Re: [Freesurfer] mri_cvs_register: no such file or directory

[Vinny K]

External Email - Use Caution

Hi,

I figured out the mistake.  I had to remove the forward slashes from the
command line.  Its running fine now.

Thanks,

Vinny

On Sat, Nov 16, 2019 at 12:13 AM Vinny K 
wrote:

> Hi,
>
> The moving subjectid directory (subjb) has a cvs folder written but it is
> empty.
>
> The template subjectid directory has the normal folder structure after
> recon-all.
>
>
> [image: moving.png]
> [image: template.png]
>
> On Fri, Nov 15, 2019 at 9:54 PM Nader Razmara  wrote:
>
>> External Email - Use Caution
>>
>> Hi
>> Check your subject and template address directory.
>>
>>
>> On Sat, 16 Nov 2019, 01:05 Vinny K >
>>> External Email - Use Caution
>>>
>>> Hi,
>>>
>>> I'm using the development version of FreeSurfer and am attempting to
>>> register two subjects using mri_cvs_register.
>>>
>>> This is the command I ran:
>>>
>>> mri_cvs_register --mov subjb/ --template subja/
>>>
>>> Below was the outputted message:
>>>
>>> The outdir:
>>> /home/vinny/Tools/freesurfer/subjects/subjb//cvs
>>>
>>> Log file is
>>> /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log
>>>
>>> /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log:
>>> No such file or directory.
>>>
>>> Thanks,
>>>
>>> Vinny
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>>
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>
>
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Re: [Freesurfer] mri_cvs_register: no such file or directory

[Vinny K]

External Email - Use Caution

Hi,

The moving subjectid directory (subjb) has a cvs folder written but it is
empty.

The template subjectid directory has the normal folder structure after
recon-all.


[image: moving.png]
[image: template.png]

On Fri, Nov 15, 2019 at 9:54 PM Nader Razmara  wrote:

> External Email - Use Caution
>
> Hi
> Check your subject and template address directory.
>
>
> On Sat, 16 Nov 2019, 01:05 Vinny K 
>> External Email - Use Caution
>>
>> Hi,
>>
>> I'm using the development version of FreeSurfer and am attempting to
>> register two subjects using mri_cvs_register.
>>
>> This is the command I ran:
>>
>> mri_cvs_register --mov subjb/ --template subja/
>>
>> Below was the outputted message:
>>
>> The outdir:
>> /home/vinny/Tools/freesurfer/subjects/subjb//cvs
>>
>> Log file is
>> /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log
>>
>> /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log:
>> No such file or directory.
>>
>> Thanks,
>>
>> Vinny
>> ___
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>
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Re: [Freesurfer] mri_cvs_register: no such file or directory

[Nader Razmara]

External Email - Use Caution

Hi
Check your subject and template address directory.


On Sat, 16 Nov 2019, 01:05 Vinny K  External Email - Use Caution
>
> Hi,
>
> I'm using the development version of FreeSurfer and am attempting to
> register two subjects using mri_cvs_register.
>
> This is the command I ran:
>
> mri_cvs_register --mov subjb/ --template subja/
>
> Below was the outputted message:
>
> The outdir:
> /home/vinny/Tools/freesurfer/subjects/subjb//cvs
>
> Log file is
> /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log
>
> /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log:
> No such file or directory.
>
> Thanks,
>
> Vinny
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Re: [Freesurfer] mri_cvs_register: no such file or directory

[Vinny K]

External Email - Use Caution

Hi,

I'm using the development version of FreeSurfer and am attempting to
register two subjects using mri_cvs_register.

This is the command I ran:

mri_cvs_register --mov subjb/ --template subja/

Below was the outputted message:

The outdir:
/home/vinny/Tools/freesurfer/subjects/subjb//cvs

Log file is
/home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log

/home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log:
No such file or directory.

Thanks,

Vinny
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[Freesurfer] bias field correction Freesurfer

[Adam Rytina]

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Hello all,

I have an input MR T1w series of images. I want to apply the bias field 
correction. According to some articles that I´ve read, bias field correction is 
automatically done in the standard "recon-all". Is that right - in which of 31 
stages of recon-all bias filed correction is implemented?

Moreover, I´ve read it´s possible to run "nu_correct" - does it perform also 
bias field correction? Or does it perform only intensity inhomogenity?

Thanks a lot
Adam
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[Freesurfer] Question about the input for longitudinal processing pipeline

[Darko Komnenić]

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Dear Freesurfer experts,
I wanted to run the Freesurfer's longitudinal processing pipeline
(described here
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
series of MRI scans from a single patient. However, after looking at the
scans, i realized that for most time points, the patient doesn't have a
"simple/normal" T1 MPRAGE sequence available. Instead, they have a T1
sequence with a contrast agent, as well as T1 mp2rage sequences.

Is it possible/advisable to run recon-all in general or this pipeline in
particular on T1 MPRAGE scans that have a contrast agent, or that are
mp2rage instead of MPRAGE?

Thanks in advance!
Best,
Darko
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Re: [Freesurfer] Cortical thickness values on a vertex base level

[Aicha Dijkshoorn]

External Email - Use Caution

Thank you so much for your repsonse.
Could you maybe please tell us which input file we should use?

Best wishes,
AIcha

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 namens Greve, Douglas N.,Ph.D. 

Verzonden: donderdag 31 oktober 2019 19:16
Aan: freesurfer@nmr.mgh.harvard.edu 
Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level

You can run mri_surfcluster with your fdr threshold as the --thmin
value. This will output cluster number (ocn) map. This will assign the
cluster number to a vertex. You can then use mri_segstats with --seg
ocn.mgz --excludeid 0 and input being the mean thickness or area maps.
When you use area as thhe input, make sure to --accumulate to get the
total area. You can get an area map in the same way that you got the
thickness map, ie, mris_preproc, etc

On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
>
> External Email - Use Caution
>
> Dear Greve,
>
> Thank you for your quick respons.
>
> Yes, I believe that is what I mean. Let me illustrate with some
> (fictive) data;
> We were able to prove these data for the entire hemisphere as can be
> seen below.
>
>
>
>
>
> *Group 1*
>
>
>
> *Group 2*
>
>
>
> *Difference*
>
>
>
> */Sig./*
>
> Thickness
>
> (in mm)
>
>
>
> Left
>
>
>
> 1.48
>
>
>
> 1.46
>
>
>
> .004
>
>
>
> .19
>
> Right
>
>
>
> 1.46
>
>
>
> 1.46
>
>
>
> .003
>
>
>
> .03
>
>
>
>
>
>
> However, we would like to provide similar data in our vertex-base
> analyses:
>
> *Significantly different clusters between group 1 and group 2*
>
>
>
> *Cortical thickness group 1*
>
>
>
> *Cortical thickness group 2*
>
>
>
> *Difference in mm2*
>
>
>
> */Sig./*
>
> Left Cuneus
>
>
>
> ?
>
>
>
> ?
>
>
>
> ?
>
>
>
> 0.013
>
> Left Fusiform gyrus
>
>
>
> ?
>
>
>
> ?
>
>
>
> ?
>
>
>
> 0.021
>
> Right Paracentral lobule
>
>
>
> ?
>
>
>
> ?
>
>
>
> ?
>
>
>
> 0.001
>
> Right parahippocampal gyrus
>
>
>
> ?
>
>
>
> ?
>
>
>
> ?
>
>
>
> 0.002
>
>
> Does this clarify my question?
>
> Best wishes,
> Aicha
>
>
>
> 
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
>  namens Greve, Douglas
> N.,Ph.D. 
> *Verzonden:* donderdag 31 oktober 2019 16:25
> *Aan:* freesurfer@nmr.mgh.harvard.edu 
> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
> base level
> I'm not sure what you mean. Do you want the mean thickness of a cluster
> and/or its surface area?
>
> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
> >
> > External Email - Use Caution
> >
> > Dear developers,
> >
> > For a case-control study we are comparing the cortical thickness and
> > cortical surface area on a vertex-base level, for which we found
> > significant differences throughout the brain.
> >
> > Is it possible that, in addition to the significance values (p < .05
> > after FDR correction) on a vertex-base level, we can include the exact
> > thickness or surface area value (or difference) of the significant
> > clusters on a vertex base-level between the groups. In order words, to
> > provide some measures to highlight the size of the significant cluster
> > or the differences in cortical thickness / cortical surface area to
> > provide clinically useful context. For instance, a command comparable
> > to 'voxel size' in TBSS.
> >
> > As this is my first time using Freesurfer any help that you could
> > offer on this matter would be highly appreciated.
> >
> > Best wishes,
> > Brigitte Dijkshoorn
> >
> > ___
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>
>
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Re: [Freesurfer] HBT hippocampal segmentation

[Iglesias Gonzalez, Juan E.]

Dear Daniel,
I’ll defer to Jean Augustinack (CCed) on this one.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Thursday, 14 November 2019 at 19:02
To: Freesurfer support list 
Subject: [Freesurfer] HBT hippocampal segmentation


External Email - Use Caution
Hello,

I was just asked by a reviewer how the head body and tail of the Freesurfer 
subfield segmentation is determined. I know that there is no differentiation of 
the tail, however, there are differentiations between the head and body of the 
different subfields. Are there specific anatomical boundary rules that drive 
the algorithm to differentiate between head and body in the HBT segmentation 
output.

Thank you for any guidance you can provide!

Best,
Daniel Callow
Graduate Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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Re: [Freesurfer] Processor speed/cores vs cache size

[fsbuild]

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Hello Pradyumna,
I have not read thru the mailing list posts so see what other comments there 
may be about this, but the posted system 
requirements,https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements- do 
not mention anything like Xeon class server chips.
Desktop (non-server class) machines with a modern Intel i7 or i9 chip with base 
(non-turbo, non-overclocked) CPU speeds of ~3 GHz are common. I’ve run a 
complete recon-all in about 7-8 hours on a mid-2016 MacBook Pro with a 2.9Ghz 
i7 chip (4 physical, 8 virtual cores) with 16GB of old higher latency 
DDR3 memory using all SSD disk storage (with the machine doing nothing else).
I don’t have any data w.r.t the pros/cons of L2 or L3 level cache. I 
don’t know the details of how many threads the commands executed by recon-all 
can exploit. From my own experience of running various commands, 4 or 8 
physical cores (hyperthreaded to yield 8 or 16 cores) should be fine.  
I’ve also found that 24G to 32G of RAM is helpful with performance. Since 
data/files will be read/written from disk, at certain points performance could 
be I/O bound by how fast disk read/writes occur. This can be helped by 
having your data stored on a 7200, 10,000 RPM disk drive (or better an SSD 
drive) to speed things up that is physically separate from the drive with the 
boot partition.

But you could certainly meet or upgrade the specs to outfit a server machine 
with Xeon class chips and drives for multiple users.
- R.

On Nov 13, 2019, at 15:00, Pradyumna Bharadwaj p...@email.arizona.edu 
wrote:External Email - Use 
CautionHello,For running 
recon-all or tracula on a local workstation, is it recommended to go for a 
higher processor speed/number of cores, or a larger cache size for the 
processor (Intel Xeon W series). Or is it likely to be a more complex interplay 
between the number of recon-all processes running at any given 
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[Freesurfer] Questions for PetSurfer

[Soo-Jong Kim]

External Email - Use Caution

Dear FreeSurfer experts,

I am a student in neuroimaging using FreeSurfer.
I have some questions and I don't know where to send questions.
That's why I found this mail and writing.

I've studied PetSurfer for partial volume correction of PET.
I saw the tutorial in website.
Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.

After generating gtmseg and coregistration to make lta file, I followed
this code and changed some.

*mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz *
*--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv
--o output_pvc*

After this, rbv.nii.gz file was generated. and SUVR analysis was performed
as reference region (cerebellar cortex).  But Compared to original un-pvc
PET, Cortex SUVR was reduced...

In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.

Is is okay if I use the output file as rbv.nii.gz ?

in Thomas et al, 2011,
He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET
using RBV method)

In that case, What are the regions to make rbv.nii.gz method in PetSurfer?

Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?

If not, Please tell me what is the correct command of mri_gtmpvc.
I need only partial volume corrected PET using RBV method.

Sincerely,

Soo-Jong Kim
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Re: [Freesurfer] Custom location of license file

[fsbuild]

External Email - Use Caution

Hello Karsten,
I think the location for license.txt in the freesurfer 6 release needs to be 
under $FREESURFER_HOME, ie., $FREESURFER_HOME/license.txt, and cannot be 
relocated from there by an environment variable.. But you can try using a 
soft link to point to it in another location. 
While it does not work to preserve $HOME/license.txt as a reference in another 
environment variable like FREESURFER_HOME or within a soft link, I believe the 
shorthand notation ~/license.txt does work in a soft link.  So in your 
common installation under $FREESURFER_HOME you could try,
$ cd $FREESURFER_HOME$ ln -s ~/license.txt license.txt
- and see if freesurfer complains if an individual users $HOME/license.txt (or 
~/license.txt) is missing.
In the newer code base on the freesurfer development branch, it should work to 
set the FS_LICENSE environment variable to point to the path of the license.txt 
file, but I don’t think that works in the 6.0.0 release.
Ideally, I think the freesurfer group would prefer if each user signed up for 
their own license in order to track usage, so maybe try the soft link.

- R.

On Nov 14, 2019, at 12:58, Siller, Karsten H (khs3z) kh...@virginia.edu 
wrote:External Email - Use 
CautionHi,We’d like to 
install FreeSurfer globally for our users on a CentOS HPC system. Is it 
possible to define an alternative location for the FreeSurfer license file, 
e.g. ~/.license, so that users can use their individual license files 
with the globally installed software? Perhaps the license file location 
and name can be customized via an environment variable at runtime?If that 
is not possible, is it ok to install a single “global” license file for all 
users in the shared FreeSurfer installation 
directory?Thanks,Karsten--Karsten SillerResearch 
ComputingUniversity of 
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Re: [Freesurfer] Volume (WM Parcellation) of RightCerebralCortex -- Freesurfer 6.0

[Tim Schäfer]

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You should ask that at the AFNI mailing list.

I would guess it refers to the files /mri/lh.ribbon.mgz and 
/mri/rh.ribbon.mgz, but I do not know that program and that is nothing 
but a wild guess.

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


> On November 15, 2019 at 6:05 AM An Lijun  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
> I am trying to use ADNI MERGE R package to get 'wholebrain' volume.
> 
> It requires CerebralCortex. The information I get from ADNI merge 
> is "Volume (WM Parcellation) of RightCerebralCortex".
> 
> But when I ran Freesurfer reconall 6.0, I could not find 
> CerebralCortex under 'stats' folder, do you know where it could 
> be? Thanks so much.
> 
> Best Regards,
> An Lijun
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