[Freesurfer] ATTACHMENT REMOVED--asegstats2table

[John Absher]

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Hi,

We run freesurfer 6 on an HPC environment. We received this error when trying 
to run an asegstats2table script:

[jabsher@node0130 results]$ ./asegstats2table_scr
  File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
[jabsher@node0130 results]$

We are running this version:
You are running this version of FreeSurfer: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Here are the loaded modules:
Currently Loaded Modules: 1) libxml2/2.9.10-gcc/8.3.1 2) 
openblas/0.3.10-gcc/8.3.1 3) matlab/2021b 4) anaconda3/5.1.0-gcc/8.3.1 5) 
openmpi/3.1.6-gcc/8.3.1-cuda10_2-ucx 6) cuda/10.2.89-gcc/8.4.1

The script is attached.

We've gone to the wiki page (asegstats2table - Free Surfer Wiki 
(harvard.edu)
 and tried essentially all permutations, including specifying the aseg.stats 
files by name for each subject. The "use -subjects" error comes up every time, 
and we tried this as specified, with -subjects followed by all the 
directory/subject names, with a \ at the end of each line for readability.

I know this must be something very straightforward, but hoping you can help. 
Thanks,


Warm Regards,

John R. Absher, MD, FAAN
Associate Professor, University of South Carolina School of Medicine Greenville
Department of Internal Medicine, Division of Neurology
Clinical Assistant Professor, Clemson University School of Health Research 
(CUSHR)
Graduate Faculty, Clemson University School of Public Health Sciences
Prisma Health-Upstate
200 Patewood Drive, Suite 350B
Greenville, SC 29615
john.abs...@prismahealth.org or 
abs...@mailbox.sc.edu or 
jabs...@clemson.edu
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)

[cid:image001.jpg@01D89871.8F9C2110]

Inspire health. Serve with compassion. Be the difference.

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A MIME attachment of type  was removed here
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[Freesurfer] FS educ links

[John Absher]

External Email - Use Caution

Hi,
We're implementing freesurfer and other neuroimaging applications on the High 
Performance Computing center. To help more users get up to speed quickly, I'm 
trying to pull together up-to-date freesurfer/freeview educational materials 
into a single online resource. Is it OK to link directly to available online 
resources/tutorials/videos/datasets as long as I include appropriate 
attributions? If not, how do I go about getting permissions?

Warm Regards,

John R. Absher, MD, FAAN
Clinical Associate Professor, University of South Carolina School of Medicine 
Greenville
Department of Internal Medicine, Division of Neurology
Clinical Assistant Professor, Clemson University School of Health Research 
(CUSHR)
Graduate Faculty, Clemson University School of Public Health Sciences
Prisma Health-Upstate
200 Patewood Drive, Suite 350B
Greenville, SC 29615
john.abs...@prismahealth.org or 
jabs...@greenvillemed.sc.edu or 
jabs...@clemson.edu
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)

[cid:image001.jpg@01D67ADF.953C21D0]

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If you have received this communication in error, please notify me immediately.
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[Freesurfer] SC20

[John Absher]

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I thought some people from this list might want to attend SC20, the 2020 
supercomputing conference. It looks interesting, and could be relevant to your 
work.

Examples of activities at SC can be found in the previous year's program at the 
SC19 
website.


Warm Regards,

John R. Absher, MD, FAAN
Clinical Associate Professor, University of South Carolina School of Medicine 
Greenville
Department of Internal Medicine, Division of Neurology
Clinical Assistant Professor, Clemson University School of Health Research 
(CUSHR)
Prisma Health-Upstate
200 Patewood Drive, Suite 350B
Greenville, SC 29615
john.abs...@prismahealth.org or 
jabs...@greenvillemed.sc.edu or 
jabs...@clemson.edu
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)

[cid:image002.png@01D52510.7E96E3A0]

Inspire health. Serve with compassion. Be the difference.

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If you have received this communication in error, please notify me immediately.
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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)



Inspire health. Serve with compassion. Be the difference.




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If you have received this communication in error, please notify me immediately.


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[Freesurfer] GPU/supercomputer adaptation of freesurfer?

[John Absher]

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Hi,

I'm planning a freesurfer analysis of a large MRI dataset, and want to use the 
"380 GPU nodes" (and other cores/nodes) on the Palmetto Cluster 
(https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html) to 
speed up the process. Since I am not a programmer, I'm hoping someone can give 
me a quick tutorial:


a)  Is this going to speed up recon-all and the data analysis?

b)  How much programming/expertise is required to enable freesurfer to take 
advantage of a supercomputer's resources?

c)   Has anyone done this already?

d)  The Palmetto Cluster is more or less limited to command-line. As long 
as I visualize the data on another system, I assume this will not be a problem, 
right?

Thanks,

John R. Absher, MD

jabs...@ghs.org
GHS Neuroscience Associates
University of South Carolina School of Medicine Greenville
864-350-6655 (mobile)

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[Freesurfer] Sag T1 3D post-contrast

[John Absher]

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Has anyone else tried to do recon-all with Sagittal 3D T1 post-contrast volumes?

We're getting hung in recon-all at the Talairach registration step, and I 
wonder if the vascular enhancement at the pial surface might be throwing the 
algorithm off. About half the scans will run smoothly, but the other half --- 
not so much.

Another question is whether a linear registration (e.g., using David 
MacDonald's register program) would allow us to do the recon-all ... -notal 
option?

Thanks,
John

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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[Freesurfer] symbolic link problem

[John Absher]

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Hi,

Running recon-all on sag T1 post-contrast MRI (for archival study) on 
virtualBox with centOS7 and freesurfer 6. The virtual box runs on a windows 
server and is allocated 8 processors and 16 GB memory by the windows server on 
which it resides. A citrix share provides the bulk of our filesystem storage 
space (/cifs). This filesystem appears not to allow symbolic links, such as 
these:

rh.white.H
rh.white.K
lh.white.H
lh.white.K

These are symbolic links to [lr]h.white.preaparc.[HK], and recon-all stalls at 
the step during which these symbolic links are created. If we run the process 
in our /home directories on a linux filesystem, all is well, and recon-all runs 
correctly. However, only 8 GB of disc storage space there, and we have ~100 
subjects to process. We thought we'd just run ~10 subjects or so, then move 
their data to the /cifs filesystem, but those 4 symbolic links won't copy.

Questions:

1.  If we ignore this error and copy everything else to the /cifs 
filesystem, is that OK, since the recon-all is complete?

2.  If we try to run a GLM contrast on all the subjects (e.g., compare 50 
to the other 50) in the /cifs filesystem, where we have space to keep all the 
data in one place, will the inability to create a symbolic link in that 
filesystem crash our analysis?

3.  One post suggested copying the linked files into the SUBJECTS_DIR 
directory, but that won't work on /cifs and isn't necessary on the linux 
filesystem; is there another workaround?

Thank you so much for you any guidance you can provide, and forgive me if 
there's some easy solution I've overlooked.

John

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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[Freesurfer] parallel openmp

[John Absher]

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We are trying to run many subjects through recon-all in batches on an 8 core 
Windows Server on which we have virtualBox running CentOS7 and freesurfer 6.

Can you tell me if this command will utilize all 8 cores effectively to process 
all 8 subjects simultaneously?

recon-all -subjid TBI1_002 -i TBI1_002_v1.nii.gz \
-subjid TBI1_003 -i  TBI1_003_v1.nii.gz \
-subjid TBI1_005 -i TBI1_005_v1.nii.gz \
-subjid TBI1_006 -i TBI1_006_v1.nii.gz \
-subjid TBI1_007 -i TBI1_007_v1.nii.gz \
-subjid TBI1_009 -i TBI1_009_v1.nii.gz \
-subjid TBI1_012 -i TBI1_012_v1.nii.gz \
-subjid TBI1_013 -i TBI1_013_v1.nii.gz \
-all -parallel -openmp 8

Thanks,

John

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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[Freesurfer] degrees of freedom

[John Absher]

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In group analysis, is it better to have matched controls (1:1) or to use age, 
education and other characteristics as confounds in the glm? In the latter 
situation, we would control for these demographic variables in the glm and the 
control group n could be smaller, the same or larger than the test group. We 
are looking at TBI+ and TBI- subjects across a broad age range to look at 
patterns of cortical thinning. Thanks.

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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[Freesurfer] Analyzing slice data with freesurfer?

[John Absher]

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We are attempting to analyze archival MRI data obtained during routine clinical 
care. Unfortunately, the standard clinical MR sequences do not include 3D 
volumes. Will the freesurfer algorithm work on slice data so that each slice 
could be marked with the pial and white matter boundaries? Then, the next 
question is how to apply seg and parc templates to analyze correctly defined 
subcortical structures, and cortical regions? Has anyone tried to do this type 
of archival data analysis? Unfortunately, our standard sequences do not include 
3D volumes, so to do the retrospective work we'll need a workaround.

Thank you.

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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[Freesurfer] segmentation and parcellation advances

[John Absher]

During the last lectures of the recent 4/2-5 course, Dr. Fischl referenced code 
that would properly segment/parcellate sub-par images. If we don't have a good 
3D MPRAGE or SPGR T1 image, is there a specific command I need to use for these 
alternate/sub-par inputs into recon-all ? If not, when might this code be 
available? I'm looking at archival images and often only a sagittal T1 volume 
is available. Also, can I just change this to 1mm voxels and leave it as a 
sagittal for recon-all, or should I reformat as axials first?

Great course, by the way.

Thanks,

John

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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[Freesurfer] MCR

[John Absher]

Hi,

I was pleased to learn freesurfer runs with the standalone matlab runtime, and 
installed this on CentOS7. It seems to be working well. I noticed that there's 
also a version of spm12 that runs using this runtime, "with limitations." Two 
questions:


1.  Are there freesurfer limitations using this runtime that can be 
overcome by having the full matlab version installed?

2.  Can I use the same runtime I've already installed for freesurfer to run 
spm12, or will I need a new one?

Thanks,

John

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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