Re: [Freesurfer] SynthSeg

[Fischl, Bruce]

Sure. I should add that because the method is sequence agnostic doesn’t mean 
the results won’t be biased by differences in contrast in the input sequence.

Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of AJ
Sent: Saturday, November 27, 2021 11:03 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] SynthSeg


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Many thanks.
Best
AJ

On Sat, Nov 27, 2021, 20:04 Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Sorry, what is the “sb” in sbTIV? I’m sure you can use it from samseg, or just 
use samseg for the segmentation as well if you want, since it is agnostic with 
respect to MRI sequence as well.
Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of AJ
Sent: Saturday, November 27, 2021 10:03 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] SynthSeg


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Hi
Thank you for your help.  I ran SynthSeg successfully.   How do you derive 
sbTIV value ?  Could one use sbTIV from SAMSEG?

Many thanks
AJ
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Re: [Freesurfer] SynthSR

[Douglas N. Greve]

Also samseg, see https://pubmed.ncbi.nlm.nih.gov/33940143/

On 11/26/2021 11:16 AM, Fischl, Bruce wrote:

Hi AJ

you might try SynthSeg, as that is one of the advantages of it - it 
isn't biased towards any particular MRI sequence


cheers
Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of AJ 


*Sent:* Thursday, November 25, 2021 9:00 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] SynthSR

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Hi,
Could synthetic MRIs generated by the SynthSR script be potentially 
used to harmonize T1w weighted images acquired on different scanners?  
Then used harmonized images for volumetric analyses?

Many thanks
AJ

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Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Help: Using a Different Atlas for Anatomical ROI Analysis

[Douglas N. Greve]

That is a label atlas; you cannot run that through FS. You will need a 
t1-weighted image to use as input to recon-all to start.


On 11/19/2021 1:59 PM, Flanagan, Shawn D wrote:


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Hello,

I would like to use the Brainnectome atlas for cortical thickness 
analysis parcellations. The T1 template volume (nifti file type) is 
attached if helpful. I have seen a couple of posts on this, but am not 
clear about the process. For example, the response to a similar 
comment was to “run recon-all on the AAL anatomical T1w volume 
template”. At this point, I do not know what files, transformations, 
and/or code modifications are needed. For example, does the 
brainnectome template volume need to be preprocessed in any way, does 
it need to be saved in the MGH format? If so, how is this done? Does 
the process require any other files or subroutines?


In summary, I am wondering if you can “walk me through” the process or 
provide a detailed example. Any help would be greatly appreciated! 
Thank you for your time.


Best,

Shawn

*---*

*Shawn Flanagan*, Ph.D.
Assistant Professor

University of Pittsburgh
School of Health and Rehabilitation Sciences
Department of Sports Medicine and Nutrition

Neuromuscular Research Laboratory
Warrior Human Performance Research Center

3860 South Water Street
Pittsburgh, PA 15203
sd...@pitt.edu  Email
412.246.0460 Office
630.854.0547 Mobile

Neuromuscular Research Laboratory 




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Re: [Freesurfer] interhemispheric registration: xhemi vs. mris_left_right_register

[Douglas N. Greve]

I see what you mean, though I don't think either one look that great. 
The first thing to do is to backup and look at the registration to 
fsaverage_sym by mapping the lh and rh curv to lh.fsaverage_sym and see 
if the curv patterns match up with those in fsaverage_sym and to each 
other (use mris_apply_reg)


On 11/20/2021 12:34 PM, Dr. Cornelius Kronlage wrote:

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Dear freesurfer community,

concerning interhemispheric registration: What are differences between 
mris_left_right_register and the xhemi pipeline (including the fsaverage_sym 
subject)? I understand that xhemi/fsaverage_sym are meant to provide an 
unbiased reference as opposed to simply mapping all data to one hemisphere.

I am trying to map a label from one hemisphere to the other on individual 
subjects. I noticed that mris_left_right_register results in output quite 
different from using fsaverage_sym via the xhemi process as an intermediate. As 
an example, see the figure file attached (original label on rh, mapped labels 
on lh). At the first glance, the output of mris_left_right_register seems to 
align with the curvature a lot better...

For reference, the following code was used. Is that correct?
surfreg --s ${subject} --t fsaverage_sym
surfreg --s ${subject} --t fsaverage_sym --lh --xhemi
mris_apply_reg \
   --src-label rh.label --trg rh_on_lh.xhemi.label \
   --streg ${SUBJECTS_DIR}/${subject}/xhemi/surf/lh.fsaverage_sym.sphere.reg 
${SUBJECTS_DIR}/${subject}/surf/lh.fsaverage_sym.sphere.reg

mris_left_right_register \
   ${SUBJECTS_DIR}/${subject}/surf/lh.sphere \
   ${SUBJECTS_DIR}/${subject}/surf/rh.sphere \
   ${SUBJECTS_DIR}/${subject}/surf/lh.sphere.left_right \
   ${SUBJECTS_DIR}/${subject}/surf/rh.sphere.left_right
mris_apply_reg \
   --src-label rh.label --trg rh_on_lh.left_right.label \
   --streg ${SUBJECTS_DIR}/${subject}/surf/rh.sphere.left_right 
${SUBJECTS_DIR}/${subject}/surf/lh.sphere.left_right

Thank you and
with best wishes
Cornelius


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Re: [Freesurfer] Difficulty Running Single Subject Surfaced Based GLM

[Douglas N. Greve]

I noticed that you are explicitly setting the mask and funcstem in 
mkanalysis-sess. Is there a reason for that? Also, I'd set -poly to 5.


On 11/21/2021 1:11 PM, Hiersche, Kelly J. wrote:


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Hello FreeSurfer Developers,

First, I am new to using Freesurfer, so I apologize if any information 
is unclear.


I am attempting to use the following tutorial *MailScanner has 
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to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel 
 to 
do a surface based GLM in an individual subject (using my own data, 
not the tutorial data), but I am getting the following error:


Error using MRIread (line 76)
ERROR: cannot determine format of
/*subnum/bold/runnum/masks*/fmcpr.brainmask.fsaverage.lh
(MRIread)

I am getting that error because the fmcpr.brainmask.fsaverage.lh does 
not exist. To fix this error, I re-ran preprocessing using the 
following tutorial: *MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc 
 



After preprocessing, I still got the same error.

*Here are the files that do exist in that path: 
*subnum/bold/run-num/masks* *
brain.e3.nii.gz            brain.fsaverage.lh.pr.nii.gz 
 brain.fsaverage.rh.pr.nii.gz  brain.mni305.2mm.pr.nii.gz 
 brain.nii.gz.mkbrainmask.log
brain.fsaverage.lh.nii.gz  brain.fsaverage.rh.nii.gz 
brain.mni305.2mm.nii.gz       brain.nii.gz


*There are some fmcpr files in this folder: subnum/bold/run-num*
fmcpr.brainmask.norm.2x2x2.nii.gz     fmcpr.mcdat fmcpr.norm.nii.gz   
           fmcpr.sm5.fsaverage.rh.nii.gz
fmcpr.brainmask.normtmp.2x2x2.nii.gz  fmcpr.nii.gz 
 fmcpr.sm0.norm.nii.gz          fmcpr.sm5.mni305.2mm.nii.gz
fmcpr.mat.aff12.1D                    fmcpr.nii.gz.mclog 
 fmcpr.sm5.fsaverage.lh.nii.gz  fmcpr.sm5.norm.nii.gz



*Here are the commands I am running:*
*These commands work: *
*mkanalysis-sess* -fsd bold -rlf $analysis_stem-$run_set.rlf -surface 
fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 
-nconditions $nconditions -mask $func_stem.brainmask -gammafit 2.25 
1.25 -nuisreg mcprextreg 6 -TR 1. -polyfit 1 -analysis 
$analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude 
$tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run


*mkcontrast-sess* -analysis 
$analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -contrast 
Con1-Con2 -a 1 -c 2


*preproc-sess* -fsd bold -rlf $analysis_stem-$run_set.rlf -surface 
fsaverage lhrh -mni305 -fwhm 5 -per-run


*This command errors *
mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface 
fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 
-nconditions $nconditions -gammafit 2.25 1.25 -nuisreg mcprextreg 6 
-TR 1. -polyfit 1 -analysis 
$analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude 
$tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run


 1. I am running freesurfer through matlab on the Ohio Supercomputer;
freesurfer/6.0.0

Thank you for all your troubleshooting help!

Kelly


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Re: [Freesurfer] register.dat

[Douglas N. Greve]

Yes, but if there is an anat2orig2diff.bbr.lta file, use that instead

On 11/22/2021 12:48 PM, Zeng, Qi wrote:


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Sorry for the trouble, I seemed to find the registration matrix 
located in xfms/anatorig2diff.bbr.dat. Is that one correct?


Best,
Jackie



On Mon, Nov 22, 2021 at 12:36 PM Zeng, Qi  wrote:

Hi Experts,

My tracula completed with no error. So I was trying to view the
fa.nii with the following command:
freeview -v mri/brain.mgz  mri/orig.mgz
mri/wmparc.mgz:colormap=lut:opacity=0.2

dmri/dtifit_FA.nii:reg=touch/rusage.mri_ca_register.dat:colormap=heat:heatscale=.2,.2,1
-colorscale -viewport coronal.

It returned with an error message saying: "reading
registration failed". I have looked at the register.dat from the
following link: RegisterDat - Free Surfer Wiki (harvard.edu)

.
My register.dat is nothing like that (attached below). So where
should the file locate?

Best,
Jackie




--

Ph.D. candidate
Icahn School of Medicine at Mount Sinai


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Re: [Freesurfer] Help

[Douglas N. Greve]

Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


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Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, used 
the gcut command and edited manually after autorecon1 but in the end, 
the results don't vary significantly compared to running recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] FREESURFER Recon all not working

[Douglas N. Greve]

Just add -cw256 to the recon-all command line

On 11/23/2021 8:34 AM, Alison McDonnell wrote:


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Hi Tim,

I looked at orig.mgz and it seemed fine and could see the whole head. 
i dont know what is meant by the flag -cw256 error. I am taking over a 
project from someone else so used the same command line as them


Thanks,
Ali

On Tue, 23 Nov 2021 at 13:29, Tim Schäfer > wrote:


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Dear Alison,

Did you already try what is suggested in the error message
(include the flag -cw256 with recon-all and inspect orig.mgz)? If
so, what were the results?

Best,

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

> On 11/23/2021 2:15 PM Alison McDonnell  wrote:
>
>
> External Email - Use Caution
>
> When i run recon all the only thing created is in the mri
folder. all the
> rest are left blank. i have attached all relevant screenshots
including one
> that has the original data being used is in the right format and
right
> place and the recon all log. any advice would be appreciated.
this is being
> done via teamviewer from pc to mac but i cant see why that would
cause any
> issues[image: Xquartz_screenshot.png][image: error_screenshot.png]
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Re: [Freesurfer] Can't load ROI labels

[Douglas N. Greve]

For volumes, load labels using the "Load ROI..." under the File menu
For surfaces, use the "Load" button in the "Label" section

On 11/23/2021 2:44 PM, Shapiro, Noah Lorenz wrote:

Hello,

I am very new to FreeSurfer, and I was going through the tutorials and 
bumped into difficulties when loading ROI's. I can load volumes (e.g. 
orig.mgz) in Freeview; however, I can't load any ROIs. I can select a 
label (e.g. lh.BA45_exvivo.label) and hit "open", but then nothing 
happens. The label doesn't load at all. I don't get an error message 
either. I am using FS version 5.3, and I also tried on FS version 6. 
Quartz is updated. I am running on macOS Big Sur version 11.6. Do you 
have any ideas why I can't load ROI labels? Any help is highly 
appreciated.


Best wishes,
Noah

**

*Noah Shapiro*

Research Technician (II)

Department of Neurology

Alzheimer’s Clinical & Translational Research Unit

Massachusetts General Hospital

149 13^th  Street

Charlestown, Massachusetts02129

E-mail: nlshap...@mgh.harvard.edu


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Re: [Freesurfer] Surface-based smoothing of EPI data

[Douglas N. Greve]

That will work; it may be clearer to use mris_fwhm, eg,
mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i 
input --o output



On 11/26/2021 6:48 AM, Mason Wells wrote:


External Email - Use Caution

Hi Experts,

This question may have been addressed elsewhereon the list, but I 
can’t find a response.


I want to smooth BOLD data on the surface. First, I pre-processed the 
data in FEAT with no smoothing applied. Then I registered the 
filtered_func data to the anatomical using bbregister. I check the 
registration matrix looks good by running this command (using 
example_func as the reference):


  * tkregisterfv --mov example_func.nii.gz --reg junk.dat --lta
reg/freesurfer/anat2exf.register.dat --surfs

I then resampled my data with mri_vol2surf using the following command:

  * mri_vol2surf --src filtered_func_data.nii.gz --out
lh_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat
--hemi lh --projfrac 0.5 --out_type mgh

I then want to smooth this data on the surface. I assume it would be 
best to run mri_surf2surf and set the target and source subject as the 
same? Such as this command:


  * mri_surf2surf --srcsubject sub-0006 --srcsurfreg lh.sphere.reg
--trgsubject srcsubject--trgsurfreg sphere.reg --hemi lh --sval
lh_func_native.mgh--tval lh_func_native_smoothed.mgz --mapmethod
nnf --fwhm 5 --cortex

Please can someone on this list give me some advice on this? Are my 
command suitible and/or am I missing anything?


Best wishes,
Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University 
webpage




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk

*/Ffôn/*: 02920 879628


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Re: [Freesurfer] SynthSR

[AJ]

External Email - Use Caution

Many thanks for this.  My experience so far with SAMSEG, SynthSeg---small
sample so far.  All images were obtained 3DT1 isomeric voxel.  Just wanted
to see how the two pipelines would compare.

2 subjects who went on 6 different clinical scanners, GE or Philips:listed
below.
The coefficient of variation in the structures I'm interested in was:
normalized by the ICV (sbTIV, segmentation based TIV).
*SAMSEG*
interscan sbTIV NBrain-StemNcortical-vol   NPutamen NCaudate
NThalamus
COV 1.620754 1.937988 0.996077 1.971807 1.863897 1.549882

*SynthSEG (normalized to ICV (sbTIV)--which was obtained from running
SAMSEG on synthetic MRI (SynthSR):*
BrainstemCortical vol  PutamenCaudateThalamus
1.48696 1.61017 2.20072 2.51099 2.16196

  Since head size does not change in the short period of time, my test
subjects (n=50) repeated scan x 2 had a sbTIV coefficient of variation of
0.93 based on SAMSEG.
 Across the 6 clinical scanners that I used (listed below), I think there
was enough tissue contrast similarities across the scanners to give a COV
around 2%, which I think is NOT bad.Even in clinical trials with MRIs
performed on the same vendor scanner across different sites, I think the
goal is to produce variability < 2%.

  From what I can see from my data, I think you could compare across
vendors with a reasonable overall COV of around 2%, that is if the
biological effect is > 2% per time of interest.

my best,
AJ

Scanners used for controls and test subjects:
Achieva_TFE_R1
Achieva_TFE_R2
Ingenia_R1
Ingenia_R2
GE_SPGR_1529_R1
GE_SPGR_1529_R2
GE_SPGR_R1
GE_SPGR_R2
Phillip_Achieva_R1
Achieva_R2
GE_R1
GE_R2

On Sun, Nov 28, 2021, 20:41 Douglas N. Greve  wrote:

> Also samseg, see 
> https://secure-web.cisco.com/1vp8CpJRiQKmY2Jw2cEv7mIT6pEjTqFspCV00PtwvCROFBQ4enl56APRMm5vjCelLMOKTLsWx15btdt_HhgYgXyFx2liCxCnsyVuAie9mcFQKtBWyJCW52VClhUXJEaUpXlqzWLs5daHkP5TL9dUJ-iBFLSAzyXGsJH2wtHdkKGTDzh-wbeUSOVjMBNN73JLXj1DWaZd5PYDBBRcyuOXcE7q8qgXcZRkUXTWsCZ-QxenmUNJo0I-ZX_TRRmRXTl2iSj4S3VgFkY6HpZvnCw2QDxv6kepjoXi0vDAV9exqeEr_0pudttpPAtIHJVBeurZP/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F33940143%2F
>
> On 11/26/2021 11:16 AM, Fischl, Bruce wrote:
>
> Hi AJ
>
> you might try SynthSeg, as that is one of the advantages of it - it isn't
> biased towards any particular MRI sequence
>
> cheers
> Bruce
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> 
>  on behalf of AJ
>  
> *Sent:* Thursday, November 25, 2021 9:00 PM
> *To:* Freesurfer support list 
> 
> *Subject:* [Freesurfer] SynthSR
>
>
> External Email - Use Caution
> Hi,
> Could synthetic MRIs generated by the SynthSR script be potentially used
> to harmonize T1w weighted images acquired on different scanners?  Then used
> harmonized images for volumetric analyses?
> Many thanks
> AJ
>
> ___
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>
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Re: [Freesurfer] fsaverage_sym lobes parcellation mri_annotation2label

[Douglas N. Greve]

This is a bug. I've put a new version of mri_annotation2label here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/
username 'guest'
password 'collab'

copy it into $FREESUFER/bin (after making a copy of the one that is there).


On 11/22/2021 12:23 PM, Dr. Cornelius Kronlage wrote:
>  External Email - Use Caution
>
> Dear freesurfer community,
>
> when trying to obtain lobe labels for fsaverage_sym, mri_annotation2label 
> segfaults - see terminal output below. It works smoothly for fsaverage and 
> any other subjects. Is there any workaround?
>
>> mri_annotation2label --subject fsaverage_sym --hemi lh --lobes 
>> fsaverage_sym_lh.lobes.annot
> subject = fsaverage_sym
> annotation = aparc
> hemi = lh
> surface   = white
>
> Reading surface
>   /home/ckronlage/epi/DATA/tmp4_working//fsaverage_sym/surf/lh.white
> Loading annotations from 
> /home/ckronlage/epi/DATA/tmp4_working//fsaverage_sym/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 1036 entries read (originally 
> /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
> Seg base 1000
> MRISmergeAnnotations: parcCount=10, newparcname=frontal
> mri_annotation2 supposed to be reproducible but seed not set
> Segmentation fault (core dumped)
> Thank you and
> best wishes
> Cornelius
>
>
>
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Re: [Freesurfer] SynthSR

[Douglas N. Greve]

Are you correcting for gradient distortion? That could easily make 2%. 
It looks like you used different ROIs in your comparisons.


On 11/28/2021 10:14 PM, AJ wrote:


External Email - Use Caution

Many thanks for this.  My experience so far with SAMSEG, 
SynthSeg---small sample so far.  All images were obtained 3DT1 
isomeric voxel.  Just wanted to see how the two pipelines would compare.


2 subjects who went on 6 different clinical scanners, GE or 
Philips:listed below.
The coefficient of variation in the structures I'm interested in was:  
normalized by the ICV (sbTIV, segmentation based TIV).

*SAMSEG*
interscan 	sbTIV 	NBrain-Stem 	   Ncortical-vol 	  NPutamen 	    
NCaudate 	   NThalamus

COV 1.6207541.9379880.9960771.971807
1.8638971.549882


*SynthSEG (normalized to ICV (sbTIV)--which was obtained from running 
SAMSEG on synthetic MRI (SynthSR):*

Brainstem      Cortical vol  Putamen   Caudate     
Thalamus
1.48696 1.61017 2.20072 2.51099 2.16196


  Since head size does not change in the short period of time, my test 
subjects (n=50) repeated scan x 2 had a sbTIV coefficient of variation 
of 0.93 based on SAMSEG.
 Across the 6 clinical scanners that I used (listed below), I think 
there was enough tissue contrast similarities across the scanners to 
give a COV around 2%, which I think is NOT bad.    Even in clinical 
trials with MRIs performed on the same vendor scanner across different 
sites, I think the goal is to produce variability < 2%.


  From what I can see from my data, I think you could compare across 
vendors with a reasonable overall COV of around 2%, that is if the 
biological effect is > 2% per time of interest.


my best,
AJ

Scanners used for controls and test subjects:
Achieva_TFE_R1
Achieva_TFE_R2
Ingenia_R1  
Ingenia_R2  
GE_SPGR_1529_R1
GE_SPGR_1529_R2
GE_SPGR_R1
GE_SPGR_R2
Phillip_Achieva_R1
Achieva_R2
GE_R1   
GE_R2


On Sun, Nov 28, 2021, 20:41 Douglas N. Greve  
wrote:


Also samseg, see *MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be*
https://pubmed.ncbi.nlm.nih.gov/33940143/



On 11/26/2021 11:16 AM, Fischl, Bruce wrote:

Hi AJ

you might try SynthSeg, as that is one of the advantages of it -
it isn't biased towards any particular MRI sequence

cheers
Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu

 on behalf of AJ
 
*Sent:* Thursday, November 25, 2021 9:00 PM
*To:* Freesurfer support list 

*Subject:* [Freesurfer] SynthSR

External Email - Use Caution

Hi,
Could synthetic MRIs generated by the SynthSR script be
potentially used to harmonize T1w weighted images acquired on
different scanners? Then used harmonized images for volumetric
analyses?
Many thanks
AJ

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The information in this e-mail is inten

Re: [Freesurfer] FREESURFER Recon all problem

[Douglas N. Greve]

If they are not part of the T1w series, then you can delete them (but 
then they should not have caused the error). If they are part of the 
series, then they are probably corrupted or perhaps the output of a very 
aggressive anonymization.


On 11/25/2021 8:40 AM, Alison McDonnell wrote:


External Email - Use Caution

Hi
I tried to running recon all on a large amount of data and got the 
below error message. the listed files that say the tag image 
orientation can't be found aer in the folder but seem to be blank. i 
was wondering is there a way to run recon all and skip/ignore those 
seemingly blank files or should i delete them from the folder?


Thanks
error_message.png

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Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] SynthSR

[AJ]

External Email - Use Caution

These are the same ROIs, just labeled differently by me late at night. They
are all normalized by the ICV.  Just didn't  add the N next to the ROI in a
different row.

Good point.  I am not correcting for gradient distortions.  Will do.

Many thanks
AJ

On Sun, Nov 28, 2021, 21:40 Douglas N. Greve  wrote:

> Are you correcting for gradient distortion? That could easily make 2%. It
> looks like you used different ROIs in your comparisons.
>
> On 11/28/2021 10:14 PM, AJ wrote:
>
> External Email - Use Caution
> Many thanks for this.  My experience so far with SAMSEG, SynthSeg---small
> sample so far.  All images were obtained 3DT1 isomeric voxel.  Just wanted
> to see how the two pipelines would compare.
>
> 2 subjects who went on 6 different clinical scanners, GE or Philips:listed
> below.
> The coefficient of variation in the structures I'm interested in was:
> normalized by the ICV (sbTIV, segmentation based TIV).
> *SAMSEG*
> interscan sbTIV NBrain-StemNcortical-vol   NPutamen NCaudate
> NThalamus
> COV 1.620754 1.937988 0.996077 1.971807 1.863897 1.549882
>
> *SynthSEG (normalized to ICV (sbTIV)--which was obtained from running
> SAMSEG on synthetic MRI (SynthSR):*
> BrainstemCortical vol  PutamenCaudateThalamus
> 1.48696 1.61017 2.20072 2.51099 2.16196
>
>   Since head size does not change in the short period of time, my test
> subjects (n=50) repeated scan x 2 had a sbTIV coefficient of variation of
> 0.93 based on SAMSEG.
>  Across the 6 clinical scanners that I used (listed below), I think there
> was enough tissue contrast similarities across the scanners to give a COV
> around 2%, which I think is NOT bad.Even in clinical trials with MRIs
> performed on the same vendor scanner across different sites, I think the
> goal is to produce variability < 2%.
>
>   From what I can see from my data, I think you could compare across
> vendors with a reasonable overall COV of around 2%, that is if the
> biological effect is > 2% per time of interest.
>
> my best,
> AJ
>
> Scanners used for controls and test subjects:
> Achieva_TFE_R1
> Achieva_TFE_R2
> Ingenia_R1
> Ingenia_R2
> GE_SPGR_1529_R1
> GE_SPGR_1529_R2
> GE_SPGR_R1
> GE_SPGR_R2
> Phillip_Achieva_R1
> Achieva_R2
> GE_R1
> GE_R2
>
> On Sun, Nov 28, 2021, 20:41 Douglas N. Greve 
> wrote:
>
>> Also samseg, see *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1cS13xAGgITfUHMGUyFsvweyVHbmcsaFQ23MTyl96k0V_BXD-oDHReEm2IXNR2eu7Pzj0jjh-1HcIJisCPg76g1WGEmZbfGm0rwdrTIyi6Atj0OeeJe2RtBYeGGnuEAEHxJrRrHanvrRcJrwyCrBuSirjC42m6ffbl66cAJYHeSp8UiBz_yBmUspGNjiqI_2cWJw9oUPGYvx_M_nzhx8yxfRz1Ne12ZzoCWAdn18whA4dnUHfFQHA3kXWbBR0R_IYHqsIkHU7R8LSGkGQRh9Fcmo4j9Es1Z4UIccpgqGmFkbxZHK34e0qsiGidAY94p12/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F33940143%2F
>> 
>>
>> On 11/26/2021 11:16 AM, Fischl, Bruce wrote:
>>
>> Hi AJ
>>
>> you might try SynthSeg, as that is one of the advantages of it - it isn't
>> biased towards any particular MRI sequence
>>
>> cheers
>> Bruce
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> 
>>  on behalf of AJ
>>  
>> *Sent:* Thursday, November 25, 2021 9:00 PM
>> *To:* Freesurfer support list 
>> 
>> *Subject:* [Freesurfer] SynthSR
>>
>>
>> External Email - Use Caution
>> Hi,
>> Could synthetic MRIs generated by the SynthSR script be potentially used
>> to harmonize T1w weighted images acquired on different scanners?  Then used
>> harmonized images for volumetric analyses?
>> Many thanks
>> AJ
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1QhFmTXCfi2HiS1aDKz0TMt25WAH7a67WZbOPeg-vsSYv3JBlQzxHVVFtEfhUzti6zjuN7Bq3GD1lC2zuBhn9MR8HKtt-GAWYUjwTyvL0cwRhmm3LQ_o5DgaTU2rp6YlAtx7ilcSbDVPqGmf3Gzw6hizAXLnJXaJPl5UFW6Wkj_J-pMBhwCaVRS8WZHNSmAhQgUacaRxYfj4ePteCIRJqK6KzvPfXSaSNM3VzBA0eiWk9fWmIz3X90g6k_rbmXV_Hb1v8NaVA6Gp7CA-5YN9sW75ShStu84XruOYxWyrjcQCWBaSoelZX94AT-LHJx1XN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> 

[Freesurfer] Visualization error in freeview from recon-all

[achille.teillac]

External Email - Use Caution

Dear experts,

We are working with a large MRI dataset (FLAIR, T1) and we are performing 
recon-all based on the 3D T1. At the end, no error is detected but the 
visualization of the pial, white and inflated surfaces in freeview is somehow 
bad as you can see on the picture attached (lh.pial_freeview, 
lh.white_freeview, lh.inflated_freeview). Can it be an error that I missed and 
is there a way to correct it ? Or could it be a 3D rendering issue that can be 
fixed with visualization options ? Oddly, when I zoom really close for all 
surfaces, it seems perfectly smoothed... I thought first it could be linked to 
the topological defect correction (which I didn't do) but when I display the 
surfaces with paraview it works fine as you can also see on the picture 
attached (lh.pial_paraview, lh.white_paraview, lh.inflated_paraview). 
Everything works fine otherwise.

Thanks in advance for any help you may provide and I can send you some 
screenshots highlightening the issue or the recon-all log.

Best,

Achille Teillac
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