[Freesurfer] question for preprocessing

[ping cao]

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Dear expert，

Thank you for reading!

I want to do these four pre-processing steps:

1. Re-sampling each MR image to 256*256*256;
2. Using the N3 algorithm for intensity inhomogeneity correction;

3. Skull stripping;

4. Removing the cerebellum.

Does " *recon-all"*  do all the above 4 steps automatically? If so, which
file is just finished with these four steps? If not, how can I do these
steps?

Your help is greatly appreciated.


Best,
ping
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[Freesurfer] unable to create symbolic link, and GPU error

[John Absher]

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Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm 
hoping someone can help me troubleshoot:

First, recon-all exits with error indicating that it is unable to create a 
symbolic link:

[GHS\026278@vmcntdsktp10 fs_sample1]$ tail 
/neuro_images_isilon/026278/fs_sample1/sample001/scripts/recon-all.log
ICI = 216.7, FI = 1989.1, variation=32373.324
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample001 exited with ERRORS at Sat Jun 22 17:10:41 EDT 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The error occurs in CentOS 7 running on a virtual machine environment, with the 
latest stable freesurfer release, 6.0. 

The recon-all process was being run on the sample_001.mgz file to test the 
installation, and ran for about 7 hours.

Second, when I tried to use the -use-gpu flag, the process seems to be missing 
a library:

[GHS\026278@vmcntdsktp10 fs_sample1]$ recon-all -subject sample001 -i 
./sample-001.mgz -use-gpu -all
Testing for CUDA device:
/usr/local/freesurfer/bin/mri_em_register_cuda: error while loading shared 
libraries: libcudart.so.5.0: cannot open shared object file: No such file or 
directory
Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample001 exited with ERRORS at Sat Jun 22 10:05:12 EDT 2019

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

[GHS\026278@vmcntdsktp10 fs_sample1]$

Can you suggest workarounds for one or both of these errors? Thanks,

John


Warm regards, 


Please, note my new email address, john.abs...@prismahealth.org

John R. Absher, MD, FAAN
Division of Neurology, Department of Medicine

Prisma Health-Upstate 
200 Patewood Drive, Suite 350B
City, SC 29615
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)



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[Freesurfer] Post-doctoral Research Position at the Yale Alzheimer's Disease Research Unit

[Adam Mecca]

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The Yale University Alzheimer’s Disease Research Unit and the Yale PET
Center has an opening for a highly qualified and motivated individual at
the post-doctoral level to work on research involving the development of
analysis techniques integrating human imaging data including PET and fMRI
for NIH-funded studies and clinical trials in Alzheimer’s disease.
Applicants must have obtained a Ph.D. in neuroscience, biomedical
engineering, or a related field.

Qualifications:
Strong experimental, analytical, and programming skills are essential.
Experience in fMRI, image analysis, algorithm development, and biological
applications is highly desirable. The selected candidate will work under
the direction of Drs. Christopher van Dyck and Adam Mecca.

The successful candidate should have a Ph.D. or an M.D./Ph.D. with at least
three years of experience in fMRI and/or PET imaging.

Application Instructions:
Interested individuals should email a CV to adam.me...@yale.edu.
Adam Mecca, M.D. Ph.D.
Yale School of Medicine, Department of Psychiatry
Geriatric Psychiatry and the Alzheimer's Disease Research Unit
Tel: (203) 764-8100
Fax: (203) 764-8111
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Re: [Freesurfer] WARNING: no voxels in AR1 computation

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

This is not a problem with the contrasts, it is an issue with the mask. How did 
you create the mask? Can you send the full terminal output?

On 6/21/2019 6:16 PM, Francesca Pentimalli wrote:

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Dear FreeSurfer experts,

I am trying to run mri_glmfit on a series of concatenated volumes.

mri_glmfit --y $SUBJECTS_DIR/concat/new_glm_input.mgh --fsgd Qdec/qdec.fsgd 
--mask fsaverage/label_volume/mask.mgz --glmdir glm_output --C 
$SUBJECTS_DIR/qdec/Untitled/contrasts/lh-Avg-Intercept-volume.mat

I am getting the following : WARNING: no voxels in AR1 computation.  I am 
guessing that this is due to the results of the analysis, or is this 
potentially a problem with the specific contrast used? If so, what should be 
kept in mind while creating new contrasts?

Regards,
Francesca

Francesca Pentimalli Biscaretti di Ruffia
Via S. Eufemia 3, 35121 Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.edu



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Re: [Freesurfer] Group mean tracer uptake images

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

you can use something like
mri_concat overlay1.mgh overlay2.mgh --mean --o mean.overlay.mgh

On 6/22/2019 4:18 PM, Boris Rauchmann wrote:
>  External Email - Use Caution
>
> Dear FS community,
>
> how can I create group mean tracer uptake images in surface space with FS 
> from several overlays?
>
> Thanks,
> Boris
>
> Von meinem iPhone gesendet
>
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Re: [Freesurfer] aseg annotation2label

[Bruce Fischl]

mri_vol2label should do the trick

cheers
Bruce
On Sat, 22 Jun 2019, Sam W. wrote:



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Hello,

I'm trying to create label files of the aparc+aseg ROIs but cannot find the 
aseg annotations. The
?h.aparc.annot does not contain subcortical regions that exist in the 
aparc+aseg.mgz volume. Is
there a way to apply mri_annotation2label to aseg labels?
Thanks!

Best regards,
Sam

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[Freesurfer] aseg annotation2label

[Sam W.]

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 Hello,

I'm trying to create label files of the aparc+aseg ROIs but cannot find the
aseg annotations. The ?h.aparc.annot does not contain subcortical regions
that exist in the aparc+aseg.mgz volume. Is there a way to apply
mri_annotation2label to aseg labels?
Thanks!

Best regards,
Sam
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[Freesurfer] Group mean tracer uptake images

[Boris Rauchmann]

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Dear FS community,

how can I create group mean tracer uptake images in surface space with FS from 
several overlays?

Thanks,
Boris

Von meinem iPhone gesendet

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Re: [Freesurfer] Within-subject vertexwise correlation

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

I don't know. There is no way for me to answer that. It depends on the 
signal-to-noise of each of the modalities. You'll probably have to experiment a 
bit

On 6/22/2019 8:08 AM, Matthieu Vanhoutte wrote:

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I effectively smoothed both modalities the same amount.

The question is whether I should or not smooth before calculating 
within-subject correlation?

Best,
Matthieu

Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure that this is a question we can answer. If you do smooth, then you 
should smooth both modalities the same amount.

On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:

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Dear FS experts,

I would like to compute within-subject correlation between two modalities based 
on vertexwise maps in fsaverage space. I wonder whether I have to smooth the 
normalized surface-based maps before computing vertexwise within-subject 
correlation?

I have noted that smoothing surface maps before computing correlation increases 
the output correlation value.

Thanks for your lights.

Best,
Matthieu



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Re: [Freesurfer] Applying Pial edits to Longitudinal

[Martin Reuter]

Hi Sierra, 

the long command should be

recon-all -long C002d C002.base -mprage …..

same way as you called it the first time when using the -all flag.

Best, Martin



> On 8. Jun 2019, at 20:28, Sierra Ann Jarvis  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello Freesurfers, 
> 
> I am trying to apply Pial edits to my longitudinal time point. I have tried 
> the command,
> 
> recon-all -long C002d.long.C002.base/ C002.base -mprage -3T -norm2-b 20 
> -norm2-n 5 -autorecon2 -autorecon3
> 
> But receive the error, 
> 
> Unmatched “.
> 
> I am using  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> 
> Do you know what could be the reason for this?
> Sierra 
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Re: [Freesurfer] Advantage of having skull for longitudinal processing?

[Martin Reuter]

Hi Adam, 

the longitudinal registration should not care, but the regular stream would 
like to have the skull in the image. This will help for a couple steps (full 
head talairach registration -> eTIV etc). 

Best, Martin


> On 5. Jun 2019, at 03:57, Adam Martersteck  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Freesurfer team,
> 
> I'm thinking of pre-skullstrip'ing my brains prior to being input into 
> FreeSurfer.
> 
> My fear was this information in the skull might be useful during 
> mri_robust_register or mri_robust_template for longitudinal analyses:
> 
> Martin discusses this in his Freesurfer workshop talk at 9 minutes in 
> (youtube: http://www.youtube.com/watch?v=vxJODPBLd3M=9m21s 
> ) where the heatmap 
> covers parts of the skull and the Freesurfer wiki which mentions that the 
> Tukey biweight will deweight regions of noise like tongue/eye/neck 
> differences.
> 
> But it appears the longitudinal stream registers everything on each 
> cross-sectional's norm.mgz to create the fused norm -- which is skullstripped 
> and missing neck/tongue/eyes/skull already.
> 
> Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz, 
> etc. do not have a skull for longitudinal processing?
> 
> Thanks,
> Adam 
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Re: [Freesurfer] Within-subject vertexwise correlation

[Matthieu Vanhoutte]

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I effectively smoothed both modalities the same amount.

The question is whether I should or not smooth before calculating
within-subject correlation?

Best,
Matthieu

Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> I'm not sure that this is a question we can answer. If you do smooth, then
> you should smooth both modalities the same amount.
>
> On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> I would like to compute within-subject correlation between two modalities
> based on vertexwise maps in fsaverage space. I wonder whether I have to
> smooth the normalized surface-based maps before computing vertexwise
> within-subject correlation?
>
> I have noted that smoothing surface maps before computing correlation
> increases the output correlation value.
>
> Thanks for your lights.
>
> Best,
> Matthieu
>
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>
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