I want?
  >
  > Thank You
  > Regards
  >
  > Fariha Muazzam
  > Research Officer
  >
  > 
--
  > Al-Khawarizmi Institute of Computer Science (KICS)
  >
  > University of Engineering and Technology (UET), Lahore
  >
  > Email: fariha.muaz...@kics.edu.pk  | Web: www.kics.edu.pk 
  >
  >
  >___
  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] GPU/supercomputer adaptation of freesurfer?

[Morgan Hough]

External Email - Use Caution

Hi Richard,

That is a very good point. I knew it was being deprecated and there was
talk of OpenCL but I have not been keeping up. Multicore systems were
getting the most benefit from newer releases. Certainly, to run the
existing CUDA code involved making sure your sysadmin would give you the
older CUDA libs too.

Thank you for your input. I know it was a long time ago but I remember your
GTC presentation for sure.

Cheers,

-Morgan

On Thu, Dec 13, 2018 at 2:55 AM R Edgar  wrote:

> External Email - Use Caution
>
> Sorry I'm coming to this a bit late I'm not sure that the CUDA
> implementation is supported these days. I've not done much work on em_
> and ca_register since 2012; I'm not sure about the surface stream (I
> didn't do that port). Furthermore, I don't see CUDA being included in
> the new CMake build system. Some differences to the CPU stream are
> inevitable (floating point arithmetic and all that), but if the
> workflow in those binaries has changed since when I was working on
> them, then those changes may not be reflected in the GPU code.
>
> Regards,
>
> Richard
>
> ___
> 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 : LME and limits of model

[Martin Reuter]

Hi Matthieu, 

no, sorry. Maybe you can find a local biostatistician who knows. 

A slope estimate with less time points is more uncertain than one with
more time points (obviously). Also a slope estimate with time points on
a line is more certain than one with time points values all over the
place. This information is used in the LME model. But I don't know to
what extend any potential biases are removed. For example, if one group
has only 2 time points and the other had 5, I would be very suspicious.
You can, of course, always reduce the number of time points in the
second group to match the first and see if your results remain stable. 

Best, Martin



On Fri, 2018-12-07 at 22:33 +0100, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> Hi Martin,
> 
> I come back on my previous question concerning survival bias in LME.
> 
> Do you have an advice ?
> 
> Best,
> Matthieu
> 
> > Le 19 oct. 2018 à 16:30, Matthieu Vanhoutte  > l.com> a écrit :
> > 
> > Hi Martin,
> > 
> > Do you mean that high attrition (less time points with time) would
> > induce more variance on the slope estimates but this effect would
> > be compensated by LME modeling ?
> > 
> > Would there be proportion of early drop outs to respect in order to
> > compensate bias with LME ?
> > 
> > Thanks,
> > Matthieu
> > 
> > 
> > Le ven. 19 oct. 2018 à 16:19, Martin Reuter  > d.edu> a écrit :
> > > Hi Matthieu, 
> > > 
> > > in LME it is OK if subjects have differently many time points in
> > > general. You need to ask a statistician about your specific
> > > setup, but
> > > I think it might be OK (basically less time points, means more
> > > variance
> > > on the slope estimates, but that should be considered in LME).
> > > But I am
> > > not a statistician. 
> > > 
> > > Best, Martin
> > > 
> > > 
> > > On Wed, 2018-10-17 at 18:46 +0200, Matthieu Vanhoutte wrote:
> > > > External Email - Use Caution
> > > > Hi Martin,
> > > > 
> > > > Thanks for your answer.
> > > > 
> > > > I actually compare neurospychological scores at baseline
> > > between
> > > > drop-out subjects and subjects with full time-points. If I ever
> > > find
> > > > that drop-out subjects are more severely affected than the
> > > subjects
> > > > with full time-points, then there might be a bias in the
> > > results of
> > > > my LME study ?
> > > > 
> > > > How could I argue that significant patterns found in my LME
> > > study
> > > > between both groups are still valid accounting for this bias ?
> > > Is LME
> > > > method robust enough for compensating this kind of drop-out ?
> > > > 
> > > > Best,
> > > > Matthieu
> > > > 
> > > > 
> > > > Le mer. 17 oct. 2018 à 18:33, Martin Reuter  > > rvard.
> > > > edu> a écrit :
> > > > > Hi Matthieu, 
> > > > > 
> > > > > 1) survival analysis is typically used if you want to detect
> > > if the
> > > > > time to an event is longer in one group vs the other (e.g.
> > > one
> > > > > group
> > > > > gets placebo the other drug and we want to know if recurrence
> > > is
> > > > > later
> > > > > in the drug group). Not sure this is what you need. The nice
> > > thing
> > > > > is,
> > > > > it can deal with drop-outs
> > > > > 
> > > > > 2) No, you can directly test that (e.g. do more dieseased
> > > drop out
> > > > > than
> > > > > healthy, or are the dropouts on average more advanced (test-
> > > scores,
> > > > > hippo-volume etc) than the diseased at baseline... many
> > > options.
> > > > > you
> > > > > could also test interactions with age , gender etc. However,
> > > not
> > > > > finding an interaction may not mean there is no bias, it is
> > > just
> > > > > small
> > > > > enough to go undetected with your data size. 
> > > > > 
> > > > > 3) Survival analysis is a different analysis than LME. 
> > > > > 
> > > > > Best, Martin
> > > > > 
> > > > > On Tue, 2018-10-16 at 16:15 +, Matthieu Vanhoutte wrote:
> > > > > > External Email - Use Caution
> > > > > > Hi Martin,
> > > > > > 
> > > > > > It's been a long time since this discussion but I return on
> > > this
> > > > > from
> > > > > > now... The problem is that I followed longitudinal images
> > > of two
> > > > > > groups where I had mainly missing time points at the end.
> > > Than
> > > > > you
> > > > > > suggested:
> > > > > > If you have mainly missing time points at the end, this
> > > will bias
> > > > > > your analysis to some extend, as the remaining ones may be
> > > > > extremely
> > > > > > healthy, as probably the more diseased ones drop out. You
> > > may
> > > > > want to
> > > > > > do a time-to-event (or survival-analysis) which considers
> > > early
> > > > > drop-
> > > > > > out.
> > > > > > 
> > > > > > 1) I know the survival analysis toolbox on matlab, but now
> > > I
> > > > > would
> > > > > > like to know what information will this survival analysis
> > > give to
> > > > > me
> > > > > > ? 
> > > > > > 2) Will this analysis tell me if there is a bias ?
> > > > > > 3) How to consider 

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

[Martin Reuter]

Hi Elena, 

FreeSurfer put inputs in RAS coordinates (during the conform step at
the very beginning), so it will take care of this. But only if the
correct information is available from the input image header. If that
header was corrupted earlier, it is impossilbe to know what coordinates
the input is in and then this can happen. 

One thing you can try is to open the orig.mgz from both time points in
freeview. Are they in the same orientation? If so , there might be a
different problem. If not, you should go back to the original scans
(dicom) and convert them to nifti directly (if possible) using
mri_convert. 

Best, Martin


On Fri, 2018-12-07 at 11:32 +1100, Elena Pozzi wrote:
> 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
> 
> 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal Stream - LONG step

[Martin Reuter]

It says "Could not find file ..". I wonder which one it is looking for.

Did you try to completely delete this long subject dir and re-run from
scratch?
Do other time points with this base go through? If not, you could re-
run the base also. 

Also when you open orig of all time points (from the long dirs), are
they nicely registered?

Best, Martin


On Thu, 2018-12-06 at 18:06 +, Figueiro Longo, Maria Gabriela
wrote:
> 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  mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.  vard.edu>
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal processing and paralllel flag

[Martin Reuter]

Hi Erik, 

usually we parallelize the number of subjects, rather than the
individual pipelines. That gives us the best performance. 

Best, Martin

On Thu, 2018-12-06 at 11:07 +, Erik O'Hanlon wrote:
> 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
> 
> 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
> 
> 
> 
> 
> ___
> 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 analyses after lesion segmentation

[Martin Reuter]

Hi Kathleen, 

if you map one image to the other, this introduces interpolation
artefacts, which will bias your analysis (any type of analysis, so this
is already a problem in the lesion segmentation part). 

Technically you run longitudinal freesurfer on these images but
(similar to the lesion analysis) you will never know if changes across
time are due to the processing bias or if they are real. 

Get the original data, not the mapped images, and work with those. (And
you may want to warn your colleague that lesion change estimates are
probably biased, if one image is mapped to the other). 

Best, Martin

On Thu, 2018-11-29 at 11:50 -0500, kathleen Gerbino wrote:
> External Email - Use Caution
> Sorry, I was thinking that my question may not have been very clear.
> Baseline T1 images were rigidly registered to 1mm^3 MNI template and
> then all follow-up images were rigidly registered to the individual's
> baseline T1. My question is whether I could still apply the
> Freesurfer longitudinal pipeline (i.e. using  recon-all -base
>  -tp    -tp  -all) to these images as they are
> (i.e. rigidly registered to the baseline scan) or if you had any
> guidance as to how to best proceed. 
> 
> thank you in advance and sorry to email twice!
> 
> Kathleen
> 
> On Thu, Nov 29, 2018 at 6:35 AM kathleen Gerbino  ail.com> wrote:
> > Hi FreeSurfer experts:
> > 
> > I hope you are well. I need to segment quite a few longitudinal T1
> > scans from patients with multiple sclerosis. A colleague has
> > applied an automated lesion segmentation algorithm to segment and
> > fill the lesions. During this process, the follow-up scans were
> > registered to the baseline scan. My question is whether I could
> > still apply the Freesurfer longitudinal pipeline to these images or
> > whether your had any recommendations on the appropriate steps to
> > take if this is not appropriate. 
> > 
> > Kind regards,
> > Kathleen 
> > 
> 
> ___
> 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