External Email - Use Caution        

Dear Freesurfer experts,

Many thanks for your prompt reply and all the helpful information.
Below are few remaining questions I have (in red), based on your responses.

Many thanks again,

Pilar


Dear Freesurfer experts,

We are conducting a PETSurfer analysis, and have some questions on the best way to proceed.  Briefly, this is what we have done:

After running the standard Freesurfer analysis an all the T1 images, we have generated the segmentation for the GTM.
Afterwards, we have registered the PET images with the anatomicals, obtaining the template.reg.lta.
To check the preliminary results without any PVC, we have used the template.reg.lta to sample the PET volume onto the surface, with the following command:
 mri_vol2surf --mov subject_PET.nii \
 --reg subject_template.reg.lta \
 --projfrac 0.5 --interp nearest \
 --hemi lh --o lh.sig.mgh

We therefore obtained the lh.sig.mgh

First question. Is this procedure correct?
Yes (though you should always check the reg.lta with tkregisterfv). Also, why are you calling the output lh.sig.mgh? My question is about "sig"; it is not wrong to call it this, but "sig" is usually reserved for significance files and I wanted to make sure you were not confused by it. 

Yep yep, sorry I’ve forgotten to specify we also checked the reg.lta for each subject with tkregisterfv. As regards the name of the output you are totally right, we just called it in this way cause we found an example of the mri_vol2surf command application which used this name for the output, but yeah, without any significance it would be more appropriate to call the output in a different way to avoid any confusion.

Second question. Is the format of the of the output (.mgh) correct?
Any format (mgh, mgz, nifti) is ok. 

Perfect, thanks, but it is unclear to me which would be the best way to visualize this output (and this aspect might influence the type of format we would choose). Do you have any suggestions?


In the wiki it is reported that: “If you are not using PVC, you can use the template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, then apply standard surface-based analysis”.

Third question. At this point should we directly run the mri_glmfit with the previously obtained lh.sig.mgh?
This is probably not right. You  will need to run the mri_vol2surf command above for each subject to generate an output (and using --trgsubject fsaverage to put them into the same space), then concatenate all into one file (mri_concat lh.subj1.mgh lh.subj2.mgh ... --o lh.all.mgh), then possibly smooth (mris_fwhm), then feed that output as input to mri_glmfit.

Sounds good, I’ll proceed in this way. Only one remaining question. Is it really ok to smooth even if it creates PV effects? 

Many thanks as always for the precious help,

Pilar







Like in this way:

 mri_glmfit \
 --y lh.sig.mgh \
 --fsgd fsgd file dods\
 --C cor.mtx file \
--surf fsaverage lh \  
--cortex \
--glmdir glmdir

Many thanks for any information you’ll be able to provide,

 Best,

Pilar Maria Ferraro




Il giorno 15 apr 2020, alle ore 5:18 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:

Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. Re: Trac-All Error (Hua, Jessica)
  2. Re: Compiling Freesurfer 6 on Centos7 Install not working due
     to annex files missing (Hoopes, Andrew)
  3. FreeSurfer UbuntuVM password (sapere-aude@tuta.io)
  4. Re: FreeSurfer UbuntuVM password (fsbuild)
  5. Re: [External] Re: Freesurfer display resolution very low
     compared to other viewers (Ruopeng Wang)
  6. Re: [External] Re: Freesurfer display resolution very low
     compared to other viewers (Douglas N. Greve)
  7. Re: [External] Re: Freesurfer display resolution very low
     compared to other viewers (Renner, Brian)
  8. Re: Trac-All Error (Yendiki, Anastasia)
  9. Re: Error in Tracula-all -prep (Salah Showiheen)
 10. Question on using T2 or FLAIR data to improve pial surfaces
     (Tim Sch?fer)
 11. Data onto the Freesurfer surface (Mason Wells)
 12. Manipulating MRI volume data in Matlab (Safi Ullah .)


----------------------------------------------------------------------

Message: 1
Date: Tue, 14 Apr 2020 20:38:52 +0000
From: "Hua, Jessica" <jphc55@mail.missouri.edu>
Subject: Re: [Freesurfer] Trac-All Error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>,
"AYENDIKI@mgh.harvard.edu" <AYENDIKI@mgh.harvard.edu>
Message-ID:
<BY5PR01MB56524C9896B67B67B00E48AE93DA0@BY5PR01MB5652.prod.exchangelabs.com>

Content-Type: text/plain; charset="iso-8859-1"

       External Email - Use Caution        

Attached are bvecs and bvals.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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------------------------------

Message: 2
Date: Tue, 14 Apr 2020 20:40:35 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] Compiling Freesurfer 6 on Centos7 Install
not working due to annex files missing
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"jn63@nyu.edu" <jn63@nyu.edu>
Message-ID: <99CCA833-A66F-4C89-9727-A87335FFCDAD@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Jorge,

Some v6.0 binary data must have been pruned from the public server. I just synced it all back, so now you should be able to download the extra files with:

git fetch datasrc
git annex get .

Sorry about that. Glad to see you got everything else working ? compiling 6.0 externally is not an easy task nowadays!

best
Andrew


From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jorge Naranjo <jn63@nyu.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 8, 2020 at 6:18 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Compiling Freesurfer 6 on Centos7 Install not working due to annex files missing


       External Email - Use Caution
Hi all

I?m building Freesurfer version 6 (stable6 branch) in a fresh centos7 OS


git clone https://github.com/freesurfer/freesurfer.git

cd freesurfer

git checkout stable6

git remote add datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git

git fetch datasrc

git annex get --metadata fstags=makeinstall .

I do this since the options in the wiki using CMAKE and everything don?t work for this version and BTW I can?t find the instruction to build it in Linux anymore. I don?t know if this instructions were removed or what

After some small tweaks in the configure and packages I do:

./setup_configure


./configure --with-cuda=/usr/local/cuda/lib64  --enable-openmp --disable-Wall --disable-Werror --enable-emu LDFLAGS=-lQt5X11Extras CFLAGS=-fpermissive CXXFLAGS=-fpermissive  --disable-Werror --with-pkgs-dir=/opt/freesurfer/packages  --prefix=/share/apps/NYUAD4/freesurfer/6/  --with-cppunit-dir=/usr --with-itk-dir=/opt/freesurfer/packages/itk/3.16.0/  --with-vtk-dir=/opt/freesurfer/packages/vtk/5.6.0/  --with-gts-dir=/opt/freesurfer/packages/gts/0.7.6/ --with-ann-dir=/opt/freesurfer/packages/ann/1.1.2/ --with-petsc-dir=/opt/freesurfer/packages/petsc/2.3.3/ --with-mni-dir=/opt/freesurfer/packages/mni/current/ --with-mpi-dir=/usr/lib64/openmpi/ --with-vxl-dir=/opt/freesurfer/packages/vxl/1.14.0 --with-kwwidgets-dir=/opt/freesurfer/packages/KWWidgets/5.6.0


make

Up to this point, everything goes OK!

Now the "make install" fails:


/bin/install: cannot stat ?face.gca?: No such file or directory

/bin/install: cannot stat ?talairach_mixed_with_skull.gca?: No such file or directory

/bin/install: cannot stat ?wmsa_new_eesmith.gca?: No such file or directory

/bin/install: cannot stat ?aseg+spmhead.ixi.gca?: No such file or directory

/bin/install: cannot stat ?aseg+spmhead+vermis+pons.ixi.gca?: No such file or directory

/bin/install: cannot stat ?pons.mni152.2mm.mgz?: No such file or directory

/bin/install: cannot stat ?lh.atlas2002_simple.gcs?: No such file or directory

/bin/install: cannot stat ?lh.atlas2005_simple.gcs?: No such file or directory

/bin/install: cannot stat ?lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs?: No such file or directory

/bin/install: cannot stat ?lh_trans_toSulc.gcs?: No such file or directory

/bin/install: cannot stat ?lh.destrieux.simple.2009-07-29.gcs?: No such file or directory

/bin/install: cannot stat ?rh.atlas2002_simple.gcs?: No such file or directory

/bin/install: cannot stat ?rh.atlas2005_simple.gcs?: No such file or directory

/bin/install: cannot stat ?rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs?: No such file or directory

/bin/install: cannot stat ?rh_trans_toSulc.gcs?: No such file or directory

/bin/install: cannot stat ?rh.destrieux.simple.2009-07-29.gcs?: No such file or directory

/bin/install: cannot stat ?rh.DKTatlas40.gcs?: No such file or directory

/bin/install: cannot stat ?lh.DKTatlas40.gcs?: No such file or directory

/bin/install: cannot stat ?rh.DKTatlas100.gcs?: No such file or directory

/bin/install: cannot stat ?lh.DKTatlas100.gcs?: No such file or directory

/bin/install: cannot stat ?lh.average.curvature.filled.buckner40.tif?: No such file or directory

/bin/install: cannot stat ?lh.average.CURVATURE.tif?: No such file or directory

/bin/install: cannot stat ?lh.average.tif?: No such file or directory

/bin/install: cannot stat ?rh.average.curvature.filled.buckner40.tif?: No such file or directory

/bin/install: cannot stat ?rh.average.CURVATURE.tif?: No such file or directory

/bin/install: cannot stat ?rh.average.tif?: No such file or directory

/bin/install: cannot stat ?rigidly_aligned_brain_template.tif?: No such file or directory

/bin/install: cannot stat ?label_scales.dat?: No such file or directory

/bin/install: cannot stat ?mni305.cor.mgz?: No such file or directory

/bin/install: cannot stat ?mni305.mask.cor.mgz?: No such file or directory

/bin/install: cannot stat ?mni305.cor.subfov1.mgz?: No such file or directory

/bin/install: cannot stat ?mni305.cor.subfov2.mgz?: No such file or directory

/bin/install: cannot stat ?mni305.cor.subfov1.reg?: No such file or directory

/bin/install: cannot stat ?mni305.cor.subfov2.reg?: No such file or directory

/bin/install: cannot stat ?mni152.register.dat?: No such file or directory

/bin/install: cannot stat ?mni152.mni305.cor.subfov1.dat?: No such file or directory

/bin/install: cannot stat ?mni152.mni305.cor.subfov2.dat?: No such file or directory

make[2]: *** [install] Error 1

The problem arises when moving to the stable6 branch, and I need that one.

I tried what suggested here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51895.html


 $> git annex get distribution/average/mult-comp-cor.tar.gz

 $> make install



But didn?t work either



Any help??



Thanks in advance

Jorge A. Naranjo
Senior HPC Computational Specialist
NYU Abu Dhabi
Office Tel (UAE): +971 2 628 4750
Mobile (UAE): +971 56 319 2814
New York University - Abu Dhabi (NYUAD)
Saadiyat Campus - A2, Room-131
P.O. Box 129188
Abu Dhabi, United Arab Emirates

http://nyuad.nyu.edu<http://nyuad.nyu.edu/>
Please consider the environment before printing this email.
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------------------------------

Message: 3
Date: Tue, 14 Apr 2020 22:53:28 +0200 (CEST)
From: sapere-aude@tuta.io
Subject: [Freesurfer] FreeSurfer UbuntuVM password
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <M4uSxmC--3-2@tuta.io>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

Hi,


the FreeSurfer Ubuntu VirtualBox Virtual Machine asks for a password to log in (see the attached image).
I can't find any information about what this password is on the tutorial page:

https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_win

Could anyone help me with the password to the VM?


kind regards,
Sapere-Aude
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------------------------------

Message: 4
Date: Tue, 14 Apr 2020 22:59:00 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] FreeSurfer UbuntuVM password
To: freesurfer@nmr.mgh.harvard.edu
Cc: sapere-aude@tuta.io
Message-ID: <1586897940.5e962414c022d@trashmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

I will send it directly to your email in a minute.
R.

On Apr 14, 2020, at 16:53, sapere-aude@tuta.io wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi,the FreeSurfer Ubuntu VirtualBox Virtual Machine asks for a password to log in (see the attached image).I can't find any information about what this password is on the tutorial page:https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_winCould anyone help me with the password to the VM?kind regards,Sapere-Aude&lt;Ubuntu password.PNG&gt;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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------------------------------

Message: 5
Date: Tue, 14 Apr 2020 16:59:22 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution
very low compared to other viewers
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <0EB085F5-24A0-4F73-A9DC-1F2CAD75BAA7@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Brian,

I honestly can?t tell the difference, even when the high dpi rendering is turned on. The volume is low res to begin with. There is a smooth display check box you can try in freeview. It will remove the pixelation of the rendering.

Best
Ruopeng

On Apr 14, 2020, at 4:28 PM, Renner, Brian <Brian.Renner@cshs.org> wrote:

       External Email - Use Caution        
Hi Rupoeng!

Attached is a direct flair opening in same without flags, freeview (L) fsleyes (R), set with 0-168 min-max for each window (fig 1). I did notice a tick box in fsleyes was set to "render in high DPI" was checked (fig 2), so I unchecked it for fig 1.

<Screen Shot 2020-04-14 at 1.27.06 PM.png>
fig 1

<Screen Shot 2020-04-14 at 1.23.18 PM.png>
fig 2.

Perhaps that is the culprit; is there a similar render mode for freeview or is that the driver not optimized as Andrew previously wrote?

Much thanks all!

BR
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Sent: Tuesday, April 14, 2020 11:10 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers

Hi Brian,

Can you load a single volume in freeview to compare? Maybe also use similar window/level? The one in the picture appears smoothed to me (may due to trilinear sampling if it is not the first loaded volume).

Best,
Ruopeng


On Apr 14, 2020, at 1:14 PM, Renner, Brian <Brian.Renner@cshs.org <mailto:Brian.Renner@cshs.org>> wrote:

       External Email - Use Caution        
Hey Andrew;

Thanks for the response! To answer your questions, yes, We?re all respectively on Macbook Pro retina displays. I hadn't compared the visualization on a Windows machine, though I ostensibly could in the near future. I have loaded up single vs. multiple volumes and noticed what you say; would it be best to load the hypothetical highest resolution scan first? ie. freeview -v highest.nii lower.nii. lowest.nii. --trilinear?

An example picture of this is shown below, with a standard 1mm^3 t2 flair loaded in freeview with a higher resolution t2* as the first loaded scan, ie. on the left freeview -v t2*file flair --trilinear vs. fsleyes t2*file flair on the right:

<Screen Shot 2020-04-14 at 9.40.57 AM.png>
Fig 1. This is the flair file compared side by side (fv --trilinear vs. fsleyes, respectively).

<Screen Shot 2020-04-14 at 9.43.58 AM.png>
Fig 2. This is the t2*file (0.65mm voxel width), which has both noticeable quality drop and a different baseline intensity threshold at baseline between freeview and fsleyes.

<Screen Shot 2020-04-14 at 10.00.10 AM.png>
Fig 3. This is the flair --trilinear vs. flair (noflags) vs. fsleyes flair, respectively.

Let me know what you think, and again thank you for the response!

BR

From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu <mailto:AHOOPES@mgh.harvard.edu>>
Sent: Tuesday, April 14, 2020 9:25:08 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Freesurfer display resolution very low compared to other viewers

Hi Brian,

A couple questions - are you visualizing on a mac retina screen? If so, there will be a slight decrease from the standard resolution because the underlying rendering library that we use unfortunately does not support retina capabilities at this time. Also, are you loading single or multiple volumes? Freeview uses the first volume loaded as the base image geometry, and all the following volumes are resampled (if necessary) into this base geometry using nearest neighbor interpolation. So if you?re working with different-resolution images, it might help to enable linear interpolation as the default resampling method by using the `--trilinear` freeview flag. If that?s not the case, it?d be helpful to see a couple screenshots of the issue.

Hope that helps,
Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Renner, Brian" <Brian.Renner@cshs.org <mailto:Brian.Renner@cshs.org>>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 13, 2020 at 8:54 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer display resolution very low compared to other viewers

       External Email - Use Caution        
Hello all!

Inaugural message to the list; I will attempt to be brief with the project description.

The setup is consistent between both versions 6.0.0 and 7.0.0-beta, run on a high performance cluster, accessed through macOS terminal + Xquartz, most recent versions all.

As it stands, our group is attempting to do subfield analysis of hippocampal analysis and lesion measurement in MS subjects. We have noticed that there is a major discrepancy of resolutions between files, which has irked some of our physicians undertaking the lesion measurement. We need to resolve the lesions down to 3mm and have noticed the quality between freeview and fsleyes of the same nifti files will yield much lower display resolution. This is true for most scans, though it has been compared using 1mm T2 FLAIR sequences as well as T2* sequences with 0.65mm voxel space. I have been attempting to find a workaround as the current solution for the physicians is to look at the files in fsleyes and then measure them with the ruler tool in freeview. I can send supporting pictures as necessary.

Thank you in advance for any thoughts you may have!

BR

--
Brian Renner, MD
Research Associate, Neurology
brian.renner@cshs.org <mailto:brian.renner@cshs.org>

Cedars-Sinai
127 S. San Vicente Blvd, Suite A6600  :  Los Angeles CA 90048
office 310-423-1589  :  mobile 310-658-3492  :  cedars-sinai.org <https://www.cedars-sinai.org/>



IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
<Screen Shot 2020-04-14 at 9.40.57 AM.png>_______________________________________________
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Message: 6
Date: Tue, 14 Apr 2020 17:09:27 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution
very low compared to other viewers
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <41d1740d-2018-5e12-29bf-13fa7449e173@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I could not tell a difference either.

On 4/14/2020 4:59 PM, Ruopeng Wang wrote:
Hi Brian,

I honestly can?t tell the difference, even when the high dpi rendering
is turned on. The volume is low res to begin with. There is a smooth
display check box you can try in freeview. It will remove the
pixelation of the rendering.

Best
Ruopeng

On Apr 14, 2020, at 4:28 PM, Renner, Brian <Brian.Renner@cshs.org
<mailto:Brian.Renner@cshs.org>> wrote:

????????External Email - Use Caution
Hi Rupoeng!

Attached is a direct flair opening in same without flags, freeview
(L) fsleyes (R), set with 0-168 min-max for each window (fig 1). I
did notice a tick box in fsleyes was set to "render in high DPI" was
checked (fig 2), so I unchecked it for fig 1.

<Screen Shot 2020-04-14 at 1.27.06 PM.png>
fig 1

<Screen Shot 2020-04-14 at 1.23.18 PM.png>
fig 2.

Perhaps that is the culprit; is there a similar render mode for
freeview or is that the driver not optimized as Andrew previously wrote?

Much thanks all!

BR
------------------------------------------------------------------------
*From:*freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Ruopeng
Wang <rpwang@nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>>
*Sent:*Tuesday, April 14, 2020 11:10 AM
*To:*Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*Re: [Freesurfer] [External] Re: Freesurfer display
resolution very low compared to other viewers
Hi Brian,

Can you load a single volume in freeview to compare? Maybe also use
similar window/level? The one in the picture appears smoothed to me
(may due to trilinear sampling if it is not the first loaded volume).

Best,
Ruopeng


On Apr 14, 2020, at 1:14 PM, Renner, Brian <Brian.Renner@cshs.org
<mailto:Brian.Renner@cshs.org>> wrote:

????????External Email - Use Caution
Hey Andrew;

Thanks for the response! To answer your questions, yes, We?re all
respectively on Macbook Pro retina displays. I hadn't compared the
visualization on a Windows machine, though I ostensibly could in the
near future. I have loaded up single vs. multiple volumes and
noticed what you say; would it be best to load the hypothetical
highest resolution scan first? ie. freeview -v highest.nii
lower.nii. lowest.nii. --trilinear?

An example picture of this is shown below, with a standard 1mm^3 t2
flair loaded in freeview with a higher resolution t2* as the first
loaded scan, ie. on the left freeview -v t2*file flair --trilinear
vs. fsleyes t2*file flair on the right:

<Screen Shot 2020-04-14 at 9.40.57 AM.png>
Fig 1. This is the flair file compared side by side (fv --trilinear
vs. fsleyes, respectively).

<Screen Shot 2020-04-14 at 9.43.58 AM.png>
Fig 2. This is the t2*file (0.65mm voxel width), which has both
noticeable quality drop and a different baseline intensity threshold
at baseline between freeview and fsleyes.

<Screen Shot 2020-04-14 at 10.00.10 AM.png>
Fig 3. This is the flair --trilinear vs. flair (noflags) vs. fsleyes
flair, respectively.

?Let me know what you think, and again thank you for the response!

BR

------------------------------------------------------------------------
*From:*freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of
Hoopes, Andrew <AHOOPES@mgh.harvard.edu
<mailto:AHOOPES@mgh.harvard.edu>>
*Sent:*Tuesday, April 14, 2020 9:25:08 AM
*To:*Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*[External] Re: [Freesurfer] Freesurfer display resolution
very low compared to other viewers
Hi Brian,

A couple questions - are you visualizing on a mac retina screen? If
so, there will be a slight decrease from the standard resolution
because the underlying rendering library that we use unfortunately
does not support retina capabilities at this time. Also, are you
loading single or multiple volumes? Freeview uses the first volume
loaded as the base image geometry, and all the following volumes are
resampled (if necessary) into this base geometry using nearest
neighbor interpolation. So if you?re working with
different-resolution images, it might help to enable linear
interpolation as the default resampling method by using the
`--trilinear` freeview flag. If that?s not the case, it?d be helpful
to see a couple screenshots of the issue.

Hope that helps,
Andrew

*From:*<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of
"Renner, Brian" <Brian.Renner@cshs.org <mailto:Brian.Renner@cshs.org>>
*Reply-To:*FS Help <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Date:*Monday, April 13, 2020 at 8:54 PM
*To:*FS Help <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*[Freesurfer] Freesurfer display resolution very low
compared to other viewers

*????????External Email - Use Caution *
Hello all!

Inaugural message to the list; I will attempt to be brief with the
project description.

The setup is consistent between both versions 6.0.0 and 7.0.0-beta,
run on a high performance cluster, accessed through macOS terminal +
Xquartz, most recent versions all.

As it stands, our group is attempting to do subfield analysis of
hippocampal analysis and lesion measurement in MS subjects. We have
noticed that there is a major discrepancy of resolutions between
files, which has irked some of our physicians undertaking the lesion
measurement. We need to resolve the lesions down to 3mm and have
noticed the quality between freeview and fsleyes of the same nifti
files will yield much lower display resolution. This is true for
most scans, though it has been compared using 1mm T2 FLAIR sequences
as well as T2* sequences with 0.65mm voxel space. I have been
attempting to find a workaround as the current solution for the
physicians is to look at the files in fsleyes and then measure them
with the ruler tool in freeview. I can send supporting pictures as
necessary.

Thank you in advance for any thoughts you may have!

BR

--
*Brian Renner, MD*
*Research Associate, Neurology*
brian.renner@cshs.org <mailto:brian.renner@cshs.org>

*Cedars-Sinai*
127 S. San Vicente Blvd, Suite A6600??:??Los Angeles?CA?90048
office 310-423-1589??:??mobile 310-658-3492? : cedars-sinai.org
<https://www.cedars-sinai.org/>



IMPORTANT WARNING: This message is intended for the use of the
person or entity to which it is addressed and may contain
information that is privileged and confidential, the disclosure of
which is governed by applicable law. If the reader of this message
is not the intended recipient, or the employee or agent responsible
for delivering it to the intended recipient, you are hereby notified
that any dissemination, distribution or copying of this information
is strictly prohibited. Thank you for your cooperation.
<Screen Shot 2020-04-14 at 9.40.57
AM.png>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Message: 7
Date: Wed, 15 Apr 2020 00:45:27 +0000
From: "Renner, Brian" <Brian.Renner@cshs.org>
Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution
very low compared to other viewers
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BY5PR01MB59226EF9D2161E4406B329A3FDDB0@BY5PR01MB5922.prod.exchangelabs.com>

Content-Type: text/plain; charset="windows-1252"

       External Email - Use Caution        

Thanks all; I've added --trilinear --smoothing and --contrast so the images run with them natively. I agree with some calibration they actually do look similar. A question: is there some basis for which level/window values are loaded? The initial image comes up very saturated, though is corrected by raising both of these levels significantly.

I will update if I hear more from my side. Thank you, both!

BR
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, April 14, 2020 2:09 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers

I could not tell a difference either.

On 4/14/2020 4:59 PM, Ruopeng Wang wrote:
Hi Brian,

I honestly can?t tell the difference, even when the high dpi rendering is turned on. The volume is low res to begin with. There is a smooth display check box you can try in freeview. It will remove the pixelation of the rendering.

Best
Ruopeng

On Apr 14, 2020, at 4:28 PM, Renner, Brian <Brian.Renner@cshs.org<mailto:Brian.Renner@cshs.org>> wrote:

       External Email - Use Caution
Hi Rupoeng!

Attached is a direct flair opening in same without flags, freeview (L) fsleyes (R), set with 0-168 min-max for each window (fig 1). I did notice a tick box in fsleyes was set to "render in high DPI" was checked (fig 2), so I unchecked it for fig 1.

<Screen Shot 2020-04-14 at 1.27.06 PM.png>
fig 1

<Screen Shot 2020-04-14 at 1.23.18 PM.png>
fig 2.

Perhaps that is the culprit; is there a similar render mode for freeview or is that the driver not optimized as Andrew previously wrote?

Much thanks all!

BR
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu<mailto:rpwang@nmr.mgh.harvard.edu>>
Sent: Tuesday, April 14, 2020 11:10 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers

Hi Brian,

Can you load a single volume in freeview to compare? Maybe also use similar window/level? The one in the picture appears smoothed to me (may due to trilinear sampling if it is not the first loaded volume).

Best,
Ruopeng


On Apr 14, 2020, at 1:14 PM, Renner, Brian <Brian.Renner@cshs.org<mailto:Brian.Renner@cshs.org>> wrote:

       External Email - Use Caution
Hey Andrew;

Thanks for the response! To answer your questions, yes, We?re all respectively on Macbook Pro retina displays. I hadn't compared the visualization on a Windows machine, though I ostensibly could in the near future. I have loaded up single vs. multiple volumes and noticed what you say; would it be best to load the hypothetical highest resolution scan first? ie. freeview -v highest.nii lower.nii. lowest.nii. --trilinear?

An example picture of this is shown below, with a standard 1mm^3 t2 flair loaded in freeview with a higher resolution t2* as the first loaded scan, ie. on the left freeview -v t2*file flair --trilinear vs. fsleyes t2*file flair on the right:

<Screen Shot 2020-04-14 at 9.40.57 AM.png>
Fig 1. This is the flair file compared side by side (fv --trilinear vs. fsleyes, respectively).

<Screen Shot 2020-04-14 at 9.43.58 AM.png>
Fig 2. This is the t2*file (0.65mm voxel width), which has both noticeable quality drop and a different baseline intensity threshold at baseline between freeview and fsleyes.

<Screen Shot 2020-04-14 at 10.00.10 AM.png>
Fig 3. This is the flair --trilinear vs. flair (noflags) vs. fsleyes flair, respectively.

Let me know what you think, and again thank you for the response!

BR

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu<mailto:AHOOPES@mgh.harvard.edu>>
Sent: Tuesday, April 14, 2020 9:25:08 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Freesurfer display resolution very low compared to other viewers

Hi Brian,



A couple questions - are you visualizing on a mac retina screen? If so, there will be a slight decrease from the standard resolution because the underlying rendering library that we use unfortunately does not support retina capabilities at this time. Also, are you loading single or multiple volumes? Freeview uses the first volume loaded as the base image geometry, and all the following volumes are resampled (if necessary) into this base geometry using nearest neighbor interpolation. So if you?re working with different-resolution images, it might help to enable linear interpolation as the default resampling method by using the `--trilinear` freeview flag. If that?s not the case, it?d be helpful to see a couple screenshots of the issue.



Hope that helps,
Andrew



From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Renner, Brian" <Brian.Renner@cshs.org<mailto:Brian.Renner@cshs.org>>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 13, 2020 at 8:54 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer display resolution very low compared to other viewers



       External Email - Use Caution
Hello all!



Inaugural message to the list; I will attempt to be brief with the project description.



The setup is consistent between both versions 6.0.0 and 7.0.0-beta, run on a high performance cluster, accessed through macOS terminal + Xquartz, most recent versions all.



As it stands, our group is attempting to do subfield analysis of hippocampal analysis and lesion measurement in MS subjects. We have noticed that there is a major discrepancy of resolutions between files, which has irked some of our physicians undertaking the lesion measurement. We need to resolve the lesions down to 3mm and have noticed the quality between freeview and fsleyes of the same nifti files will yield much lower display resolution. This is true for most scans, though it has been compared using 1mm T2 FLAIR sequences as well as T2* sequences with 0.65mm voxel space. I have been attempting to find a workaround as the current solution for the physicians is to look at the files in fsleyes and then measure them with the ruler tool in freeview. I can send supporting pictures as necessary.



Thank you in advance for any thoughts you may have!



BR



--
Brian Renner, MD
Research Associate, Neurology
brian.renner@cshs.org<mailto:brian.renner@cshs.org>

Cedars-Sinai
127 S. San Vicente Blvd, Suite A6600  :  Los Angeles CA 90048
office 310-423-1589  :  mobile 310-658-3492  :  cedars-sinai.org<https://www.cedars-sinai.org/>




IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
<Screen Shot 2020-04-14 at 9.40.57 AM.png>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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------------------------------

Message: 8
Date: Wed, 15 Apr 2020 07:34:16 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Trac-All Error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MN2PR04MB57575BFF2A5748AB3FE936658ADB0@MN2PR04MB5757.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

Hi Jessica - A couple of things to fix. The bvecs file has commas in it. The bvals file, if you view it with the more command on linux, you'll see that instead of line changes it has "^M" in between the values. This can happen if it's saved in a windows text editor. You can open it in a linux text editor and save it again.

Hope this helps!

a.y


________________________________
From: Hua, Jessica <jphc55@mail.missouri.edu>
Sent: Tuesday, April 14, 2020 4:38 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Subject: Re: Trac-All Error


       External Email - Use Caution

Attached are bvecs and bvals.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Message: 9
Date: Wed, 15 Apr 2020 17:42:27 +1000
From: Salah Showiheen <sshowiheen@gmail.com>
Subject: Re: [Freesurfer] Error in Tracula-all -prep
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFc5RtcP7C2qEJV6YSZXG3MUdnWc2+BrZz9tB1=_KhYPK3g_1w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

Thanks Freesurfer developer
I have followed what you have suggested and it did work for me.

Thanks once again for your help.

Regards
Salah

On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia, <AYENDIKI@mgh.harvard.edu>
wrote:

Hi Salah - You're probably running into this problem:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for
tkregister2, change it to tkregister2_cmdl, then try again.

a.y
------------------------------
*From:* freesurfer-bounces@nmr.mgh.harvard.edu <
freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen <
sshowiheen@gmail.com>
*Sent:* Friday, April 10, 2020 12:33 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Error in Tracula-all -prep


       External Email - Use Caution

Hi Anastasia,

It is true that this file was missing. When I added it, the processing in
trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in
executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is
unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.


Regards,
Salah

On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia <
AYENDIKI@mgh.harvard.edu> wrote:

Hi Salah - It looks like it didn't find your subject's freesurfer recon
when it was doing the pre-processing, so it skipped some steps that you
need to go beyond that point. Based on your SUBJECTS_DIR and your subject
name, it looked for this file:
/Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y
------------------------------
*From:* freesurfer-bounces@nmr.mgh.harvard.edu <
freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen <
sshowiheen@gmail.com>
*Sent:* Monday, April 6, 2020 11:49 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Error in Tracula-all -prep


       External Email - Use Caution

Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has
been asked about back in (17/12/2016) and the title is ([Freesurfer]
Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)



Regards,
Salah
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
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Message: 10
Date: Wed, 15 Apr 2020 12:51:38 +0200 (CEST)
From: Tim Sch?fer <ts+ml@rcmd.org>
Subject: [Freesurfer] Question on using T2 or FLAIR data to improve
pial surfaces
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <226129081.1112889.1586947898539@ox.hosteurope.de>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around?
2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images, so I feel it should be fine, but I wanted to hear your opinion.

Best,

Tim



[1] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimprovepialsurfaces

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



------------------------------

Message: 11
Date: Wed, 15 Apr 2020 13:32:29 +0000
From: Mason Wells <WellsMT1@cardiff.ac.uk>
Subject: [Freesurfer] Data onto the Freesurfer surface
To: "FSL - FMRIB's Software Library" <FSL@JISCMAIL.AC.UK>, Freesurfer
support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <15D9C7C5-3921-4EBA-A570-CD10ECAD5403@cardiff.ac.uk>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

Hi all,

I apologise for cross-posting to both FSL and Freesurfer lists.

I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface?

Thanks in advance,
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: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
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: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
Ff?n: 02920 879628

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Message: 12
Date: Thu, 16 Apr 2020 00:17:30 +0900
From: "Safi Ullah ." <safi.ullah@uog.edu.pk>
Subject: [Freesurfer] Manipulating MRI volume data in Matlab
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CACzMhqwRa-AoHqT95k5QRcQLh5t3bvPqy2dkaQM87emeTKY4wg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

Dear Freesurfers,

I recently started working on an brain sMRI related project. I have a minor
(may be a major) issue.
when I generate label files for a tissue e.g midbrain by using the command
mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173
--l midbrain.label
or in voxel space
mri_vol2label --c
$SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz --id 173 --l
midbrain1.label
?Now I want to lad the label file and the MRI volume, brainstemSsLabels.v10
, in Matlab (I can do this by using MRIread function given in FSmatlab
directory. the function read mri in a matlab struct, which along with other
info also contain a 'vol' 3D data matrix)
? Using the coordinates given in label file, how to extract a specific
slice, row, column from a matlab matrix? as the label file need some
transformation, I dont know this part.

Any help shall be highly appreciated.

Regards,

Safi

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