Re: [Freesurfer] segment_subregions stats files missing?

[Hoopes, Andrew]

To mimic the original matlab implementation, segment_subregions saves stats as 
*.txt files in the mri subdirectory of the subject.

But maybe we should just save things in the stats folder to be consistent. 
Eugenio/Doug, what do you think?

Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alvarado, Luis 

Date: Monday, July 18, 2022 at 4:11 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] segment_subregions stats files missing?

External Email - Use Caution
Hi all,

I ran the segment_subregions thalamus --cross on some of my subjects but I 
cannot find the *.stats files in the stats folder. I was wondering if I am 
missing something?

I need the *.stats files to aggregate the results via asegstats2table to feed 
the mri_glmfit tool. Is there another way to do this without the *.stats files?

I am using the freesurfer-linux-ubuntu20_x86_64-dev-20220716-015eeb0 build on 
Ubuntu 20.04.4 LTS.

Best,

Luis
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Re: [Freesurfer] SynthSR: Illegal Hardware Instruction

[Hoopes, Andrew]

Unfortunately, tensorflow and M1 don’t mix well at the moment. Not sure if 
there is a universal fix yet.

Rob, do you remember where the mac-specific TF package can be installed from?

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Abdelkarim, Ahmed 

Date: Tuesday, July 12, 2022 at 9:29 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] SynthSR: Illegal Hardware Instruction

External Email - Use Caution
Hello

I have an issue getting SynthSR working with FreeSurfer dev.
I have MacBook Pro with apple M1 chip and MacOS Monterey.
In bash terminal, after setting up FreeSurfer, and running the SynthSR command, 
I get this error ‘’Illegal instruction: 4’’.
Have you had a similar issue before? Any advice?

Many thanks in advance.

Regards
Ahmed


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Re: [Freesurfer] [ext] Amygdala Subfields - longitudinal volumes differ a lot from the cross-sectionals

[Hoopes, Andrew]

This might be related to a small bug in the previous longitudinal code, which 
affected volume rescaling. It should be fixed now. You could try out the new 
implementation: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Andrea Dell'Orco 

Date: Tuesday, June 21, 2022 at 10:06 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] [ext] Amygdala Subfields - longitudinal volumes 
differ a lot from the cross-sectionals
External Email - Use Caution

Ops I have forgot:

Freesurfer 7.1.1,

no special flags in recon-all.

Just the subjects have a little processing before recon-all, but I do
not think this can lead to some problem only on the left hemisphere.



>  External Email - Use Caution
>
> Dear all,
>
> I have a Cohort of subjects with multiple time points. I have segmented
> the T1w with the normal recon-all and sub fields and then with the
> longitudinal pipeline as described in the wiki.
>
> When I compare the sub fields Volumes, there is a good agreement, with
> the expected variability,  between longitudinal and not longitudinal for
> the Whole Hippocampus rh and lh.
>
> The Volumes for the amygdala are on the other hand, really different,
> especially for the left Whole amygdala.
>
> Here some plots with the correlation longitudinal vs non-longitudinal
> pipeline:
> https://secure-web.cisco.com/14VEQLZEbs96z59Y5ty9CueQKgO9cELG9hY62vKSTRXY_0S04A9X5thwWY_4fEhSd-jO6E-9ayRY0XOalS_l_UwoZfqgLuPgrHO9gy8-fJwasgdw5jxcsAEvOuetKOo_-ks3z-utNjBwTcyTVJ5QsG_G_hNIZRTFjNQBRP20TZGauK6v3qgy2ecQvHiAn_2Z03W6FA8MNcRcx0-IVMEQLNdBiosVRO60RFuEUover0QGAglNFCOaQ3eJE8ygT8xFwqhEMoHJr7BfVBb3CIlQuvLId91YmGOn-CiLE4kot2e_8d1hQvWN6cJLg5K364kF7Kkj_kAZro5kcdO-ZJthDyjWrATEXDN9DHxb4LW1KZ88/https%3A%2F%2Fcharitede-my.sharepoint.com%2F%3Ap%3A%2Fg%2Fpersonal%2Fandrea_dellorco_charite_de%2FEU3Za9DDG-pDv8XfcB4fBNAB53JTlqbZnzKhSXOnSvBYSQ%3Fe%3DGLKyYP
>
> Do someone has some idea, what can be the problem?
>
> Regards,
>
> Andrea Dell'Orco
>
--
Andrea Dell'Orco
HiWi

Charité – Universitätsmedizin Berlin
NeuroCure Clinical Research Center NCRC

AG Kognitive Neurologie
Charitéplatz 1, D-10117 Berlin
Tel  +49 30 450 560 185
Fax +49 30 450 7 560 280
Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2

http://secure-web.cisco.com/1F0p6iM7RaFZ9LS84INNpTbTRMLmoNAJurIRelhgOdUD-v6sk1MwHtQL7fwPGIb8xGMsmCh9aR4UcBXWIpJ8JGsbeyQRqfEcH2n2TYA8cVknZprBCe5beax0DeXxFBDvn7qZ8DSTYFIy9bnohrwpjYEwiH4EnLo1nW1cXSbJJj05pnErSlrSwDWDWYELuA4KOQpdhdYgEGluaLgzzqvSLSUyvHYM9AEywJTv-LR-_wvGTrR7l6zUPVWqlBCUUaoAkXAkOp9LujAj_5RVaExGgkrnNusSrNg9peQtgboqzU7OPaYsQ59u-Lb5CjQVJVmnif-y_vAct4P6l8YOQ_3IlmQ/http%3A%2F%2Fwww.charite.de%2Fservice%2Flageplan%2Fplan%2Fmap%2Fccm_sauerbruchweg_5%2F


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Re: [Freesurfer] Hippocampal segmentation Matlab crash

[Hoopes, Andrew]

I’m not sure what the cause of this would be, unfortunately. The matlab runtime 
library errors become very difficult to track down. One thing you could do is 
try to run this in a singularity or docker container, if available on your 
cluster. You could use centos7 as the base image, and mount the paths to your 
freesurfer installation and your input/output data.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Wednesday, March 9, 2022 at 12:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Tried it, but I still get the same error.

--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee

From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Tuesday, March 8, 2022 at 3:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

Hi Cait,

Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? 
You can do this in bash with:

unset LD_LIBRARY_PATH

or in cshell with:

unsetenv LD_LIBRARY_PATH

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace

Re: [Freesurfer] run_samseg output folder permissions error

[Hoopes, Andrew]

Hi Randy,

As Koen mentioned, FS support for ushort file types wasn’t added until 
recently. I just extended that support to the python (samseg) tools yesterday, 
so this should work in the most recent development (nightly) freesurfer 
distributions. You could install that, or you could convert your input image to 
a supported type, like uint8, int, or float.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Koen Van Leemput 

Date: Wednesday, March 9, 2022 at 12:44 PM
To: daedalu...@aol.com 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] run_samseg output folder permissions error

External Email - Use Caution
This seems to have something to do with the image read/write tools in FS's 
Python tools not being able to handle ushort pixel types. One way around this 
would be to convert the input image into e.g., floats before calling samseg, 
but for a real fix in the code I'm looking at Andrew... (?)

On Wednesday, March 9, 2022, mailto:daedalu...@aol.com>> 
wrote:
Thank you Koen,

Your suggestion allowed run_samseg to run for a few minutes, but...


daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg 
--input o_ADNI_002_S_4654__MRI-m072.nii --output T1-only
##--
  Samsegment Options
##--
output directory: T1-only
input images: o_ADNI_002_S_4654__MRI-m072.nii
modelSpecifications: {'FreeSurferLabels': [0, 165, 258, ...

 process ran for an additional few minutes and then crashed with the 
following statements (Any Thoughts?) ..


maximalDeformation=0.0750 minLogLikelihood=-0.8762
maximalDeformation=0. minLogLikelihood=-0.8762
appliedScaling: 1.0021
INFO: This is an unsigined short.
Traceback (most recent call last):
  File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 179, in 

reg_only=args.reg_only
  File 
"/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 
252, in segment
initTransform=initTransform
  File 
"/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 
271, in register
initTransform=initTransform
  File 
"/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 
72, in registerAtlas
self.saveResults( savePath, worldToWorldTransformMatrix, 
imageToImageTransformMatrix )
  File 
"/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 
473, in saveResults
inputImage = fs.Volume.read(self.imageFileName)
  File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/ndarray.py", 
line 103, in read
result = bindings.vol.read(filename)
ValueError: unknown MRI data type ID: 10
daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$


The image that I am trying to test with this process is a standard T1-weighted 
image from ADNI, and Freesurfer had been able to run the basic segmentation 
(-recon-all, took about four hours and ran to completion without errors), so 
I'm not sure why Samseg can't identify the "MRI data type".

Thanks in advance for any insights you might be able to share.

-Randy



-Original Message-
From: Koen Van Leemput mailto:leem...@gmail.com>>
To: daedalu...@aol.com 
mailto:daedalu...@aol.com>>; Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Tue, Mar 8, 2022 11:18 pm
Subject: Re: [Freesurfer] run_samseg output folder permissions error
It looks like you have an extra slash in front of the output file name, so 
you're trying to write in the root directory...

On Tuesday, March 8, 2022, mailto:daedalu...@aol.com>> 
wrote:
External Email - Use Caution
Dear experts,

Having installed Freesurfer on WSL2, I was able to get the basic FS 
segmentation to run without error.  However, when I tried to run_samseg on a 
single T1 image, I received the following error message (permissions denied 
creating the "output folder")

Is there anything in the trace (below) that provides a clue?

daedalus@DESKTOP-TILLA3B:/usr/ local/freesurfer/7-dev/ subjects$ run_samseg 
--input o_ADNI_002_S_4654__MRI-m072. nii --output /T1-only
-samsegOutput/
Traceback (most recent call last):
  File "/usr/local/freesurfer/7-dev/ python/scripts/run_samseg", line 67, in 

os.makedirs(args. outputDirectory, exist_ok=True)
  File "/usr/local/freesurfer/7-dev/ python/lib/python3.6/os.py", line 220, in 
makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/T1-only-samsegOutput/'

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Re: [Freesurfer] Gcut error: gcutted brain is much smaller than the mask

[Hoopes, Andrew]

Hi Begum,

You could try the just-recently released SynthStrip command `mri_synthstrip` 
available in the dev distributions of freesurfer (as of today, march 15th). It 
should be more robust than the watershed utility.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Begüm Cerrahoğlu 

Date: Tuesday, March 15, 2022 at 5:26 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Gcut error: gcutted brain is much smaller than the mask

External Email - Use Caution
Dear developers,
I am trying to clean up the extra dura left after skullstripping. Watershed 
parameter does not prove to be much helpful and when I try gcut I get the error 
below.

I checked the release notes of freesurfer 5.1 and mri_gcut is not run by 
default. In the archives I came across this exact problem before, under this 
message: 
msg18797
However, there was not an end solution available in the archived email exchange.

I am not interested in cerebellum and am okay with cutting the cerebellum out 
of the brain mask as long as it does not interfere with being able to 
distinctly separate cortex from cerebellum in the following steps.
>From skullstripping tutorials,I have read that one should not start erasing 
>cerebellum from the brainmask directly and was wondering if you could let me 
>know why?

In sum, are there important reasons to keep the cerebellum despite only being 
interested in analyzing the cortex?

If not, could you please let me know what could be the reason for gcut's 
failure and if there is anyway to disable failure detection so I can see if the 
gcutted
brain is usable?

>> " rm -f brainmask.gcuts.mgz

>> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz

>> brainmask.gcuts.mgz

>>

>> INFO: Care must be taken to thoroughly inspect your data

>>  when using mri_gcut. In particular, inspect the edges of

>>  gm and cerebellum for over-aggressive cutting.

>>  Add -segmentation brainmask.gcuts.mgz to the tkmedit

>>  command string to view the voxels which gcut has removed.

>>

>> reading mask...

>> white mean: 107.529232

>> threshold set to: 107.529232*0.40=43.011693

>> calculating weights...

>> doing mincut...

>> now doing maxflow, be patient...

>> g-cut done!

>> post-processing...

>> post-processing done!

>> masking...

>> ** Gcutted brain is much smaller than the mask!

>> ** Using the mask as the output instead!

>>

>> cp brainmask.auto.mgz brainmask.mgz "


1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.

2) Platform: Linux Mint 20.2

Thank you greatly for your time and efforts.

Kindest regards,

Begum Cerrahoglu
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 .
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Re: [Freesurfer] Hippocampal segmentation Matlab crash

[Hoopes, Andrew]

Hi Cait,

Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? 
You can do this in bash with:

unset LD_LIBRARY_PATH

or in cshell with:

unsetenv LD_LIBRARY_PATH

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace (captured):
[  0] 0x2baa65422f4e 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478
 _ZN2fl4diag5linux12context_base12capture_dataEv+0030
[  1] 0x2baa65420424 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428
[  2] 0x2baa740ef0f5 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597
[  3] 0x2baa740f12ca 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258
[  4] 0x2baa740f13c1 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505
[  5] 0x2baa740f1743 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403
[  6] 0x2baa740f17b3 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515
[  7] 0x2

Re: [Freesurfer] R: SAMSEG "lesion" (Illegal instruction) ~ running VM_67

[Hoopes, Andrew]

Hi Randy,

I agree with Stefano that this is likely due to your CPU not supporting AVX 
instructions, since this is not a reproducible error when running VM 67 on our 
mac and linux test machines. Here’s some more info:

https://github.com/tensorflow/tensorflow/issues/46108

Unfortunately, there is not much we can do to fix this on our side of things, 
because the main solution requires recompiling tensorflow from scratch.

Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Cerri, Stefano 

Date: Monday, February 28, 2022 at 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: daedalu...@aol.com 
Subject: [Freesurfer] R: SAMSEG "lesion" (Illegal instruction) ~ running VM_67
Hi Randy,

Yes, Tensorflow is installed in "freesurfer_7.2.0_amd64.deb". If it wasn't you 
would have obtained "no module named tensorflow" when running the command 
"import tensorflow".

Note that you are able to run "basic" SAMSEG since it does *not* require 
tensorflow. Only the lesion version (--lesion flag) requires that library.

I'm quite sure it is a problem with your CPU instruction set and the specific 
tensorflow version installed in FreeSurfer (v2.4.1). Unfortunately, I'm not 
able to help you further here. I hope someone else on the list can solve your 
issue.

Stefano

Da: daedalu...@aol.com 
Inviato: lunedì 28 febbraio 2022 14:52
A: Cerri, Stefano ; freesurfer@nmr.mgh.harvard.edu 

Oggetto: Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67


External Email - Use Caution
Hi Stefano and thanks for your response.

I have copied the output from my terminal window below, highlighting your 
instructed inputs.

When you say "SAMSEG requires Tensorflow", I am still trying to find out if 
Tensorflow was incorporated into "freesurfer_7.2.0_amd64.deb". (Installed 
2/8/2022)
If not, do I have to import and install it from somewhere else? (if so, then 
where/how?)

A colleague suggested I check where "tensor" might be found

developer@developer-VirtualBox:~$ env | grep -i tensor
(... returned nothing)

developer@developer-VirtualBox:~$ grep -i tensor $FREESURFER_HOME/bin/*
(... returned several instances of the term "tensor", but really only in 
"trac-preproc" / "orientLAS" / "dt_recon" / dmri_tensoreig" / "dmri_ac.sh")
(these make a certain amount of sense for the diffusion MRI routines)


As far as running this on another host, I am using the Virtual Machine as 
directed to from the Freesurfer Wiki:
VM_67 - Free Surfer Wiki 
(harvard.edu)

I am running the VM on a Windows 10 Pro computer which is just a little over 2 
years old, and since the standard Freesurfer segmentation and the basic SAMSEG 
cross-sectional routines both work just fine, I don't know if the age of this 
system is truly the issue here.  This "illegal instruction (core dumped)" issue 
only happens when I try to use the --lesion flag.


x

Device secifications: (XXX's substituted for security reasons)

Device name DESKTOP-XX
Processor Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz   3.60 GHz
Installed RAM 32.0 GB (31.8 GB usable)
Device ID CA89F214-3517-4D16-8A5D-XX
Product ID 00330-53014-11941-AAOEM
System type 64-bit operating system, x64-based processor


Windows specifications

Edition Windows 10 Pro
Version 21H2
Installed on ‎11/‎12/‎2020
OS build 19044.1526
Experience Windows Feature Experience Pack 120.2212.4170.0

x

Here is the output text-capture that I am seeing after I followed your 
instructions.  Yes, the error is replicated...


 freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.2.0
FSFAST_HOME   /usr/local/freesurfer/7.2.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.2.0/subjects
MNI_DIR   /usr/local/freesurfer/7.2.0/mni
developer@developer-VirtualBox:~$ fspython
Python 3.6.8 (default, Apr 10 2020, 02:08:58)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-23)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tensorflow
Illegal instruction (core dumped)
developer@developer-VirtualBox:~$


Thanks in advance for any further insights/directions.

-Randy

xxx
-Original Message-
From: Cerri, Stefano 
To: freesurfer@nmr.mgh.harvard.edu 
Cc: daedalu...@aol.com 
Sent: Sun, Feb 27, 2022 11:22 am
Subject: Re: [Freesurfer] SAMSEG "lesion

Re: [Freesurfer] matlab runtime error

[Hoopes, Andrew]

Hi Corinna,
Do you happen to have the LD_LIBRARY_PATH environment variable set in your 
shell? If so, I would unset it. LD_LIBRARY_PATH tends to mess with any programs 
linked to dynamic libraries. In this case, it’s forcing freeview to load the 
wrong matlab Qt libraries.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Corinna Bauer 

Date: Wednesday, September 1, 2021 at 4:58 PM
To: Mailing Freesurfer List 
Subject: [Freesurfer] matlab runtime error

External Email - Use Caution
Hi all,

I ran a few subjects successfully through7.1.1, but when I got to check the 
surfs in freeview I get an error about the Matlab runtime libraries below. 
However, I already have those libraries and the 2014b runtime environment 
installed on my Ubuntu 18.04.

freeview: 
/usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5X11Extras.so.5: no 
version information available (required by freeview)
freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Core.so.5: no 
version information available (required by freeview)
freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Gui.so.5: no 
version information available (required by freeview)
freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Widgets.so.5: 
no version information available (required by freeview)
freeview: relocation error: freeview: symbol 
_ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined 
in file libQt5Widgets.so.5 with link time reference

I also tried re-installing the 2014b MCR, but get this message:
fs_install_mcr R2014b
curl: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libcurl.so.4: no version 
information available (required by curl)
curl: (48) An unknown option was passed in to libcurl

Let me know how to best proceed.

Thanks!

Corinna

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Re: [Freesurfer] fs_install permission denied

[Hoopes, Andrew]

Are you adding sudo in front of every command? like this:

cd $FREESURFER_HOME/bin && sudo curl 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && sudo chmod +x fs_install_mcr

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Junyeon Won 

Date: Monday, August 30, 2021 at 11:38 AM
To: Freesurfer support list 
Subject: [Freesurfer] fs_install permission denied

External Email - Use Caution
Dear Freesurfer experts,

I was tiring to install fs_install using the below command.

cd $FREESURFER_HOME/bin && curl MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x fs_install_mcr
It showed an error message saying permission denied so I added sudo as 
suggested here.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg66199.html

However, even after adding sudo in front, it shows the same error message.

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0  17104  0 --:--:-- --:--:-- --:--:-- 17179
chmod: Unable to change file mode on fs_install_mcr: Operation not permitted


Could you please let me know how to resolve this?

Best,
JW









[https://secure-web.cisco.com/19DMpBEx9mw9glbcQIJcRkgtBkmhZPmAAO1cwfUwAXx_f2RafPXmmCeQSK-zNW3acuD9BoxMVg2Wi3sdZu2UCEJbwUYPZ7hS2gYKqqHq4XbFc-RAcOeC28wzNYkyKhUv9qo5WpujkG9--MH58fK8nzmU_YS0rmAbLVqVFgve9X6t3bsuzdTeWUrKL7ETMcgpHtOR2kxpbJD6DjgKS3sOkkLCtq2JhDFz8RXUmLbI7WmXGM_T7t5PLv_MPV9NbZ8EgoXuCzqz5ZwGDJlvNLQg2kQ/https%3A%2F%2Fmailfoogae.appspot.com%2Ft%3Fsender%3Dad29uMjVAdW1kLmVkdQ%253D%253D%26type%3Dzerocontent%26guid%3D51fe252b-2fc2-4de3-9526-88b58670325d]ᐧ
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The information in this e-mail is intended only for the person to whom it is 
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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, 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Shiny new 7.2!

[Hoopes, Andrew]

Yes! And thanks for the reminder – I just pushed 7.2.0 to dockerhub
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Andy Worth 

Date: Tuesday, August 31, 2021 at 3:45 PM
To: Freesurfer support list 
Subject: [Freesurfer] Shiny new 7.2!

External Email - Use Caution
Is it true that all that is needed for a new official FS docker container to 
come into existence is to merge pull request 
#866?
  That would be so very nice.  We like the official release!  4.1K pulls of 
previous versions on dockerhub can't be wrong.

Kind regards,
Andy Worth
Senior Scientific Solutions Engineer
he, him, his
[https://secure-web.cisco.com/1GDKx1YAS8d7j3ghh8LVHIYDBol75pmm1NA5OzfsAwJ651N7-hg_VmOJ3eXexi6mXA5WG8l7ei3-7hqy3ytscFsrtEM_7Avd7ikgwRDXzt0Yu-FKT94IGucDoaus5xeMtsfpo5OlaccJVzyYnlCXi4Rg-U2kUNdUSxa_jTDKOwcriB-SAEaBFEl2N8XlT5_TjyN8EM-VLVt9FBajVWQK7PuJlK3s3dIIEcHa-p3Ssft5CiTE_2M3oujHjp-IZAalc9wq7WVOT4lG72T3D-pVzLQ/https%3A%2F%2Fdrive.google.com%2Fuc%3Fid%3D1oozBEoFHbBP_5xYyw59-9YNoEOsX6Ghd%26export%3Ddownload]
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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Hippocampal, thalamus and brainstem subfields: Matlab crash bump on macOS Big Sur

[Hoopes, Andrew]

Honestly, I’m not sure. Without tracebacks it’s getting very difficult to debug 
these matlab runtime errors. It seems like Big Sur is the common culprit here, 
but we really don’t know why. Hopefully we can release the python port soon... 
Cico, could you try running freesurfer through a docker container instead?

https://hub.docker.com/r/freesurfer/freesurfer

Best
Andrew


From: Iglesias Gonzalez, Juan E. 
Date: Thursday, August 12, 2021 at 2:57 PM
To: Freesurfer support list 
Cc: Hoopes, Andrew 
Subject: Re: [Freesurfer] Hippocampal, thalamus and brainstem subfields: Matlab 
crash bump on macOS Big Sur
Thanks a bit lot, Cico. The screensaver thing blew my mind.
We need to move these tools into python to avoid this type of problems.
In the meantime:  Andrew, do you have any ideas?
Cheers,
/Eugenio

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


On Aug 12, 2021, at 12:58, Francesco Cardinale 
mailto:cico1...@icloud.com>> wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute hippocampal, thalamus and brainstem subfields on my 
laptop (MacBook Pro, MacOS Big Sur, Freesurfer 7.1.1 or 7.2.0) with 
segmentHA_T1.sh, segmentThalamicNuclei.sh and segmentBS.sh scripts, 
respectively. All the three pipelines fail because of a Matlab Crash Dump. You 
can find the error logged in the bash console text reported in the last part of 
this email. I also attached the file brainstem-substructures-T1.log

Please, note that everything works fine with previous versions of MacOS, 
including Mojave. All the updates of Big Sur didn’t solve the problem.
Is it possible to use these tools with an updated Matlab Runtime?

Another note, probably helpful to somebody else: sometimes these tools fail 
also in previous version of MacOS, but I discovered that it happens for a 
different Matlab Crash Dump due to some screen savers. Avoiding the use of 
screen savers solved the problem under Mojave (but not under Big Sur).


Best regards


Cico Cardinale



   Segmentation violation detected at Thu Aug  5 00:29:40 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : US-ASCII
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 
05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 78 Stepping 3, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX =   RBX = 
  RCX =   RDX = 
  RSP =   RBP = 
  RSI =   RDI = 

   R8 =    R9 = 
  R10 =   R11 = 
  R12 = 78d9bd00  R13 = 7fff205294bd
  R14 = 7fff87277d38  R15 = 78d9bda0

  RIP = 3002  RFL = 7f8b5b737b30

   CS =    FS =    GS = 00010c5bb560

Stack Trace (from fault):
[  0] 0x00010c208e64 
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x00010c20ca2a 
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x00010c20c477 
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x000111b3db7a 
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x000111b3de58 
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x000111b3b733 
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff205a9d7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x000109c546ca 
/Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178 
_ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+0186


If this problem is reproducible, please submit a Service Request via:
MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://www.mathworks.com/sup

Re: [Freesurfer] Issue with tksurfer-sess

[Hoopes, Andrew]

Hi Lauri,

This is fixed in v7.2, but if you want to patch your current freesurfer 
distribution, you can try these commands:

cd $FREESURFER_HOME/bin
sudo mv fsvglrun fsvglrun.backup
sudo curl -O 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun
sudo chmod +x fsvglrun

Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lauri Tuominen 

Date: Wednesday, August 18, 2021 at 10:42 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Issue with tksurfer-sess
External Email - Use Caution

Dear Surfers,
I ran into a problem with tksurfer-sess. See below. I have a mac big sur.

I wonder if there is a bug. Any help would be appreciated.
Thank you
Lauri Tuominen

tksurfer-sess -s subj1 -d ../subjects -analysis ftap.sm05.rh -c ftap -freeview
Surface fsaverage rh
Map Surface fsaverage rh
FreeSurferEnv.csh 7.1.1
Darwin Lauris-MacBook-Pro.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 
00:26:31 PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64 x86_64
Wed 18 Aug 2021 10:35:41 EDT
tksurfer: Command not found.

list ftap
con/map ftap 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz
maplist 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz
mri_concat 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz
 --o 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Writing to 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii
cd /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/mkanalysis
setenv SUBJECTS_DIR 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/SUBJECTS_DIR
tksurferfv fsaverage rh inflated -overlay 
/Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii
 -annot aparc -surf white -surf pial -fminmax 2 4

Contrasts
0 ftap


/Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: conditional binary 
operator expected
/Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v 
FS_ALLOW_VGLRUN ]]; then'





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Re: [Freesurfer] LGI - output issue

[Hoopes, Andrew]

This is fixed in v7.2, but if you want to patch your current freesurfer 
distribution, you can try these commands:

cd $FREESURFER_HOME/bin
sudo mv fsvglrun fsvglrun.backup
sudo curl -O 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun
sudo chmod +x fsvglrun

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lab of Autism and 
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 

Date: Tuesday, August 17, 2021 at 2:43 PM
To: Freesurfer support list 
Subject: [Freesurfer] LGI - output issue

External Email - Use Caution
Good afternoon FreeSurfer experts,

Hope that everyone is well and staying safe!

I tried opening LGI freeview (or tksurferfv) output, and I have been running 
into the following issues (see code and error message outputs below). Any ideas 
how I could fix this? Please let me know if additional details are needed.

Bolded code is what I inserted. Outputs are not bolded.

tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi
zsh: command not found: tksurfer
tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi
ERROR: cannot find lh.pial_lgi
cd $SUBJECTS_DIR/HAR30303_srs2_2/surf
tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi
freeview -f 
/Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5
 -viewport 3d
/Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator 
expected
/Applications/freesurfer/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; 
then'

Also within the surf folder, I tried something like: freesurfer -v lh.pial_lgi
Output in freeview was just a dark screen - tried changing the color map but 
nothing improved this issue.

Thank you so much!


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Re: [Freesurfer] about FreeSurfer QA tools errors

[Hoopes, Andrew]

Hi Xin,

Are you using the QA tools from 
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools? Those are specific to FS 5.3 
(we should update the wiki). v7.1 includes an executable named `qatools.py` 
that functions similarly.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Xin Qi 

Date: Thursday, August 12, 2021 at 12:00 AM
To: Freesurfer support list 
Subject: [Freesurfer] about FreeSurfer QA tools errors

External Email - Use Caution
Hi Freesurfer Community Support Team:

We would like to use FreeSurfer QA tools.

After installing it, I tested it on one subject that finished Freesurfer 
recon-all processing using the latest FreeSurfer 7.1. but got errors that seem 
many files are missing in the mri, surf, stat folders created by FreeSurfer.

I attach the recon_checker summary log and zipped snaps file for your reference.

Looking forward to hearing from you. Thank you very much.

Best regards
Xin
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] error running samseg on cluster

[Hoopes, Andrew]

Hi Rito, which freesurfer version are you using here?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ritobrato Datta 

Date: Wednesday, August 11, 2021 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] error running samseg on cluster

External Email - Use Caution
Hi All,

I am trying to run samseg as follows on a cluster and am getting a message that 
I need to install tensorflow (which is already installed). Please see below.
Please advise how to fix this.

Many thanks

Rito
-
run_samseg --input t12t2.nii.gz t2_brain.nii.gz --lesion --lesion-mask-pattern 
0 1 --save-posteriors --output t2_lesions
error: This tool requires tensorflow, but fspython does not ship with tensorflow
by default. You (or a sys admin) can install the CPU version via:fspython -m 
pip install tensorflow==1.13.1

fspython -m pip install tensorflow==1.13.1

Requirement already satisfied: tensorflow==1.13.1 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (1.13.1)
Requirement already satisfied: protobuf>=3.6.1 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (3.17.3)
Requirement already satisfied: keras-applications>=1.0.6 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (1.0.8)
Requirement already satisfied: absl-py>=0.1.6 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (0.13.0)
Requirement already satisfied: six>=1.10.0 in 
/home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) 
(1.14.0)
Requirement already satisfied: grpcio>=1.8.6 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (1.39.0)
Requirement already satisfied: termcolor>=1.1.0 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (1.1.0)
Requirement already satisfied: astor>=0.6.0 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (0.8.1)
Requirement already satisfied: gast>=0.2.0 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (0.5.2)
Requirement already satisfied: numpy>=1.13.3 in 
/home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) 
(1.18.4)
Requirement already satisfied: keras-preprocessing>=1.0.5 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (1.1.2)
Requirement already satisfied: wheel>=0.26 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (0.37.0)
Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (1.13.1)
Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow==1.13.1) (1.13.0)
Requirement already satisfied: h5py in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
keras-applications>=1.0.6->tensorflow==1.13.1) (3.1.0)
Requirement already satisfied: markdown>=2.6.8 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.3.4)
Requirement already satisfied: werkzeug>=0.11.15 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (2.0.1)
Requirement already satisfied: mock>=2.0.0 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1) (4.0.3)
Requirement already satisfied: cached-property; python_version < "3.8" in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
h5py->keras-applications>=1.0.6->tensorflow==1.13.1) (1.5.2)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (4.6.3)
Requirement already satisfied: dataclasses; python_version < "3.7" in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
werkzeug>=0.11.15->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (0.8)
Requirement already satisfied: zipp>=0.5 in 
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
importlib-metadata; python_version < 
"3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.5.0)
Requirement already satisfied: typing-extensions>=3.6.4; python_version < "3.8" 
in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from 
importlib-metadata; python_version < 
"3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) 
(3.10.0.0)
You are using pip version

Re: [Freesurfer] fsaverage file download

[Hoopes, Andrew]

We don’t release the fsaverage subject alone. You might be able to work some 
magic with the curl and tar commands to pull and extract just the fsaverage 
subdirectory from a freesurfer release archive, but I’m not sure how (or if) 
that can be done. Plus, it still probably requires downloading most or even all 
of the distribution.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shruthi Srinivasan 

Date: Saturday, July 17, 2021 at 2:16 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] fsaverage file download

External Email - Use Caution
Good afternoon!

I would like to ask if there is there anyway that I would be able to redownload 
just fsaverage to my WSL without redownloading the whole Freesurfer 
distribution?

I was trying to understand how to find the location of the output data for 
recon-all on my windows system, and accidentally deleted the fsaverage folder 
without understanding it’s importance. Thus, I need just the fsaverage folder. 
Please let me know, thank you
___
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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

[Hoopes, Andrew]

The line of code you sent doesn’t seem changed though

best
andrew

From: Kaija Sander 
Date: Thursday, July 29, 2021 at 5:40 PM
To: Hoopes, Andrew , Freesurfer support list 

Cc: Iglesias Gonzalez, Juan E. 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution
Hi Andrew,

I just meant that upon going to make those changes, it appears the change has 
already been made, therefore I am not entirely sure what the issue is...

Best,
Kaija

From: Hoopes, Andrew 
Sent: 29 July 2021 16:45
To: Kaija Sander ; Freesurfer support list 

Cc: Iglesias Gonzalez, Juan E. 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing


Hi Kaija,



Not sure I follow. Have you tried making the change I suggested in the last 
email?



Best,

Andrew



From: Kaija Sander 
Date: Wednesday, July 28, 2021 at 2:30 PM
To: Freesurfer support list 
Cc: Hoopes, Andrew , Iglesias Gonzalez, Juan E. 

Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution

Hi Andrew and Eugenio,



Sorry for taking so long to follow up on this again, but after checking 
MCR_CACHE_ROOT path, it seems that it has already been changed. It is currently 
set to



 MCR_CACHE_ROOT=$( echo "/tmp/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;



I'm not sure where I am going wrong...



Best,
Kaija



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: 23 June 2021 14:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing



Hi Kaija,



I believe this is related to limitations in temporary file handling. You could 
try manually replacing the MCR_CACHE_ROOT path on line 49 of:



$FREESURFER_HOME/bin/run_SegmentSubfieldsT1Longitudinal.sh



With something like:



MCR_CACHE_ROOT=$( echo "$HOME/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;



That seems to have fixed this problem in the past.



Best,

Andrew





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kaija Sander 

Date: Monday, June 14, 2021 at 9:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution

External Email - Use Caution

Hi Eugenio,



No problem at all, thanks for getting back to me!

All the subjects should have been acquired exactly the same way with the same 
parameters, so I don't understand... So far I've only gotten through a few 
subjects but decided to reach out when I realised it happened to at least 3 of 
them (out of 7 so far, 18 total). I did run one of the subjects multiple times, 
and even re-ran the recon-all and still got the exact same error.



I am very puzzled!



Thanks so much,

Kaija



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: 14 June 2021 14:20
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing



Sorry for not having replied earlier, Kaija.

This is very strange. Do these subjects have more time points or a larger field 
of view? Did you run all the subjects on the same platform? Is the issue with 
these few subjects reproducible?

Cheers,

/Eugenio





Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com<http://secure-web.cisco.com/1bmGWc_BEDrYMr5MiQIaYmEfT3rZLKMKv6fH6XeQkUQQb2MRdyqahVMJklYsz5EwPo-ecqc9F67VZm88jliW-5RRCOkzjNQqbAXONth-G3a5VSHRB-h4Mc_FZ1PHqCzNVrrphgmJ5f1CwTCotzX2r4yM0h5jKcoYyAMKI3WYbRbH-CWudWDoy_0W-0uYFxOu_OrsZ_IS3ZB11ByCtGcYbTdNs4zxpdwlzY5AL3rax0YmrzOKGNLvbchEZOBiEaZwN_8riuHMAUWozkHCvGbmjfA/http%3A%2F%2Fwww.jeiglesias.com>



On Jun 14, 2021, at 11:11, Kaija Sander 
mailto:kaija.san...@mail.mcgill.ca>> wrote:



External Email - Use Caution

External Email - Use Caution

Hello,



I just wanted to follow up on this issue as it seems other people experience 
problems with hippocampal subfields segmentation but not this same issue.



Does anyone please have any idea how to help??



Thank you very much,

Kaija



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Kaija Sander 
mailto:kaija.san...@mail.mcgill.ca>>
Sent: 02 June 2021 14:15
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in hippocampal subfields longitudinal processing



External Email - Use Caution

Hello all,



I am attempting to obt

Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

[Hoopes, Andrew]

Hi Kaija,

Not sure I follow. Have you tried making the change I suggested in the last 
email?

Best,
Andrew

From: Kaija Sander 
Date: Wednesday, July 28, 2021 at 2:30 PM
To: Freesurfer support list 
Cc: Hoopes, Andrew , Iglesias Gonzalez, Juan E. 

Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution
Hi Andrew and Eugenio,

Sorry for taking so long to follow up on this again, but after checking 
MCR_CACHE_ROOT path, it seems that it has already been changed. It is currently 
set to

 MCR_CACHE_ROOT=$( echo "/tmp/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;

I'm not sure where I am going wrong...

Best,
Kaija

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: 23 June 2021 14:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing


Hi Kaija,



I believe this is related to limitations in temporary file handling. You could 
try manually replacing the MCR_CACHE_ROOT path on line 49 of:



$FREESURFER_HOME/bin/run_SegmentSubfieldsT1Longitudinal.sh



With something like:



MCR_CACHE_ROOT=$( echo "$HOME/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;



That seems to have fixed this problem in the past.



Best,

Andrew





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kaija Sander 

Date: Monday, June 14, 2021 at 9:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution

External Email - Use Caution

Hi Eugenio,



No problem at all, thanks for getting back to me!

All the subjects should have been acquired exactly the same way with the same 
parameters, so I don't understand... So far I've only gotten through a few 
subjects but decided to reach out when I realised it happened to at least 3 of 
them (out of 7 so far, 18 total). I did run one of the subjects multiple times, 
and even re-ran the recon-all and still got the exact same error.



I am very puzzled!



Thanks so much,

Kaija



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: 14 June 2021 14:20
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing



Sorry for not having replied earlier, Kaija.

This is very strange. Do these subjects have more time points or a larger field 
of view? Did you run all the subjects on the same platform? Is the issue with 
these few subjects reproducible?

Cheers,

/Eugenio





Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com<http://secure-web.cisco.com/1bmGWc_BEDrYMr5MiQIaYmEfT3rZLKMKv6fH6XeQkUQQb2MRdyqahVMJklYsz5EwPo-ecqc9F67VZm88jliW-5RRCOkzjNQqbAXONth-G3a5VSHRB-h4Mc_FZ1PHqCzNVrrphgmJ5f1CwTCotzX2r4yM0h5jKcoYyAMKI3WYbRbH-CWudWDoy_0W-0uYFxOu_OrsZ_IS3ZB11ByCtGcYbTdNs4zxpdwlzY5AL3rax0YmrzOKGNLvbchEZOBiEaZwN_8riuHMAUWozkHCvGbmjfA/http%3A%2F%2Fwww.jeiglesias.com>



On Jun 14, 2021, at 11:11, Kaija Sander 
mailto:kaija.san...@mail.mcgill.ca>> wrote:



External Email - Use Caution

External Email - Use Caution

Hello,



I just wanted to follow up on this issue as it seems other people experience 
problems with hippocampal subfields segmentation but not this same issue.



Does anyone please have any idea how to help??



Thank you very much,

Kaija



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Kaija Sander 
mailto:kaija.san...@mail.mcgill.ca>>
Sent: 02 June 2021 14:15
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in hippocampal subfields longitudinal processing



External Email - Use Caution

Hello all,



I am attempting to obtain the hippocampal subfields segmentation in a small 
longitudinal dataset (18 participants, 2 time points each). I have successfully 
been able to run recon-all, recon-all -base and recon-all -long (or at least, 
these steps appear to be completed without errors). However, when trying to run 
segmentHA_T1_long.sh, I encountering the following error (I have also attached 
the full log file of one of the subjects):



Open file failed because file 
'/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m'
 has invalid content. Details: 'file is closed.failbit is set.'

The file

   
"/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/user

Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

[Hoopes, Andrew]

Hi Kaija,

I believe this is related to limitations in temporary file handling. You could 
try manually replacing the MCR_CACHE_ROOT path on line 49 of:

$FREESURFER_HOME/bin/run_SegmentSubfieldsT1Longitudinal.sh

With something like:

MCR_CACHE_ROOT=$( echo "$HOME/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;

That seems to have fixed this problem in the past.

Best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kaija Sander 

Date: Monday, June 14, 2021 at 9:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution

External Email - Use Caution
Hi Eugenio,

No problem at all, thanks for getting back to me!
All the subjects should have been acquired exactly the same way with the same 
parameters, so I don't understand... So far I've only gotten through a few 
subjects but decided to reach out when I realised it happened to at least 3 of 
them (out of 7 so far, 18 total). I did run one of the subjects multiple times, 
and even re-ran the recon-all and still got the exact same error.

I am very puzzled!

Thanks so much,
Kaija

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: 14 June 2021 14:20
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

Sorry for not having replied earlier, Kaija.
This is very strange. Do these subjects have more time points or a larger field 
of view? Did you run all the subjects on the same platform? Is the issue with 
these few subjects reproducible?
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com


On Jun 14, 2021, at 11:11, Kaija Sander 
mailto:kaija.san...@mail.mcgill.ca>> wrote:

External Email - Use Caution
External Email - Use Caution
Hello,

I just wanted to follow up on this issue as it seems other people experience 
problems with hippocampal subfields segmentation but not this same issue.

Does anyone please have any idea how to help??

Thank you very much,
Kaija

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Kaija Sander 
mailto:kaija.san...@mail.mcgill.ca>>
Sent: 02 June 2021 14:15
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution
Hello all,

I am attempting to obtain the hippocampal subfields segmentation in a small 
longitudinal dataset (18 participants, 2 time points each). I have successfully 
been able to run recon-all, recon-all -base and recon-all -long (or at least, 
these steps appear to be completed without errors). However, when trying to run 
segmentHA_T1_long.sh, I encountering the following error (I have also attached 
the full log file of one of the subjects):

Open file failed because file 
'/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m'
 has invalid content. Details: 'file is closed.failbit is set.'
The file
   
"/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m"
cannot be executed.

Error in SegmentSubfieldsT1Longitudinal (line 1795)

What is strange is that this has only happened for a couple of subjects, and 
has worked fine for the few others I did.

Does anyone have any suggestions of what might be going wrong and how to fix it?

Thank you very much,
Kaija

FreeSurfer version: freesurfer-local-build-dev-20200116
Platform: Ubuntu 18.04.5
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Re: [Freesurfer] Recon-all running on a loop

[Hoopes, Andrew]

Hi Diana,

If there are a lot of obvious holes in the surface topology, it might be worth 
doing some manual fixing of the white-matter segmentation. The tutorial at 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 walks 
through that process.

Best
Andrew

From: DIANA ORTEGA CRUZ <100315...@alumnos.uc3m.es>
Date: Thursday, May 27, 2021 at 3:32 AM
To: Freesurfer support list , Hoopes, Andrew 

Subject: Re: [Freesurfer] Recon-all running on a loop

External Email - Use Caution
Dear Andrew,

Thank you for your reply. I shared with you the recon-all.cmd file via Drive, 
since I could not upload it directly to the mail. I also copy here (down) the 
last lines in this file.

I checked the resulting volumes and surfaces up to that point and the 
smoothwm.nofix surfaces look like they have a lot of holes, which I understand 
could cause the error. I also run again recon-all for that subject without 
parallelizing as you advised, but the process was again stuck at the same step.

Do you think it would be possible to change anything in the original file or 
the recon-all configuration to fix this issue?

Thanks a lot for your help!!! Best,
Diana

#@# Fix Topology rh Tue May 18 04:37:48 UTC 2021
 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig 
orig.nofix -out orig.premesh -ga -seed 1234 NoUMA0233 rh
 mris_euler_number ../surf/lh.orig.premesh
 cp ../surf/lh.orig.nofix ../surf/lh.orig.premesh
 mris_euler_number ../surf/rh.orig.premesh
 cp ../surf/rh.orig.nofix ../surf/rh.orig.premesh
 cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
 cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
 mris_topo_fixer -orig_name orig.nofix -out_name orig.premesh -mgz -warnings 
-seed 1234 NoUMA0233 lh
 cp ../surf/rh.qsphere.nofix ../surf/rh.qsphere
 cp ../surf/rh.smoothwm.nofix ../surf/rh.smoothwm
 mris_topo_fixer -orig_name orig.nofix -out_name orig.premesh -mgz -warnings 
-seed 1234 NoUMA0233 rh

 mris_remesh --remesh --iters 3 --input 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/lh.orig.premesh
 --output 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/lh.orig

 mris_remesh --remesh --iters 3 --input 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/rh.orig.premesh
 --output 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/rh.orig
F

El mié, 26 may 2021 a las 1:59, Hoopes, Andrew 
(mailto:ahoo...@mgh.harvard.edu>>) escribió:
Hi Diana,

Can you send the recon-all.cmd file? Have you tried running without parallel 
processing enabled?

Best,
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of DIANA ORTEGA CRUZ 
<100315...@alumnos.uc3m.es<mailto:100315...@alumnos.uc3m.es>>
Date: Friday, May 21, 2021 at 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Recon-all running on a loop

External Email - Use Caution
Dear FreeSurfer team,

My name is Diana Ortega, I am a Neuroscience PhD student at Universidad 
Politécnica of Madrid. I run a job to compute recon-all in parallel for 30 
subjects remotely on a supercomputer at my research institution. This job 
finished due to timeout, and all subjects but one finished without errors. 
However, one of the subjects was not finished and it appears as if it was stuck 
on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB 
in size), and from recon-all-status.log it appears to be stuck in the "Fix 
Topology" step. Have you ever encountered a similar situation? Would you know 
why this could have occurred?
Here are the details:

FreeSurfer version: 7.1.1-centos8_x86_64
Operative System: CentOS8
Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem 
SD530<https://secure-web.cisco.com/1Bch1AH1AvTKzQqcdunZ0FIqTIHtdhvL6XMYZuyZxpRjtV9TB6kEZn1nh48ZtbJGIw41ngjalVrelQDieE52ynIv7RkZ7f4BZtvzTIxvrOmGmA3JirLjPRIeUkGZzhBEi_NAarb-drp-U-IpLwb1OwHc9qiofX0w5uSIqj3r6yvgPVMj00Wrwio5IAMXe7yXue7tddIlb73tamNyfvbBKIuqQ_TSHGyNsCNyd4NSVZUxvMlbsarqYSxR1oVHqb0XP2bkT1mGLxlsjaijzsxSTjw/https%3A%2F%2Fwww.lenovo.com%2Fes%2Fes%2Fdata-center%2Fservers%2Fhigh-density%2FThinkSystem-SD530%2Fp%2F77XX7DSSD53>
Line run for that subject:
recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16

When opening recon-all.log, it keeps adding the following lines:

Remesher::removeTria( 240873 )
Remesher::removeTria( 240876 )
 NEXTIDX : 88755
 Remesher::removeCollapsedTrias( 88755 , 120326 )
 v_to_t[vidx] :
 Trias are identical : ... removing ...

When opening the error.log of the complete job, there are several lines of this 
error:

rm: No match.

Any advice will be of great help! Thanks a big lot!
Best,
Diana Ortega Cruz.
PhD Student
Lab

Re: [Freesurfer] Multiple Versions Installed

[Hoopes, Andrew]

Hi Nárlon,

There’s no harm in installing multiple versions of freesurfer on one 
filesystem. The FS distribution is confined to the directory it’s installed to, 
so we suggest organizing a FREESURFER_HOME directory structure like:

/Applications/freesurfer/5.3
/Applications/freesurfer/6.0
/Applications/freesurfer/7.1.1

etc… when installing different distributions. Just make to correctly source the 
directories when using different versions.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Boa Sorte Silva, Narlon 

Date: Tuesday, May 25, 2021 at 6:17 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Multiple Versions Installed

External Email - Use Caution
Dear FreeSurfer experts,

I was wondering if there are any problems in having installed two different 
versions of FreeSurfer on the same MacOS computer?

We have 5.3 installed and wanted to install 7.1.1, but keep the older version 
in case older data processed in the 5.3 needed to be reanalyzed.

Would we run into any problems by installing the new version and processing new 
data with it?

Thanks,
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSFHR/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon

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Re: [Freesurfer] Recon-all running on a loop

[Hoopes, Andrew]

Hi Diana,

Can you send the recon-all.cmd file? Have you tried running without parallel 
processing enabled?

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DIANA ORTEGA CRUZ 
<100315...@alumnos.uc3m.es>
Date: Friday, May 21, 2021 at 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-all running on a loop

External Email - Use Caution
Dear FreeSurfer team,

My name is Diana Ortega, I am a Neuroscience PhD student at Universidad 
Politécnica of Madrid. I run a job to compute recon-all in parallel for 30 
subjects remotely on a supercomputer at my research institution. This job 
finished due to timeout, and all subjects but one finished without errors. 
However, one of the subjects was not finished and it appears as if it was stuck 
on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB 
in size), and from recon-all-status.log it appears to be stuck in the "Fix 
Topology" step. Have you ever encountered a similar situation? Would you know 
why this could have occurred?
Here are the details:

FreeSurfer version: 7.1.1-centos8_x86_64
Operative System: CentOS8
Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem 
SD530
Line run for that subject:
recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16

When opening recon-all.log, it keeps adding the following lines:

Remesher::removeTria( 240873 )
Remesher::removeTria( 240876 )
 NEXTIDX : 88755
 Remesher::removeCollapsedTrias( 88755 , 120326 )
 v_to_t[vidx] :
 Trias are identical : ... removing ...

When opening the error.log of the complete job, there are several lines of this 
error:

rm: No match.

Any advice will be of great help! Thanks a big lot!
Best,
Diana Ortega Cruz.
PhD Student
Laboratory for Clinical Neuroscience
Centro de Tecnología Biomédica - Universidad Politécnica de Madrid
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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur

[Hoopes, Andrew]

Hi Joe,

Is this the full command output from start to finish? There is usually some 
helpful information preceding the “Segmentation violation detected” error.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Xin Qiao 

Date: Thursday, May 20, 2021 at 12:44 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Matlab R2014b exits while executing 
segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur

External Email - Use Caution

As mentioned, recon-all function with T1 MRI data works well with no problem at 
all.
With results from recon-all, while trying to run segmentThalamicNuclei.sh, 
MATLAB quit with message as follows:


   Segmentation violation detected at Wed May 19 19:42:08 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 
21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 69 Stepping 1, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX =   RBX = 
  RCX =   RDX = 
  RSP =   RBP = 
  RSI =   RDI = 

   R8 =    R9 = 
  R10 =   R11 = 
  R12 = 729b8d00  R13 = 7fff2041d4bd
  R14 = 7fff87147cf8  R15 = 729b8da0

  RIP = 3002  RFL = 7fa5bda93250

   CS =    FS =    GS = 00010f288560

Stack Trace (from fault):
[  0] 0x00010eedce64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x00010eee0a2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x00010eee0477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x000117c5fb7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x000117c5fe58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x000117c5d733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff2049dd7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x00010df9a6ca 
/Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00063178 
_ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+0186


This crash report has been saved to disk as 
/Users/transmri/matlab_crash_dump.9882-1 **


Caught "std::exception" Exception message is:
FatalException


  std::terminate() detected at Wed May 19 19:42:10 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 
21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 69 Stepping 1, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 2


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX =   RBX = 
  RCX =   RDX = 
  RSP =   RBP = 
  RSI =   RDI = 

   R8 =    R9 = 
  R10 =   R11 = 
  R12 = 729b8d00  R13 = 7fff2041d4bd
  R14 = 7fff87147cf8  R15 = 729b8da0

  RIP = 3002  RFL = 7fa5bda93250

   CS =    FS = 00

Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields

[Hoopes, Andrew]

Hi Joana,

I agree with Eugenio that if this is failing from within python, then python is 
probably messing with your environment. Based on that error log, it’s tough to 
say whether this is a freesurfer problem or matlab. The fact that it runs fine 
on linux seems to suggest it’s a macOS-specific issue with calling the matlab 
runtime library from python. If you’re using anaconda or something, it might be 
overwriting matlab-runtime linked libraries. I’m not sure how much we can help 
out here, unfortunately.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joana Collet i Fàbregas 

Date: Saturday, May 15, 2021 at 11:18 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields

External Email - Use Caution
Ok, thanks!
I forgot to mention ut before, but this error only occurs when running it in 
IOS, in Linux it works fine...

El dv., 14 de maig 2021, 22:52, Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
va escriure:
Yes, but that doesn’t guarantee that the (library) environment is the same as 
when you run something from the terminal.
I’m CCing Andrew Hoppes to see if he can assist.
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com


On May 14, 2021, at 15:22, Joana Collet i Fàbregas 
mailto:joana.col...@gmail.com>> wrote:


External Email - Use Caution

Dear Juan Eugenio,

I'm not sure what you mean. In Python I use os.system() to run the recon-all 
command from the command line.
Thanks!

Joana

El dv., 14 de maig 2021, 21:04, Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
va escriure:
Dear Joana,
Is it possibly that Python changes somehow that libraries that are loaded, 
compared with the command line?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com


On May 14, 2021, at 06:06, Joana Collet i Fàbregas 
mailto:joana.col...@gmail.com>> wrote:


External Email - Use Caution

Good morning,

I am a Biomedical Engineering Student at Universitat de Barcelona and I am 
creating a python script that has a Watchdog which detects new patients in a 
specific folder, and we want it to run FS and Hippocampal Subfields. The FS 
runs properly, but when the script arrives to the Hippocampal Subfields 
command, it breaks.

When using the FreeSurfer's Hippocampal Subfields from a python script after 
running FS recon-all right before, the processing is not performed due to the 
error shown in the attatched file. However, when running the Hippocampal 
Subfields from the terminal it does work.

We have even tried to create a watchdog only for the Hippocampal Subfields, and 
when we move a folder obtained after running FS to a specific folder, it also 
runs properly. It is only when it is concatenated with FS that it does not work.

We have contacted MathWorks Support, but they told us to reach you. The Matlab 
versions we have are Matlab_R2020a and Matlab_R2014b.

Thanks a lot,

Joana Collet
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Re: [Freesurfer] Freeview Update using MAC

[Hoopes, Andrew]

Hi Erika,

Can you untar the file you downloaded instead of the "HighSierra" version. 
There was a small typo in the UpdateFreeview instructions that mentioned 
high-sierra. The freeview you downloaded should work fine for 10.12

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erika Nolan 

Date: Tuesday, May 18, 2021 at 2:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview Update using MAC

External Email - Use Caution

External Email - Use Caution
Hi Ruopeng,

Thank you for the quick reply.

When I attempt to untar Freeview:


erikanolan$ tar -xzvf 
/Users/erikanolan/Downloads/freesurfer-darwin-macOS-HighSierra-dev-freeview.tar.gz

tar: Error opening archive: Failed to open 
'/Users/erikanolan/Downloads/freesurfer-darwin-macOS-HighSierra-dev-freeview.tar.gz'

When I attempt to open a HCP .gii file on Freeview (also see attached 
screenshot):


** invalid: gim version = 1

mrisReadGIFTIfile: GIFTI file /Users/erikanolan/Desktop/SULCAL PAINTING 
7.1.1/103515/103515.L.pial.native.surf.gii is invalid!

MRISread failed

mrisReadGIFTIfile: GIFTI file /Users/erikanolan/Desktop/SULCAL PAINTING 
7.1.1/103515/103515.L.pial.native.surf.gii is invalid!

Thank you,

Erika

_

Erika Nolan

Ph.D. Candidate

Clinical Psychology, Department of Psychology


Montreal Neurological Institute
McGill University
Montreal, Canada

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Sent: May 18, 2021 2:50 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview Update using MAC

Hi Erika,

What error message do you get when you launch Freeview on your macOS 10.12?

Ruopeng


On May 18, 2021, at 1:57 PM, Erika Nolan 
mailto:erika.no...@mail.mcgill.ca>> wrote:

External Email - Use Caution
External Email - Use Caution
Good afternoon,

I downloaded Freesurfer 7.1.1 and am trying to open HCP .gii files in Freeview. 
I tried updating Freeview (MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview)
 using the instructions for MacOS but it fails:

Mac

  1.  Go into your $FREESURFER_HOME and create a backup of your existing 
freeview app (this may require sudo access):

2.  cd $FREESURFER_HOME

cp Freeview.app Freeview-backup.app

  1.  Download the dev, standalone freeview tarball from 
here

  1.  Untar freeview within your $FREESURFER_HOME (this may require sudo):

5.  cd $FREESURFER_HOME

tar -xzvf /path/to/freesurfer-darwin-macOS_HighSierra-dev-freeview.tar.gz

  1.  IMPORTANT: If you are replacing freeview in a freesurfer release LESS 
than 7.0, then you must also remove the line "source 
$FREESURFER_HOME/sources.csh" from the $FREESURFER_HOME/bin/freeview script


The tar file that downloads is " freesurfer-darwin-macOS-dev-freeview.tar" is 
this file correct? My Mac is a MacOS Sierra (not HighSierra), version 10.12.6. 
Is it possible for me to get a file that is compatible with my Mac?

Thank you for your help!!!

Erika
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Re: [Freesurfer] memory allocation error

[Hoopes, Andrew]

Hi Fabio,

How much memory are you allowing for this process? You might want to just try 
increasing the limit on the slurm job to see if that works.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bernardoni, Fabio 

Date: Tuesday, May 11, 2021 at 4:22 AM
To: freesurfer mailing list 
Subject: Re: [Freesurfer] memory allocation error
External Email - Use Caution

Sorry I forgot the attachment.



Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
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Von: Bernardoni, Fabio
Gesendet: Dienstag, 11. Mai 2021 10:20:19
An: freesurfer mailing list
Betreff: AW: memory allocation error

Dear Freesurfers,

when running the longitudinal preprocessing on a subject, I get the same error 
as described here (see recon-all.log attached):
https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html


my FS version is:
recon-all -version
freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e

and I did not perform any editing, so there is no control points to remove as 
suggested in the above post (which also refers to version 6). Therefore, if I 
understand correctly, my problem is a different one. Any clue what I might be 
doing wrong?

Other possibly useful information:
uname -a
Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP 
Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux




Thanks for any hint/help

Fabio Bernardoni


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52

Re: [Freesurfer] Error in SAMSEG preprocessing

[Hoopes, Andrew]

If this is the last message before crashing, it sounds like it’s probably a 
memory issue – how much do you have available? CC’ing Stefano who might have an 
idea of the total memory requirement for lesions.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Monday, May 10, 2021 at 9:31 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution
After 14th interaction the terminal wrote this message:

I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports 
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-05-10 13:40:01.273046: I 
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 
3292375000 Hz
2021-05-10 13:40:01.281440: I tensorflow/compiler/xla/service/service.cc:150] 
XLA service 0x30013a0 executing computations on platform Host. Devices:
2021-05-10 13:40:01.281470: I tensorflow/compiler/xla/service/service.cc:158]   
StreamExecutor device (0): , 
WARNING:tensorflow:From 
/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266:
 checkpoint_exists (from tensorflow.python.training.checkpoint_management) is 
deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
VAE lesion model loaded
2021-05-10 13:40:16.471711: W tensorflow/core/framework/allocator.cc:124] 
Allocation of 171720 exceeds 10% of system memory.

I tried to improve the system memory of my virtual machine but the same error 
appeared.

Any suggestions?


El vie, 7 may 2021 a las 20:59, Hoopes, Andrew 
(mailto:ahoo...@mgh.harvard.edu>>) escribió:
If the output directory is missing seg.mgz, then samseg failed. You’ll have to 
send us the log or some sort of information about the error for us to debug 
this.

Best
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alberto Del Cerro Leon 
mailto:bertocer...@gmail.com>>
Date: Friday, May 7, 2021 at 6:49 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution
Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the 
following command:

run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii' 
'/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion 
--lesion-mask-pattern 0 1 --output '/home/neuroimage/fsl/vascular/1002/'

The output files were:

  *   cost.txt
  *   priors-testing.mgz
  *   samseg.talairach.lta
  *   template.lta
  *   template_coregistered.mgz
  *   template_transforms.mat
However I don't find any file with the white matter lesions segmented or a stat 
file. I would send you the terminal outputs but is too extensive. Would you 
help me?
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continue to communicate over

Re: [Freesurfer] mri_label2vol error

[Hoopes, Andrew]

Hi Melissa,

If the command runs fine in the terminal but not from python, it’s most likely 
because python is messing with aspects of your env before running commands in a 
subshell. The easiest solution is to upgrade to FS v7, where this problem no 
longer exists, but if you’re stuck at v6, you should verify that the 
DYLD_LIBRARY_PATH env var in the python subshell is the same as in the terminal 
environment.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Melissa Marie Rundle 

Date: Friday, May 7, 2021 at 2:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_label2vol error

External Email - Use Caution
Hi,

I get the following error message when I run mri_label2vol (freesurfer v 6.0) 
in a jupyter notebook(6.1.4) with python (v3.8.5):


dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib



However, when I run mri_label2vol directly in a terminal window, the command 
runs just fine.  Nor do I have trouble

running similar commands such as mri_vol2vol or mri_convert using the jupyter 
notebook.



I tried running "sudo -E fs_update" as suggested in MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

but that didn't solve the problem.



Any suggestions would be greatly appreciated.



Sincerely,

Melissa Rundle




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contains patient information, please contact the Mass General Brigham 
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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] Freesurfer 7 crashes during mris_fix_topology

[Hoopes, Andrew]

Yes, it might be a normalization issue. You could try using the `-no-ants-n4` 
recon-all flag to fallback to the v6 normalization method.

As for the wm edits, you don’t really need to load the surfaces, just the 
norm.mgz and wm.mgz, but if you wanted to visualize the initial smooth 
tessellation as well:

freeview -v mri/norm.mgz mri/wm.mgz:colormap=heat:opacity=0.5 -f 
surf/?h.smoothwm.nofix

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yakupov, Renat /DZNE 

Date: Friday, May 7, 2021 at 6:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Hi Andrew,



thank you for looking at the data!



I did check out that tutorial first, and the first thing it tells you to do is 
load various surfaces into Freeview, which was what brought me here. In this 
subject's `surf` directory there are no ?h.white and ?h.pial surface files. 
Which files can I use instead in order to see the white matter surface and look 
for those defects?



It is also interesting, that the processing didnt fail in Freesurfer 6. Looking 
at the release notes, one of the changes was using N4 bias-field correction 
instead of N3. Do you think this might mean that N4's inadequate bias-field 
correction led to broken-up segmented white matter, which in turn caused larger 
topological defects?


Best wishes,

Renat.




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Friday, May 7, 2021 5:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology


Hi Renat,



The third defect is too large and it’s causing a crash. When I run it, it hangs 
forever at:



CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369)

An extra large defect has been detected...

This often happens because cerebellum or dura has not been removed from 
wm.mgz.

This may cause recon-all to run very slowly or crash.



There are huge gaps missing in this subject’s white matter mask, resulting in a 
bad surface tessellation (see attached pic). I would check out the info at 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview<https://secure-web.cisco.com/12gT4H7XBsnxMWWCG4F8T4qJBE2PnbITfcdxpaBTxDgzaZPjHt1Catp497o4oUcQVkGOLdV1H5oPZEhAnsBEWow0_4VGH6FsatlW_uUq3bBc-hRCpHluu5XhEuB-KQOMYmA6arEafPIf63cVVzOyZIn4hG1sVKMtcFUPlyUovEhCmOtR0jOZIyYiy7FQeC2_hSbRngcTvJKSaaE9nCnXO2Law1dP6lPrceor8a4XTA3T_mew60k5qF8QD5Vmg2YWpbOhlp1IWt2BeJQ0sfT1yQQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview>
 and fill in the wm.mgz to manually edit.



best

Andrew





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yakupov, Renat /DZNE 

Date: Thursday, May 6, 2021 at 4:21 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Hi Andrew,



thank you for your reply. I just uploaded the subject's directory under the 
name "subject_from_RenatYakupov.tar.gz".



Regarding memory, I am running these jobs on our SGE cluster, which monitors 
memory usage. Both of the subject's images had maximum memory usage of slightly 
over 3GB, which is pretty typical from my experience. Interestingly, when 
processed with Freesurfer 6, which didnt crash and finished successfully, the 
maximum memory usage was around 11GB.



Thanks again and looking forward to your findings 😊



Best wishes,

Renat.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Wednesday, May 5, 2021 7:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology



Hi Renat,



That 3rd defect is fairly large – normally it would hang but it’s possible 
you’re running out of memory. If you can zip the subject and file drop it to 
us, we can take a look:



MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange<https://secure-web.cisco.com/1u2I9K-ckbULcDN4h-_ZdylX5n2vBBOMX6EHfWnDs7-xWZI3mqQdWi7HFoMKz9tdNYKjuWfN_Nan4JpJGREsnwmGq3yxwMImknbbPMfasAVeeqV3mWyJDJQbZi7QtsM0L44JYsK6UYk_wuuwEf_p_Ed5vbQFvnR_qkoiA75YR3ueRivLu1VsrmbDCfIglg4xLUeLcU3w4JopYBtaAk1pJe5CQJ-Nwjy6wxShFB-45MwaCw2xP54Ka9a36Silz4XoVQFam74VwOrlnybPLjm3TGQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange>



best,

Andrew



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yakupov, Renat /DZNE 

Date: Friday, April 30, 2021 at 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Dea

Re: [Freesurfer] Error in SAMSEG preprocessing

[Hoopes, Andrew]

If the output directory is missing seg.mgz, then samseg failed. You’ll have to 
send us the log or some sort of information about the error for us to debug 
this.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Friday, May 7, 2021 at 6:49 AM
To: Freesurfer support list 
Subject: [Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution
Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the 
following command:

run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii' 
'/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion 
--lesion-mask-pattern 0 1 --output '/home/neuroimage/fsl/vascular/1002/'

The output files were:

  *   cost.txt
  *   priors-testing.mgz
  *   samseg.talairach.lta
  *   template.lta
  *   template_coregistered.mgz
  *   template_transforms.mat
However I don't find any file with the white matter lesions segmented or a stat 
file. I would send you the terminal outputs but is too extensive. Would you 
help me?
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Re: [Freesurfer] Multiple Freesurfer(s)

[Hoopes, Andrew]

Hi Giulio,
I’ll follow up off-list.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Giulio Degano 

Date: Friday, May 7, 2021 at 3:20 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Multiple Freesurfer(s)

External Email - Use Caution
Hi all,

I am trying to install multiple Freesurfer versions on a Linux server (academic 
purposes, Linux Ubuntu 20.04).
I was able to install 7.1 and 5.3 (I used two different folders) and I also got 
the licenses. While 7.1 runs with no problem, for 5.3 recon-all keeps giving 
the “invalid license file error”. I am probably missing something.

Thanks in advance
Best
Giulio Degano

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Re: [Freesurfer] help with SAMSEG

[Hoopes, Andrew]

The atlases used by samseg are very different from freesurfer GCAs, and the 
samseg-template creation is not an easily-accessible utility at the moment. 
Feel free to look through the GEMS code in the FS repository, but it might be 
some time before we have an easy-to-use samseg atlas building tool in 
freesurfer.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Wednesday, May 5, 2021 at 11:11 AM
To: Freesurfer support list 
Subject: [Freesurfer] help with SAMSEG

External Email - Use Caution
Hello Freesurfer team, my group is interested in using the SAMSEG tool to 
evaluate white matter lesions in MCI patients. We would like to use a 
personalized atlas for the measure. We suppose that we need to use the flag 
--atlas but we don`t know if we need a generic atlas or we need an atlas at 
each subject' spaces.

Thanks in advance for your help.
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Re: [Freesurfer] Freesurfer version 7 reconall -autorecon2-wm error

[Hoopes, Andrew]

Hi Jewelia,

Can you try running without the -parallel flag to see if that’s the issue?

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jewelia K. Yao 

Date: Tuesday, May 4, 2021 at 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer version 7 reconall -autorecon2-wm error

External Email - Use Caution

Hi Freesurfer Developers,

I am trying to run reconall -autorecon2-wm using Freesurfer version 7 after 
making some minor edits to the wm.mgz file. I've tried it on multiple subjects 
and still get the same error (recon-all.log attached) when mri_fill starts to 
run:


reading segmented volume aseg.presurf.mgz

removing CC from segmentation

Looking for area (min, max) = (350, 1400)

area[0] = 1276 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75)

no need to search

using seed (127, 124, 151), TAL = (1.0, 23.0, 4.0)

*** Error in `mri_fill': double free or corruption (!prev): 0x01c65070 
***




reconall -autorecon2-wm runs well with Freesurfer version 6, but since the data 
was run through reconall with version 7, I was hoping to to use it for 
autorecon as well. I couldn't find any similar errors (specific to version 7) 
in the list. Does anyone know if this error is specific to version 7 and if 
there's any way to troubleshoot?

Thanks!
Jewelia
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Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

[Hoopes, Andrew]

Hi Renat,

That 3rd defect is fairly large – normally it would hang but it’s possible 
you’re running out of memory. If you can zip the subject and file drop it to 
us, we can take a look:

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

best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yakupov, Renat /DZNE 

Date: Friday, April 30, 2021 at 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution

Dear all,



I have a subject whose Freesurfer processing crashes during topology fixing 
step. The last lines in `recon-all.log` are:


After retessellation of defect 2 (v0=22890), euler #=-15 (110444,329616,219157) 
: difference with theory (-18) = -3
CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369)
Segmentation fault (core dumped)
Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 81489f2bb-M12_T1_01 exited with ERRORS at Tue Apr 27 21:23:59 CEST 
2021
For the full `recon-all.log` and `recon-all.error` files please see the 
attached files.



I tried to follow the manual topology fixing instructions from MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview,
 but *.white and *.pial surface files are missing from `surf` directory. It 
only contains these files:


lh.defect_borders  lh.defect_labels   lh.orig.nofix lh.smoothwm.nofix  
rh.orig.nofix rh.smoothwm.nofix
lh.defect_chulllh.inflated.nofix  lh.qsphere.nofix  rh.inflated.nofix  
rh.qsphere.nofix
Which files can I use in place of white and pial surface files in order to look 
for WM segmentation defects?



Some additional information about the data:

- I am running Freesurfer 7.1

- overall, there are no gross errors in WM segmentation, although the subjects 
does have significant temporal lobe atrophy

- there are two images acquired at different times, and processing fails for 
both images

- interestingly, processing didnt crash with Freesurfer 6.

Thank you and have a great weekend,

Renat.


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Re: [Freesurfer] Error with mris_convert

[Hoopes, Andrew]

Hi Mudathir,

What freesurfer version are using? I haven’t been able to reproduce this 
segfault on our end. Can you run the same command on lh.aparc.annot instead to 
narrow down whether this is an issue with your lh.par.annot file or not?

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of バキット・ムダシル 

Date: Sunday, April 25, 2021 at 8:32 AM
To: Freesurfer support list 
Subject: [Freesurfer] Error with mris_convert
External Email - Use Caution

Hi,
I manually made annotation files on an inflated surface of 40 subjects. The 
labels that makes these annotfiles are 13 in total but not present in all 
subjects every time, some can be missing depending on the brains surface 
morphology. I made the ctab files manually in the label folder in eluding an 
unknown label in the first line. I tried to convert one of the annotfiles into 
gii format and got the following error:
 mris_convert --annot $SUBJECTS_DIR/spl_01/label/lh.par.annot 
$SUBJECTS_DIR/spl_01/surf/lh.white ~/Desktop/spl_01/lh.par.gii
reading colortable from annotation file...
colortable with 14 entries read (originally none)
Segmentation fault: 11

What this error exactly means, and how I can solve this issue.
Thanks

Mudathir





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Re: [Freesurfer] mri_recon-all error : number of vertices does not match surface

[Hoopes, Andrew]

Hi Josephine,
It appears that the rh.thickness file is corrupted. I would suggest rerunning 
to see if that clears things up.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 林諐庭 

Date: Tuesday, April 20, 2021 at 4:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_recon-all error : number of vertices does not match 
surface

External Email - Use Caution
Dear FreeSurfer Developers:

We analyzed MRI T1 image data on freesurfer and encountered some difficulty, 
could you help us with this?  The recon-all.log file is already attached in 
this email in case you need it. We thank you in advance.

  *   FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
  *   program versions used:$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 
nicks Exp $

Best regards,
Josephine

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Re: [Freesurfer] Freeview - manjaro

[Hoopes, Andrew]

Please check out the known issues section of 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes for a fix

Best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Vishnu S 

Date: Monday, April 19, 2021 at 8:05 AM
To: Freesurfer support list 
Subject: [Freesurfer] Freeview - manjaro

External Email - Use Caution
I'm getting a repeated error with libjpeg.so.62. is there any known fix?
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Re: [Freesurfer] docker pull freesurfer: manifest error

[Hoopes, Andrew]

Hi Christina,

You’ll need to specify the version tag. You can try:

docker pull freesurfer/freesurfer:7.1.1

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chr. Roßmanith 

Date: Friday, April 16, 2021 at 8:41 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] docker pull freesurfer: manifest error
External Email - Use Caution

Hi,

I'd like to use FS 7 in a docker container. When pulling freesurfer I
get the following error message:

docker pull freesurfer/freesurfer
Using default tag: latest
Error response from daemon: manifest for freesurfer/freesurfer:latest
not found: manifest unknown: manifest unknown

Any hint what I'm doing wrong?

Regards,
Christina Roßmanith


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Re: [Freesurfer] error installing tensorflow

[Hoopes, Andrew]

Hi AJ,

Freesurfer ships its own python distribution, so it doesn’t matter what you 
have installed on your system. Can you let us know the specific version of 
macOS you are using and send the full error report from pip?

Thanks
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of AJ 
Date: Friday, April 16, 2021 at 11:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] error installing tensorflow

External Email - Use Caution
Hi,
I have python both versions of python installed:
MacBook-Pro-4:~ AJ$ python3 --version
Python 3.9.4
MacBook-Pro-4:~ AJ$ python --version
Python 2.7.10

when installing  fspython -m pip install tensorflow==1.13.1, I get the error:
dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib
Abort trap: 6

Is the issue that freesurfer is looking for python3?  I am not sure how to get 
past this installation of tensorflow?
Thank you for your help.
AJ


On Fri, Apr 16, 2021 at 12:58 AM Vishnu S 
mailto:vishnudab...@gmail.com>> wrote:

External Email - Use Caution
Can you try downgrading to python 3.6 in a conda env? Python 3.7 support only 
TF 2.0 and higher.

On Fri, 16 Apr 2021, 11:24 AJ, 
mailto:ajcns1...@gmail.com>> wrote:

External Email - Use Caution
Hi,

I am having trouble installing:  fspython -m pip install tensorflow==1.13.1
Not sure what the issue is.  Any help would be greatly appreciated.
best
AJ
Error message while installing:

dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3
  Expected in: /usr/lib/libSystem.B.dylib


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Re: [Freesurfer] Freeview does not open files through the Freeview window (Terminal only)

[Hoopes, Andrew]

Hi Max,

You could try downloading an updated, standalone release of freeview from 
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Max Korbmacher 

Date: Wednesday, April 14, 2021 at 2:05 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freeview does not open files through the Freeview window 
(Terminal only)
External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to open files through Freeview v.2.0 (I’m using 
freesurfer-i386-apple-darwin11.4.2-stable6-20170119), but cannot do it 
“manually” but only through scripting / the terminal. The operating system is 
macOS BigSur 11.2.3 (20D91). The latest attempt to open files this way have led 
the program to crashes or freeze. Please find attached an error report from the 
program crashing.

Best,
Max
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Re: [Freesurfer] addon question perl version needed for FS5.3

[Hoopes, Andrew]

Hi Phillip,

Yes, 5.3 is getting to the point where some components are just too old to 
install correctly on modern system. I would read through this thread 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg69376.html that 
discusses this problem and a potential solution, similar to what you suggest.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Date: Monday, April 12, 2021 at 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] addon question perl version needed for FS5.3

External Email - Use Caution

Hi all,



sorry for a short additional question on the same perl topic:



I found that the critical syntax of an "if(defined(@...)" has been omitted in 
FS6.0.



Where there other changes to the perl scripts in the subfolder "mni" or could 
they be exchanged by the mni folder of FS6.0 in order to avoid the break of the 
perl script due to a version problem?



Thanks for any hints,

Philipp


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Saemann, Philipp 

Gesendet: Montag, 12. April 2021 22:06
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] perl version needed for FS5.3


External Email - Use Caution

Hi all,



we have problems in launching the recon-all command of FS5.3 (needed for a 
reconstruction of old results):

during the nu_correct command various perl commands are called with a fix



#!/usr/bin/perl -w



The primary error is some "Can't used 'define(@Array)'.



A bit of search showed that this seems perl version issue. Up to versio 5.18 
this only seems to produce a warning,

but no fatal error.



On the respective node of our cluster we have installed another perl and call 
this module before,

so the "which perl" correctly points to that perl main function.



Still, errors appear, e. g. cannot locate MNI/Startup.pm, so obviously some 
packages are not correctly linked.



What is the Installation recommendation on a Linux 64 Bit System to maFS5.3 
compatible with the local perl?



Best,

Philipp


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Re: [Freesurfer] Install issue

[Hoopes, Andrew]

I’m not totally sure of the answer here. Could be filesystem limitations or a 
permissions issue. Have you tried untar’ing without the -p flag, or ensuring 
that you can write to /usr/local?

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pål Gunnar Larsson 

Date: Tuesday, April 13, 2021 at 8:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Install issue

External Email - Use Caution
Today I tried to set up a new Freesurfer instance.
It is on a Win10 system with Vmware 6.0 and Ubuntu 18 LTS.

I have tried a local install and to /usr/local, but I get the same error  
“cannot hardlink to….” And then a row of protocol errors (see attachment).

What is the issue?

Pål G. Larsson M.D., PhD.
Department of Neurosurgery
Division of Surgery and Clinical Neuroscience

not sensitive

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Re: [Freesurfer] mri_convert problem

[Hoopes, Andrew]

Have you made sure that you have read permission to open those files? What is 
the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your 
working directory.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pierpaolo Croce 

Date: Thursday, April 8, 2021 at 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_convert problem

External Email - Use Caution
Dear List,
I have installed the ubuntu version of freesurfer (creating the VM as in the 
tutorial)
I would like to run the following command:

mri_convert -c -oc 0 0 0 asta.mgh orig.mgz

I always get the error in the screen shot. Can someone help me?
also using asta.nii format
--

Ing. Pierpaolo Croce, PhD.
Institute for Advanced Biomedical Technologies - ITAB
and
Department of Neuroscience and Imaging
University of Chieti "G. D'Annunzio"
Via dei Vestini, 33
66013 Chieti, Italy
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Re: [Freesurfer] "ERROR: crypt() returned null with 4-line file"

[Hoopes, Andrew]

Thanks for the details. We’ll look into it a bit and get back to you.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Cook, Philip 

Date: Monday, April 5, 2021 at 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file"

External Email - Use Caution
Dear FreeSurfer developers,

I have also encountered the error that Katja Zoner reported in

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg69509.html

We work on different servers within the same institution and have been in 
contact with our administrators, we are sure at this point that the error is 
caused by FIPS 140 compliance on some of our systems. It is unrelated to 
Singularity. The crypt() function, as called in freesurfer/utils/chklc.cpp, 
returns NULL with errno == EPERM on machines booted in FIPS mode. I believe 
these users have encountered the same problem

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54981.html

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57637.html

As one of the above users noted, certain institutions (such as the Veterans 
Administration) require FIPS mode, as do studies using sensitive data. Our 
administrators have agreed to provide some "insecure" machines to run 
FreeSurfer binaries and containers for the time being, but we're concerned 
about the sustainability of this longer term.

I think the issue could be resolved by using a FIPS-compliant algorithm in the 
call to crypt(). For example, I've tested crypt() with the SHA-512 algorithm in 
FIPS mode, and this works

  crypt_gkey = crypt(gkey, "$6$FS");

but this would require the license file to contain an SHA-512 encrypted gkey in 
addition to the DES one that currently exists.

Alternatively, we can check if errno == EPERM after the call to crypt(), and 
bypass the encryption check in that case.

I understand that these solutions are non-trivial and could raise backwards 
compatibility or license compliance issues. Unfortunately, I've not been able 
to find any other workaround.

Thanks

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Re: [Freesurfer] [External] Re: "ERROR: crypt() returned null with 4-line file" when running via Singularity

[Hoopes, Andrew]

Hi Katja,

Okay good to know. I will follow up off-list.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zoner, Katja 

Date: Tuesday, March 30, 2021 at 1:24 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [External] Re: "ERROR: crypt() returned null with 
4-line file" when running via Singularity

External Email - Use Caution
Hi Andrew,

After speaking with our compute cluster service providers, it seems like this 
error is due to FIPS being enabled on the cluster. Are there any existing 
solutions to FIPS conflicts with FreeSurfer?

Thanks!
Katja

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Saturday, March 27, 2021 4:19 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] "ERROR: crypt() returned null with 4-line 
file" when running via Singularity


Hi Katja,



I wonder if this is related to possible security settings. I can’t replicate 
this, but can you send your license file so that we can narrow down the 
possibilities? You can send it directly to my email, off-list.



Best

Andrew



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zoner, Katja 

Date: Monday, March 22, 2021 at 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when 
running via Singularity

External Email - Use Caution

Hi all,



I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity 
image (pulled from the FreeSurfer DockerHub) like this:

export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt

export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer



singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \

/project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \

recon-all -s sub-17867 -i 
/mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz
 -all

But it fails quickly with error message:

ERROR: crypt() returned null with 4-line file

Do you know what might be causing this error message? How can I address this?

Additional info:

  1.  FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
  2.  uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 
12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
  3.  recon-all.log: see attached

See GitHub issue: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://github.com/freesurfer/freesurfer/issues/848<https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848>

[https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44igxbFcjkvEBwioJUXRaWvFZHtoGPQqrUbSlBypgDgQbDuBWjvd-22zMLp_ozjhIwKQzVLJKCp0yPoqA5Jl_pFvhR-3OKlIQ9D5gOx-1rSy9WaziDl1r-sKmOwEbyWlYPXOi1GYxFF_5VZ3ElEqF1XxMvU2JxTpTowEWPoVTRECmtbmBdJhnEkKiBKV2AlSQcbm-ZEJyL2cL-lSnLuPDlXjKSBdlNZgzeMLSL51ug/https%3A%2F%2Favatars.githubusercontent.com%2Fu%2F6330653%3Fs%3D400%26v%3D4]<https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848>

`ERROR: crypt() returned null with 4-line file` when running via Singularity 
image · Issue #848 · 
freesurfer/freesurfer<https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848>

I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity 
image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt 
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22...

github.com



Thank you for any assistance!

Katja Zoner


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Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[Hoopes, Andrew]

Matt (cc’d) has recently posted a similar error on the last. Unfortunately, 
these mac MCR errors are difficult to debug. You could wait for the python 
subfield port to get released, but that might be a few months down the line. If 
you want to get things running immediately, one thing to try is to download the 
7.1 docker container from https://hub.docker.com/r/freesurfer/freesurfer and 
run FS through that. That should fix any system-specific problems.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ramtilak Gattu 

Date: Thursday, March 25, 2021 at 7:20 PM
To: fsbuild , freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution

External Email - Use Caution
Hi 'E' / 'R',

I even tried changing the resolution to 1.0 with no success ruling put memory 
issues.

Just wondering if its time to give up and wait for your python build to 
successfully finish the job in mac. I wonder if any other user with a similar 
MacBook pro configuration as mine
Hardware Overview:

  Model Name: MacBook Pro
  Model Identifier: MacBookPro16,1
  Processor Name: 6-Core Intel Core i7
  Processor Speed: 2.6 GHz
  Number of Processors: 1
  Total Number of Cores: 6
  L2 Cache (per Core): 256 KB
  L3 Cache: 12 MB
  Hyper-Threading Technology: Enabled
  Memory: 16 GB
  System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)
  Serial Number (system): C02DPB3BMD6M
  Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4
  Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4
  Activation Lock Status: Enabled

had successfully finished the processing or encountered the same issue and 
later fixed it to successfully run the segmentation. Is there a way to bypass 
that step and run the program till the end?

I think some Compatability issues with 'MCR' holding back the processing at 
that stage.

Again, thanks a lot for all your help in this regards.

Regards
Tilak

From: Ramtilak Gattu 
Sent: Wednesday, March 24, 2021 8:32 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

First let me thank you 'R' and 'E' for being so patient and working with me to 
resolve this issue.

As suggested by 'R' I monitored the activity monitored but unfortunately, the 
memory pressure graph remained green throughout the process. When the program 
was running memory usage jumped from 6.25gb to 7.85 gb.

As suggeted by 'E" I even tried to run the code by changing the parameters in 
the code for


set RESOLUTION="0.".

by:

set RESOLUTION="0.5";

still, the error persists.

It works fine on my Linux centos system(8gb ram) but fails on both the macs. 
surprisingly, it's the same exact error.

Does running the routine after installing full matlab instead of just mcr8.4 
would help? just a thought.

Thanks

Regards
Tilak


From: fsbuild 
Sent: Wednesday, March 24, 2021 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

I don’t see anything in your output showing say code 01 with Bus Error.  But 
code 01 could indicate a memory issue, e.g., not enough RAM.

You could bring up the Activity Monitor program and click on the memory tab to 
profile memory during the command run.  But the "memory pressure" graph does 
not go back very far in time, so you would need to be able to see it close to 
the time the command exits. See  
https://www.lifewire.com/use-activity-monitor-to-track-mac-memory-usage-2260880

- R.


On Mar 24, 2021, at 04:26, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Yes it says enabled.

[tilak:~] tilak% csrutil status
System Integrity Protection status: enabled.

Thanks

Regards,
Tilak

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Wednesday, March 24, 2021 4:22 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ramtilak Gattu mailto:rg...@med.wayne.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is 
turned on the Mac (which is the default).  The following command will report if 
it is enabled or disabled, e.g., when enabled,

$ csrutil status
System Integrity Protection status: enabled.
- R.

On Mar 24, 2021, at 01:48, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running 
"fs_install_mcr R2014b" as suggested in FSwiki.

I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (build 
1.8.0_281-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed m

Re: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity

[Hoopes, Andrew]

Hi Katja,

I wonder if this is related to possible security settings. I can’t replicate 
this, but can you send your license file so that we can narrow down the 
possibilities? You can send it directly to my email, off-list.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zoner, Katja 

Date: Monday, March 22, 2021 at 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file" when 
running via Singularity

External Email - Use Caution
Hi all,


I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity 
image (pulled from the FreeSurfer DockerHub) like this:

export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt

export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer



singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \

/project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \

recon-all -s sub-17867 -i 
/mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz
 -all

But it fails quickly with error message:

ERROR: crypt() returned null with 4-line file

Do you know what might be causing this error message? How can I address this?

Additional info:

  1.  FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
  2.  uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 
12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
  3.  recon-all.log: see attached

See GitHub issue: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://github.com/freesurfer/freesurfer/issues/848
[https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44igxbFcjkvEBwioJUXRaWvFZHtoGPQqrUbSlBypgDgQbDuBWjvd-22zMLp_ozjhIwKQzVLJKCp0yPoqA5Jl_pFvhR-3OKlIQ9D5gOx-1rSy9WaziDl1r-sKmOwEbyWlYPXOi1GYxFF_5VZ3ElEqF1XxMvU2JxTpTowEWPoVTRECmtbmBdJhnEkKiBKV2AlSQcbm-ZEJyL2cL-lSnLuPDlXjKSBdlNZgzeMLSL51ug/https%3A%2F%2Favatars.githubusercontent.com%2Fu%2F6330653%3Fs%3D400%26v%3D4]
`ERROR: crypt() returned null with 4-line file` when running via Singularity 
image · Issue #848 · 
freesurfer/freesurfer
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity 
image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt 
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22...
github.com



Thank you for any assistance!

Katja Zoner

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Re: [Freesurfer] License Agreement for re-distribution

[Hoopes, Andrew]

Hi Ezequiel,

Just including the FS license in the software as a separate text file is fine.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ezequiel Mikulan 

Date: Monday, March 22, 2021 at 12:48 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] License Agreement for re-distribution

External Email - Use Caution
Hi All, I've developed an open-source software for MRI pseudonymization that 
uses Freesurfer so I wanted to check that I'm correctly handling the licenses.

In Freesurfer's License Agreement it says that: "If you distribute Software (as 
defined below) downloaded from FreeSurfer, all of the paragraphs of Part B of 
this Agreement must be included with and apply to such Software".

It is not clear to me if we should copy the relevant part into our license or 
if it is ok if we add a text file in the software with Freesurfer's license. In 
other words, should Part B be included inside our license or inside the 
software as a file?

How should I proceed? Thanks,

Ezequiel
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Re: [Freesurfer] Freesurfer 6.0.0 Container & MCR

[Hoopes, Andrew]

Hi Ursula,

I was just reminded that we purposely don’t include MCR in the container due to 
redistribution-restrictions by the MCR license. So, it’s up to the user to 
install or provide the MCR library if needed.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Date: Friday, March 19, 2021 at 1:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer 6.0.0 Container & MCR
Hi Ursula,

Thanks for pointing this out. I think it’s just the case that MCR wasn’t 
installed in that container. I’m surprised this hasn’t been brought up before. 
We’ll update the container with it.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ursula Tooley 

Date: Friday, March 19, 2021 at 12:23 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer 6.0.0 Container & MCR

External Email - Use Caution
Hi Freesurfer experts,

I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC 
(for consistency with previous pipelines), and got the error below about not 
finding the Matlab Compiler Runtime in the container. I have worked around it 
by explicitly binding the mcr on the HPC to the container with “-B 
/cbica/software/external/matlab/mcr/v711/:/opt/freesurfer/MCRv80”, but is this 
the expected behavior? Or is there some issue? My understanding was that one of 
the advantages of mcr was that you could include it in containers and 
distribute compiled code, so was surprised to find this come up.

Thanks in advance,
Ursula
---
Ursula Tooley
Ph.D. Candidate
Neuroscience Graduate Group
University of Pennsylvania
she/her/hers
utoo...@gmail.com<mailto:utoo...@gmail.com>
202.413.5627




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Re: [Freesurfer] Freesurfer 6.0.0 Container & MCR

[Hoopes, Andrew]

Hi Ursula,

Thanks for pointing this out. I think it’s just the case that MCR wasn’t 
installed in that container. I’m surprised this hasn’t been brought up before. 
We’ll update the container with it.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ursula Tooley 

Date: Friday, March 19, 2021 at 12:23 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer 6.0.0 Container & MCR

External Email - Use Caution
Hi Freesurfer experts,

I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC 
(for consistency with previous pipelines), and got the error below about not 
finding the Matlab Compiler Runtime in the container. I have worked around it 
by explicitly binding the mcr on the HPC to the container with “-B 
/cbica/software/external/matlab/mcr/v711/:/opt/freesurfer/MCRv80”, but is this 
the expected behavior? Or is there some issue? My understanding was that one of 
the advantages of mcr was that you could include it in containers and 
distribute compiled code, so was surprised to find this come up.

Thanks in advance,
Ursula
---
Ursula Tooley
Ph.D. Candidate
Neuroscience Graduate Group
University of Pennsylvania
she/her/hers
utoo...@gmail.com
202.413.5627




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Re: [Freesurfer] Matlab Runtime error line 334

[Hoopes, Andrew]

Hi Matt,

Hopefully this isn’t specific to M1, but I’m not sure it would be in this case. 
Maybe try running fs_install_mcr with sudo in front? Some users are suggesting 
it here:
https://www.mathworks.com/matlabcentral/answers/176228-error-message-install_unix-not-found

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Cleary, Matthew 

Date: Friday, March 12, 2021 at 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Matlab Runtime error line 334
External Email - Use Caution

Hi team,

I’m wondering if I could please ask for help - I am trying to install 
fs_install_mcr R2014b on a 2020 M1 chip MacBook. I’m encountering an error at 
the end, that goes as follows;

inflating: sys/java/jre/maci64/jre/THIRDPARTYLICENSEREADME.txt
  inflating: sys/java/jre/maci64/jre/Welcome.html
  inflating: trademarks.txt
./install: line 334: 
/var/folders/2f/fyngt3b52mn39mcc6_419q8hgn/T/tmp.rt0pgVdq/bin/unknown/install_unix:
 No such file or directory
ls: 
/var/folders/2f/fyngt3b52mn39mcc6_419q8hgn/T/tmp.rt0pgVdq/install-target/v*:
 No such file or directory

Do you have any idea how I can fix this? Any help would be massively 
appreciated.

Kindest regards,
Matt

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Re: [Freesurfer] license file not working

[Hoopes, Andrew]

Hi Philipp,

Okay interesting. So it's failing on centos 8. Do you mind sending the license 
file directly to my email (off-list)?

thanks
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Sent: Monday, March 15, 2021 3:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] license file not working

External Email - Use Caution

Hi Andrew,


it works on the "frontend" of  our cluster:


NAME="Scientific Linux"
VERSION="7.9 (Nitrogen)"
ID="scientific"
ID_LIKE="rhel centos fedora"
VERSION_ID="7.9"
PRETTY_NAME="Scientific Linux 7.9 (Nitrogen)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:scientificlinux:scientificlinux:7.9:GA"
HOME_URL="http://www.scientificlinux.org//";
BUG_REPORT_URL="mailto:scientific-linux-de...@listserv.fnal.gov";
REDHAT_BUGZILLA_PRODUCT="Scientific Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.9
REDHAT_SUPPORT_PRODUCT="Scientific Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.9"



But not any more on the nodes:

NAME="CentOS Linux"

VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Linux 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/";
BUG_REPORT_URL="https://bugs.centos.org/";
CENTOS_MANTISBT_PROJECT="CentOS-8"
CENTOS_MANTISBT_PROJECT_VERSION="8"



Thanks in advance,

best,

Philipp




Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Hoopes, Andrew 

Gesendet: Montag, 15. März 2021 20:29
An: Freesurfer support list
Betreff: Re: [Freesurfer] license file not working


Hi Philipp,



Can you let us know the OS and version you’re running on? The license format 
was updated for v6. It should be backwards compatible, but it’s possible it’s 
not anymore on newer systems.



thanks

Andrew



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Date: Monday, March 15, 2021 at 2:36 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] license file not working

External Email - Use Caution

Hi FreeSurfer specalists,



for some historical reconstruction I had to download an old FS5.3-Version,

on a Linux System, untarred etc. - it seems there was no .license = hidden 
license

file coming with the download, and no license.txt file.



I requested one (usual link) and received a license.txt file, and put that

into the FS home folder. When using the command mri_convert I get the

error message that an invalid License file is used.

Questions:



(1) Is a .license file (so, a hidden file) needed for itself or in addition?

(2) Why does a freshly delivered license.txt file not work?

(3) Any other solutions or ideas?



Bw,

Philipp

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Re: [Freesurfer] license file not working

[Hoopes, Andrew]

Hi Philipp,

Can you let us know the OS and version you’re running on? The license format 
was updated for v6. It should be backwards compatible, but it’s possible it’s 
not anymore on newer systems.

thanks
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Date: Monday, March 15, 2021 at 2:36 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] license file not working

External Email - Use Caution

Hi FreeSurfer specalists,



for some historical reconstruction I had to download an old FS5.3-Version,

on a Linux System, untarred etc. - it seems there was no .license = hidden 
license

file coming with the download, and no license.txt file.



I requested one (usual link) and received a license.txt file, and put that

into the FS home folder. When using the command mri_convert I get the

error message that an invalid License file is used.

Questions:



(1) Is a .license file (so, a hidden file) needed for itself or in addition?

(2) Why does a freshly delivered license.txt file not work?

(3) Any other solutions or ideas?



Bw,

Philipp
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Re: [Freesurfer] Matlab version 2012b installation problem

[Hoopes, Andrew]

The 'matlab runtime' (MCR) installed by fs_install_mcr lets you run compiled 
matlab binaries, but it’s different from having matlab actually installed on 
your system. MCR is used to run the sub-structure segmentation tools, but 
mris_compute_lgi is a command that runs matlab scripts directly, so it’s 
required that you have matlab installed on your computer to use it.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Georgia Kapizioni 

Date: Wednesday, March 10, 2021 at 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Matlab version 2012b installation problem

External Email - Use Caution
Hello Andrew,

Thank you once again for your help and apologies for writing one more time, but 
it seems that Freesurfer cannot detect/recognise Matlab. When I tried to ran 
local gyrification index for one participant, I got the following error:

recon-all -s HD01 -localGI
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/georgina/Downloads/HDf
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 georgina  staff  1188013 Mar 10 13:20 
/Users/georgina/Downloads/HDf/HD01/scripts/recon-all.log
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64
/Users/georgina/Downloads/HDf/HD01/surf
#
#@# Local Gyrification Index lh Wed Mar 10 13:24:00 EET 2021
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64

recon-all -s HD01 exited with ERRORS at Wed Mar 10 13:24:00 EET 2021


Attached please also find the recon-all.error.

When I go to Freesurfer directory and type: ls -l 
$FREESURFER_HOME/bin/fs_install_mcr
The output is: -rw-r--r--  1 root  wheel  2010 Mar  6 12:03 
/Applications/freesurfer/bin/fs_install_mcr

Do you have any idea about what went wrong?
Thank you once more time.
Best,
Georgia



On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Thank you so much for your response.

Here is the output when running the command you suggested:

Georgias-MacBook-Pro:~ georgina$ curl MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr
  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   8170  0 --:--:-- --:--:-- --:--:--  8137
(base) Georgias-MacBook-Pro:~ georgina$ ls fs_install_mcr
fs_install_mcr




I assume, it didn’t download it, right?

Georgia





On 26 Feb 2021, at 8:03 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Please accept my apologies for such a detailed response, I had a health issue, 
and I was just able to test what you suggested.

When I use the wget command, again I have an error: -bash: wget: command not 
found

Any ideas on how to overcome this issue?



Thank you once again,
Best,
Georgia



On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Thank you for your response!
The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x) was:

 % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   5275  0 --:--:-- --:--:-- --:--:--  5261
usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] mode|entry 
file ...
chmod [-fhv] [-R [-H | -L | -P]] [-E | 

Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs

[Hoopes, Andrew]

Yes, I was just going to follow up with this disclaimer. It’s a slightly newer 
version of nu_correct, so it’s possible the result will differ very slightly. 
The problem is that the FS 5.3 version of MNI/nu_correct uses a perl version 
that reached end-of-life in 2008! So it would be quite difficult to rebuild a 
local package for centos8.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tobias, Malcolm 

Date: Monday, March 8, 2021 at 3:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on 
newer OSs

External Email - Use Caution

External Email - Use Caution

Andrew,

That's a great suggestion, thanks.

Any idea whether using the MNI from FS6 has an impact on the results?

Cheers,
Malcolm

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, March 8, 2021 2:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on 
newer OSs


* External Email - Caution *

Hi Malcolm,



Yes, this is an unfortunate bug, but I've been playing around with a few 
options and the following seems to be the best patch. This assumes you also 
have FS v6  installed and, in this case, FS_53 and FS_60 point to the 
respective freesurfer base directories:



rm -rf $FS_53/mni

cp -r $FS_60/mni $FS_53/



Then, customize the 5.3 SetUpFreeSurfer.sh (or whatever you use to source FS) 
to ensure that the following variables are set in a 5.3 environment:



export PERL5LIB="$FS_53/mni/share/perl5"

export MNI_PERL5LIB="$FS_53/mni/share/perl5"



Hope that helps,

Andrew





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tobias, Malcolm 

Date: Monday, March 8, 2021 at 10:48 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs

External Email - Use Caution

External Email - Use Caution



All,



We're setting up a new cluster (based on CentOS 8) but have many users that 
still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).

We're hitting a perl error which appears to be a known issue with newer 
versions of Perl:



[mtobias@login02 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 
50 --no-rescale --i orig.mgz --o orig_nu.mgz

/mnt/beegfs/scratch/mtobias/mri

/export/freesurfer/freesurfer-5.3.0-HCP/bin/mri_nu_correct.mni

--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

nIters 1

$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $

...

Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at 
/export/freesurfer/freesurfer-5.3.0-HCP/mni/bin/nu_estimate_np_and_em line 165.

nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=65280)

ERROR: nu_correct



One fix suggested for Ubuntu users is to install an older version of Perl.  
While we've tried that on our system, it seems the perl scripts are hard-wired 
to use /usr/bin/perl:



[root@mgt bin]# head -1 nu_estimate_np_and_em

#!/usr/bin/perl -w



So without replacing the system perl on every system in the cluster, is anyone 
aware of any other work-arounds for this issue?

Cheers,

Malcolm







The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs

[Hoopes, Andrew]

Hi Malcolm,

Yes, this is an unfortunate bug, but I've been playing around with a few 
options and the following seems to be the best patch. This assumes you also 
have FS v6  installed and, in this case, FS_53 and FS_60 point to the 
respective freesurfer base directories:

rm -rf $FS_53/mni
cp -r $FS_60/mni $FS_53/

Then, customize the 5.3 SetUpFreeSurfer.sh (or whatever you use to source FS) 
to ensure that the following variables are set in a 5.3 environment:

export PERL5LIB="$FS_53/mni/share/perl5"
export MNI_PERL5LIB="$FS_53/mni/share/perl5"

Hope that helps,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tobias, Malcolm 

Date: Monday, March 8, 2021 at 10:48 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs

External Email - Use Caution

External Email - Use Caution

All,

We're setting up a new cluster (based on CentOS 8) but have many users that 
still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).
We're hitting a perl error which appears to be a known issue with newer 
versions of Perl:

[mtobias@login02 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 
50 --no-rescale --i orig.mgz --o orig_nu.mgz
/mnt/beegfs/scratch/mtobias/mri
/export/freesurfer/freesurfer-5.3.0-HCP/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
...
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at 
/export/freesurfer/freesurfer-5.3.0-HCP/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=65280)
ERROR: nu_correct

One fix suggested for Ubuntu users is to install an older version of Perl.  
While we've tried that on our system, it seems the perl scripts are hard-wired 
to use /usr/bin/perl:

[root@mgt bin]# head -1 nu_estimate_np_and_em
#!/usr/bin/perl -w

So without replacing the system perl on every system in the cluster, is anyone 
aware of any other work-arounds for this issue?

Cheers,
Malcolm



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] PROBLEM WITH license.txt file

[Hoopes, Andrew]

If you installed freesurfer with admin permissions, you should mv or cp the 
file to the destination directory with `sudo` in front of your command to run 
as root.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Donato Romano 

Date: Monday, March 8, 2021 at 6:52 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] PROBLEM WITH license.txt file

External Email - Use Caution
Hello FreeSurfer Developers,

I have a problem with the license.txt file. I installed freesurfer MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-linux-centos7_x86_64-7.1.0.tar.gz
 on the ubuntu system and I obtained the license.txt file by following the 
guidelines on freesurfer site. I can't paste the file into the freesurfer older 
because I have not the permission to do it, how can I solve this problem?

Best regards
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Re: [Freesurfer] Matlab version 2012b installation problem

[Hoopes, Andrew]

Looks like it downloaded fine. In that case, just move that file to your FS 
install:

mv fs_install_mcr $FREESURFER_HOME/bin

and you should be good to go.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Georgia Kapizioni 

Date: Monday, March 1, 2021 at 10:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Matlab version 2012b installation problem

External Email - Use Caution
Hello Andrew,

Thank you so much for your response.

Here is the output when running the command you suggested:

Georgias-MacBook-Pro:~ georgina$ curl MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr
  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   8170  0 --:--:-- --:--:-- --:--:--  8137
(base) Georgias-MacBook-Pro:~ georgina$ ls fs_install_mcr
fs_install_mcr


I assume, it didn’t download it, right?

Georgia





On 26 Feb 2021, at 8:03 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Please accept my apologies for such a detailed response, I had a health issue, 
and I was just able to test what you suggested.

When I use the wget command, again I have an error: -bash: wget: command not 
found

Any ideas on how to overcome this issue?

Thank you once again,
Best,
Georgia



On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Thank you for your response!
The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x) was:

 % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   5275  0 --:--:-- --:--:-- --:--:--  5261
usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] mode|entry 
file ...
chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file …


However, when I type: ls -l $FREESURFER_HOME/bin/fs_install_mcr as you 
suggested, it appears ls: /Applications/freesurfer/bin/fs_install_mcr: No such 
file or directory
When I type again fs_install_mcr while being in Freesurfer/bin path again 
fs_install_mcr: command not found appears.
Any idea what went wrong?


Thanks once again,
Best,
Georgia







On 9 Feb 2021, at 1:05 AM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Dear Freesurfer experts,

I am trying to install Matlab version 2012b but a message appears: command not 
found.

Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x
Then I typed: fs_install_mcr R2012b and I receive: command not found.
My FS version is 6 and I have already install Matlab2016_b on my Mac.

Could you please help me resolve this issue?
Thank you in advance,
Georgia




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Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

[Hoopes, Andrew]

Can you run this instead:

apt-get -y install libncurses5

That should fix it. Also, please do not globally add the MCRv84 path to 
LD_LIBRARY_PATH. This shouldn’t be needed to run the subfield code and will 
likely cause problems for other freesurfer binaries.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ishi Tandon AIB, Jaipur 

Date: Thursday, March 4, 2021 at 1:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 
20.04.1 LTS

External Email - Use Caution
Yes, the same error occurred again.

It would be great if someone from the dev team could help me resolve it.



On Thu, Mar 4, 2021 at 11:29 AM Horsng Junn 
mailto:hsj...@gmail.com>> wrote:

External Email - Use Caution
You mean the following error occurred again?

libncurses.so.5: cannot open shared object file: No such file or directory

Sorry but I ran out of ideas.
Could anyone from the FreeSurfer dev team chime in?

Please delete the file you just created with the following command, so it won't 
get in the way later.
sudo rm /usr/lib/x86_64-linux-gnu/libncurses.so.5

Best,
Horsng



On Mar 4, 2021, at 2:46 PM, Ishi Tandon AIB, Jaipur 
mailto:ishi.tan...@student.amity.edu>> wrote:


External Email - Use Caution

 Thanks alot.
That seems to have executed without any errors.

But 
segmentHA_T1.sh
 seems to display the same error again.


On Thu, Mar 4, 2021 at 11:03 AM Horsng Junn 
mailto:hsj...@gmail.com>> wrote:

External Email - Use Caution

Then installing libncurses5-dev doesn't seem like the solution we've been 
seeking after all.
Could you try this instead?

sudo ln -s /usr/lib/x86_64-linux-gnu/libncurses.so.6.2 
/usr/lib/x86_64-linux-gnu/libncurses.so.5

Regards,
Horsng



On Mar 4, 2021, at 2:17 PM, Ishi Tandon AIB, Jaipur 
mailto:ishi.tan...@student.amity.edu>> wrote:


External Email - Use Caution


 Upon running sudo apt-get install libncurses5-dev.
This is what I get (attached below).



On Thu, Mar 4, 2021 at 10:36 AM Horsng Junn 
mailto:hsj...@gmail.com>> wrote:

External Email - Use Caution

Hi Ishi,

The results suggest that libncurses5-dev isn't installed at all.
(Listed files are all from the default libncurses 6)

In your previous mail you said that:

>> Also, I have tried sudo apt-get install libncurses5-dev. But that doesn't 
>> seem to resolve the issue.

What exactly happened when you ran that command?
Could you please re-run that command and attach the result?

Best,
Horsng


On Mar 4, 2021, at 1:58 PM, Ishi Tandon AIB, Jaipur 
mailto:ishi.tan...@student.amity.edu>> wrote:


External Email - Use Caution

Hello,

Thanks for your response.

I tried to look for libncurses5-dev in my home directory.
It appears to be installed on usr/share/doc.
Upon checking its permissions, it seemed to be owned by the root.

Also, upon running the aforementioned commands this is what I get (attached 
below).

On Thu, Mar 4, 2021 at 6:30 AM Horsng Junn 
mailto:hsj...@gmail.com>> wrote:

External Email - Use Caution

Hi Ishi,

Following are what I gathered:

- You're running Freesurfer 7.1.1 on an ubuntu 20.04 box
- Ubuntu 20.04 has libncurses 6 installed as default
- Freesurfer 7.1.1 is linked against libncurses 5
- So previously you were advised to install libncurses5-dev
- And you followed the advice
- But somehow your ubuntu is failing to find the shared object file of that 
library

It seems your installation of libncurses5-dev is somehow hosed.
Could you please double check if libncurses5-dev is successfully installed
by running the following commands one at a time?
(You don't need to be root to run them.)

apt list --installed *ncurses*
find /lib -name 'libncurses*'
find /usr/lib -name 'libncurses*'
find /usr/local/lib -name 'libncurses*'


Best
Horsng


On Mar 3, 2021, at 1:53 PM, Ishi Tandon AIB, Jaipur 
mailto:ishi.tan...@student.amity.edu>> wrote:


External Email - Use Caution

Hello experts,

With reference to my previous email, I am attaching the log file of 
segmentHA_T1.sh
 bert command.

Please provide your feedback.

Tha

Re: [Freesurfer] Installing freesurfer 6 in a preexisting conda environment

[Hoopes, Andrew]

Hi Bruno,

I’m not sure I fully understand the question. If you want to use freesurfer in 
combination with MNE, why not just install FS normally and source it while 
you’ve activated your conda environment?

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruno Mansur 

Date: Friday, February 26, 2021 at 9:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Installing freesurfer 6 in a preexisting conda environment

External Email - Use Caution
Dear community members,

I created a conda environment for installing MNE. Now I want to install 
freesurfer in this same environment to use freesurfer in combination with MNE.

Does anyone have already installed and configured freesurfer in an environment 
and could give me some support with it?

The mailing list has no entries related to 'conda environment' and the 
freesurfer installation guide webpage has no instructions related to this.

I would appreciate any help,

Best regards

--
Bruno
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Re: [Freesurfer] Matlab version 2012b installation problem

[Hoopes, Andrew]

Hi Georgia,

No worries. It just means you’re missing wget, but we should probably figure 
out the problem with curl. From any directory, can you run:

curl 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr
ls fs_install_mcr

What’s the output of that?

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Georgia Kapizioni 

Date: Friday, February 26, 2021 at 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Matlab version 2012b installation problem

External Email - Use Caution
Hello Andrew,

Please accept my apologies for such a detailed response, I had a health issue, 
and I was just able to test what you suggested.

When I use the wget command, again I have an error: -bash: wget: command not 
found

Any ideas on how to overcome this issue?

Thank you once again,
Best,
Georgia



On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Thank you for your response!
The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x) was:

 % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   5275  0 --:--:-- --:--:-- --:--:--  5261
usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] mode|entry 
file ...
chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file …


However, when I type: ls -l $FREESURFER_HOME/bin/fs_install_mcr as you 
suggested, it appears ls: /Applications/freesurfer/bin/fs_install_mcr: No such 
file or directory
When I type again fs_install_mcr while being in Freesurfer/bin path again 
fs_install_mcr: command not found appears.
Any idea what went wrong?


Thanks once again,
Best,
Georgia







On 9 Feb 2021, at 1:05 AM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Dear Freesurfer experts,

I am trying to install Matlab version 2012b but a message appears: command not 
found.

Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x
Then I typed: fs_install_mcr R2012b and I receive: command not found.
My FS version is 6 and I have already install Matlab2016_b on my Mac.

Could you please help me resolve this issue?
Thank you in advance,
Georgia



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Re: [Freesurfer] mincRead error

[Hoopes, Andrew]

Hi Michele,

It looks like there is a local MNI install in /opt/minc/1.9.16 that is taking 
priority over freesurfer. I would suggest rerunning freesurfer without sourcing 
this local minc.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Michele Valotti 

Date: Monday, February 22, 2021 at 5:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
Hi all,
I was wondering if anyone had a chance to look at the log to shed some light on 
this mystery error, or if more info or a different log are needed.

Thank you,
Michele

On Fri, 12 Feb 2021 at 10:05, Michele Valotti 
mailto:michele.valo...@gmail.com>> wrote:
Hi Andrew,
thank you for your help, I have attached the mri_nu_correct log from the base 
freesurfer directory, let me know if this helps

Michele

On Thu, 11 Feb 2021 at 17:16, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
If you send the mri_nu_correct.mni.log we can figure it out for sure.
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Michele Valotti 
mailto:michele.valo...@gmail.com>>
Date: Thursday, February 11, 2021 at 12:07 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
Hi Andrew,
I do think the problem is in the MINC but the minc paths point to the 
freesurfer installation, so I think it should be running using that

thank you,
Michele

On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Michele,
I think that’s the problem then. The freesurfer code is written to work with 
the specific version of minc that we distribute with the release. If possible, 
you should run freesurfer without setting any MINC paths to your local install 
to see if that fixes things.
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Michele Valotti 
mailto:michele.valo...@gmail.com>>
Date: Thursday, February 11, 2021 at 11:02 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
Hi Trisanna,
thank you for your reply, I am using minc2 (version 1.9.16) but this is the 
same version I use on my local machine and it does not give any errors there, 
and SetUpFreesurfer is sourced before exporting MINC paths and variables.

Michele

On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:

External Email - Use Caution
Hi All

As a frequent user of minctools, I know I’ve had problems in the past if I 
source minctools before sourcing freesurfer in the same terminal, because 
freesurfer uses an older version of minctools.
Also, freesurfer uses minc1 format not minc2.

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hoopes, Andrew" 
mailto:ahoo...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, February 10, 2021 at 9:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed 
minc tools separately on your local machine and do you have any of these 
variables set in your default environment?

MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR

It’s possible there’s another install of MNI that’s interfering with the 
freesurfer one.
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Michele Valotti 
mailto:michele.valo...@gmail.com>>
Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version 
on my local machine (where the command runs) and in the cloud instance

On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local 
machine I tried to run it on a server (which should however have the same 
FreeSurfer version and setup), but I am getting this error

mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz 
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like 
orig.mgz --conform
ncopen: filename "./tmp.mr

Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences

[Hoopes, Andrew]

Hi Mike,

Interesting. The FS surface file format is very straightforward, only saving 
vertex positions and face indices, so any difference between these v6 and 7 
surfaces would come down to basic geometry representation. My intuition is that 
there are either some weird intersections or mis-ordered face indices resulting 
in bad normal computations. Not sure if this is easy in blender, but it might 
be worth visualizing the surface normals to see if they’re pointing in 
reasonable directions. I haven’t been able to replicate this issue on our end.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mike Schmidt 

Date: Tuesday, February 16, 2021 at 7:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences

External Email - Use Caution
Good questions, Andrew.

In FreeView, I loaded the .pial files directly. This should rule out the 
conversion step (mris_convert or my own script) altogether, I think.

In the initial javascript viewers, I tried several debugging steps:
- I converted each version of {lh,rh}.pial with the mris_convert from each 
version of FreeSurfer with no difference. The .pial file from FS6 looked OK; 
the .pial file from FS7 looked mottled regardless of mris_convert version.
- In a more complicated pipeline, I tried loading the STL into blender and 
having it export a gltf file containing only the vertices, then generate and 
save normals alongside the vertices into a gltf file. Both versions rendered 
the same in three.js. FS6 was fine; FS7 was mottled. As I did this with a 
python script, I never actually saw the surfaces in blender. I can try that and 
see what they look like there. Perhaps I'll see some additional data that would 
be useful. The difference seems to be stored in the .pial files, though, so 
blender may assist in suggesting debugging, but is unlikely to solve the 
problem in my estimation.

Thanks for your thoughts,
Mike

On Tue, Feb 16, 2021 at 2:06 PM Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Mike,

Are you loading the STL files or the original pial files in freeview here?

If the former, have you narrowed down whether this is an issue with STL 
conversion or the actual surfaces? FS surface files only store vertex and face 
data, not normals. So, is it possible the normals are being incorrectly 
computed during the conversion? You could narrow down whether it’s a conversion 
issue by converting the same lh.pial file with both v6 and v7 mris_convert and 
comparing those STLs.

Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Date: Tuesday, February 16, 2021 at 1:32 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences
FYI, translucent surfaces in freeview do not render properly due to the 
limitation of old VTK libs being used. I would not use it for error checking in 
this case.

Ruopeng

On Feb 16, 2021, at 11:55 AM, Mike Schmidt 
mailto:mikeschm...@schmidtgracen.com>> wrote:

External Email - Use Caution

Thank you for your response, Doug. I am including two screenshots from FreeView 
side-by-side. These are from the same two lh.pial files mentioned in the first 
email.

They are very very similar and render correctly in FreeView. But when I set 
their transparency from 1.00 to 0.25, similar artifacts appear.

It's difficult to say which is "right" from this. There's nothing behind the 
pial surface to exploit the transparency. But there's a distinct difference 
between the two versions.

Thanks again. Happy to assist in figuring this out in any way I can,
Mike Schmidt


On Mon, Feb 15, 2021 at 12:10 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
Do these show up in freeview? You can turn on the mesh and vertices
On 2/14/2021 8:48 PM, Mike Schmidt wrote:
External Email - Use Caution
Hello FreeSurfer Developers and Experts,

I have written a script that reads the binary representations of the vertices 
and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged 
to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 
and several MRI images, everything working fine. Processing the identical 
input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes 
faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. The 
aliasing is identical if I avoid all of my own code and use mris_convert (from 
either FreeSurfer version) to generate an stl file from the lh.pial and rh.pial 
files.

I've spent a lot of time debugging, messing with different materials and 
textures, generating vertex normals at different stages, but I can

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

[Hoopes, Andrew]

Hi Ishi,
What FS version are you using? Can you try installing `apt-get install 
libncurses5-dev`?
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ishi Tandon 

Date: Thursday, February 18, 2021 at 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 
LTS

External Email - Use Caution
Hello experts,

I have recently installed freesurfer on Ubuntu 20 (which is on virtualbox).
I want to use hippocampal subfield segmentation in freesurfer.
I have installed MATLAB run time (2014b) through the following command -
 fs_install_mcr M2014b

However, this displayed the following warning -

on the target computer , append the following to your LD_LIBRARY_PATH 
environment variable :
/tmp/tmp.HvgiEwe6Av/install-target/v84/runtime/glnx864://tmp/tmp.HvgiEwe6Av/install-target/v84/bin/glnx864://tmp/tmp.HvgiEwe6Av/install-target/v84/sys/os/glnx864

  Next, set the XAPPLRESDIR environment variable to 
/tmp/tmp.HvgiEwe6Av/install-target/v84/X11/app-defaults

Having set that to the bashrc script. It gives me an error when I try the 
following command.

segmentHA_T1.sh
 bert. (error attached below).

I am also attaching the changes that I made in bashrc.

It would be great if you help me out.
Thank you  in advance.

Regards,
Ishi Tandon
B.tech
 + 
M.tech
 - Cognitive & Neuroscience
Amity University, Rajasthan
contact - +918239259846 ; Email- 
ishi.tando...@gmail.com

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Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences

[Hoopes, Andrew]

Hi Mike,

Are you loading the STL files or the original pial files in freeview here?

If the former, have you narrowed down whether this is an issue with STL 
conversion or the actual surfaces? FS surface files only store vertex and face 
data, not normals. So, is it possible the normals are being incorrectly 
computed during the conversion? You could narrow down whether it’s a conversion 
issue by converting the same lh.pial file with both v6 and v7 mris_convert and 
comparing those STLs.

Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Date: Tuesday, February 16, 2021 at 1:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences
FYI, translucent surfaces in freeview do not render properly due to the 
limitation of old VTK libs being used. I would not use it for error checking in 
this case.

Ruopeng


On Feb 16, 2021, at 11:55 AM, Mike Schmidt 
mailto:mikeschm...@schmidtgracen.com>> wrote:

External Email - Use Caution

Thank you for your response, Doug. I am including two screenshots from FreeView 
side-by-side. These are from the same two lh.pial files mentioned in the first 
email.

They are very very similar and render correctly in FreeView. But when I set 
their transparency from 1.00 to 0.25, similar artifacts appear.

It's difficult to say which is "right" from this. There's nothing behind the 
pial surface to exploit the transparency. But there's a distinct difference 
between the two versions.

Thanks again. Happy to assist in figuring this out in any way I can,
Mike Schmidt


On Mon, Feb 15, 2021 at 12:10 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
Do these show up in freeview? You can turn on the mesh and vertices
On 2/14/2021 8:48 PM, Mike Schmidt wrote:
External Email - Use Caution
Hello FreeSurfer Developers and Experts,

I have written a script that reads the binary representations of the vertices 
and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged 
to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 
and several MRI images, everything working fine. Processing the identical 
input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes 
faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. The 
aliasing is identical if I avoid all of my own code and use mris_convert (from 
either FreeSurfer version) to generate an stl file from the lh.pial and rh.pial 
files.

I've spent a lot of time debugging, messing with different materials and 
textures, generating vertex normals at different stages, but I can't find 
anything that makes any difference except the FreeSurfer version. I have seen 
several items in the release notes (MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes)
 that may be related, but I'm not sure how to go about investigating them.

Left cortex images are included, with links if they don't show up in the email, 
of the same brain processed with FS6 and FS7. These are rendered in Firefox 
with the three.js library.

FreeSurfer 6.0.0 works well with a smooth surface (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://dragonfruit.mfs.ms/rh_pial_oblique_from_fs6.png).
 This image is of the correctly rendered surf/lh.pial with 149,968 vertices and 
299,932 faces.


FreeSurfer 7.1.1 results in the same size and shape cortex, but renders 
strangely with mottled shading of triangles. (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://dragonfruit.mfs.ms/rh_pial_oblique_from_fs7.png).
 This image is from the same T1 image as above, but processed with FS7.1.1, 
resulting in 1

Re: [Freesurfer] mincRead error

[Hoopes, Andrew]

If you send the mri_nu_correct.mni.log we can figure it out for sure.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Michele Valotti 

Date: Thursday, February 11, 2021 at 12:07 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
Hi Andrew,
I do think the problem is in the MINC but the minc paths point to the 
freesurfer installation, so I think it should be running using that

thank you,
Michele

On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Michele,
I think that’s the problem then. The freesurfer code is written to work with 
the specific version of minc that we distribute with the release. If possible, 
you should run freesurfer without setting any MINC paths to your local install 
to see if that fixes things.
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Michele Valotti 
mailto:michele.valo...@gmail.com>>
Date: Thursday, February 11, 2021 at 11:02 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
Hi Trisanna,
thank you for your reply, I am using minc2 (version 1.9.16) but this is the 
same version I use on my local machine and it does not give any errors there, 
and SetUpFreesurfer is sourced before exporting MINC paths and variables.

Michele

On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:

External Email - Use Caution
Hi All

As a frequent user of minctools, I know I’ve had problems in the past if I 
source minctools before sourcing freesurfer in the same terminal, because 
freesurfer uses an older version of minctools.
Also, freesurfer uses minc1 format not minc2.

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hoopes, Andrew" 
mailto:ahoo...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, February 10, 2021 at 9:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed 
minc tools separately on your local machine and do you have any of these 
variables set in your default environment?

MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR

It’s possible there’s another install of MNI that’s interfering with the 
freesurfer one.
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Michele Valotti 
mailto:michele.valo...@gmail.com>>
Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version 
on my local machine (where the command runs) and in the cloud instance

On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local 
machine I tried to run it on a server (which should however have the same 
FreeSurfer version and setup), but I am getting this error

mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz 
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like 
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 
UTC 2020 x86_64 GNU/Linux

recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC 2021


Any idea what the cause of this might be?
Thank you!
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Re: [Freesurfer] mincRead error

[Hoopes, Andrew]

Hi Michele,
I think that’s the problem then. The freesurfer code is written to work with 
the specific version of minc that we distribute with the release. If possible, 
you should run freesurfer without setting any MINC paths to your local install 
to see if that fixes things.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Michele Valotti 

Date: Thursday, February 11, 2021 at 11:02 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
Hi Trisanna,
thank you for your reply, I am using minc2 (version 1.9.16) but this is the 
same version I use on my local machine and it does not give any errors there, 
and SetUpFreesurfer is sourced before exporting MINC paths and variables.

Michele

On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:

External Email - Use Caution
Hi All

As a frequent user of minctools, I know I’ve had problems in the past if I 
source minctools before sourcing freesurfer in the same terminal, because 
freesurfer uses an older version of minctools.
Also, freesurfer uses minc1 format not minc2.

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hoopes, Andrew" 
mailto:ahoo...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, February 10, 2021 at 9:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed 
minc tools separately on your local machine and do you have any of these 
variables set in your default environment?

MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR

It’s possible there’s another install of MNI that’s interfering with the 
freesurfer one.
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Michele Valotti 
mailto:michele.valo...@gmail.com>>
Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version 
on my local machine (where the command runs) and in the cloud instance

On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local 
machine I tried to run it on a server (which should however have the same 
FreeSurfer version and setup), but I am getting this error

mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz 
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like 
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 
UTC 2020 x86_64 GNU/Linux

recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC 2021


Any idea what the cause of this might be?
Thank you!
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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1JGrZCpBCSuPapkm_HHIatoVooBbQLB65QiBaa7gloZuDTas3F7Jm5NUb0Jh70_kAxkiyAieOo4vj5KWnmyBckkZfLu5nV0KX3Mgw7SIvo89FMuleCURamxNMyNKLld0AulzlbFQN38jsbEpwGx9wGmFPQS4gS9S-eUBjNstDxOMweGNSdRBNhB41QYIdh7qgt-XD01A9MibR5VGK_Izj3WoT1yzm6BsCYIFiFRg95tYg3xA3NqMoGwukf1F2NvrYpc-xnrg8KIrVPxavMFasuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Re: [Freesurfer] Installing anither Freesurfer version - lincese not working

[Hoopes, Andrew]

Can you provide a bit more information about how you installed the license(s) 
and what errors you’re encountering?

best
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fernanda Hansen P. de 
Moraes 
Date: Thursday, February 11, 2021 at 9:45 AM
To: Freesurfer support list 
Subject: [Freesurfer] Installing anither Freesurfer version - lincese not 
working

External Email - Use Caution
Dear Freesurfer experts,
I installed another Freesurfer version on my computer and used the same license 
of the version installed before. But, it is not working. How should I proceed?

Best regards,
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino (IDOR), 
Rio de Janeiro, Brazil
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Re: [Freesurfer] mincRead error

[Hoopes, Andrew]

Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed 
minc tools separately on your local machine and do you have any of these 
variables set in your default environment?

MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR

It’s possible there’s another install of MNI that’s interfering with the 
freesurfer one.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Michele Valotti 

Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version 
on my local machine (where the command runs) and in the cloud instance

On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local 
machine I tried to run it on a server (which should however have the same 
FreeSurfer version and setup), but I am getting this error

mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz 
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like 
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 
UTC 2020 x86_64 GNU/Linux

recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC 2021


Any idea what the cause of this might be?
Thank you!
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Re: [Freesurfer] Matlab version 2012b installation problem

[Hoopes, Andrew]

Hi Georgia,

I think you forgot to run the last word "fs_install_mcr" in that command (after 
chmod +x). That’s why chmod is throwing a usage error. That doesn’t solve the 
reason why it’s not downloading though. Can you try a different tool, like wget 
and let me know if anything downloaded:

wget 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr

Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Georgia Kapizioni 

Date: Tuesday, February 9, 2021 at 10:49 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Matlab version 2012b installation problem

External Email - Use Caution
Hello Andrew,

Thank you for your response!
The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x) was:

 % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   5275  0 --:--:-- --:--:-- --:--:--  5261
usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] mode|entry 
file ...
chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file …


However, when I type: ls -l $FREESURFER_HOME/bin/fs_install_mcr as you 
suggested, it appears ls: /Applications/freesurfer/bin/fs_install_mcr: No such 
file or directory
When I type again fs_install_mcr while being in Freesurfer/bin path again 
fs_install_mcr: command not found appears.
Any idea what went wrong?


Thanks once again,
Best,
Georgia







On 9 Feb 2021, at 1:05 AM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Dear Freesurfer experts,

I am trying to install Matlab version 2012b but a message appears: command not 
found.

Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x
Then I typed: fs_install_mcr R2012b and I receive: command not found.
My FS version is 6 and I have already install Matlab2016_b on my Mac.

Could you please help me resolve this issue?
Thank you in advance,
Georgia


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Re: [Freesurfer] Matlab version 2012b installation problem

[Hoopes, Andrew]

Hi Georgia,

If you downloaded the runtime installer script to FREESURFER_HOME, which it 
looks like you did, the command should be available to run as long as you’ve 
also sourced that version of freesurfer, i.e. $FREESURFER_HOME/bin is in your 
PATH.

If this is the case and it still can’t find the command, you should make sure 
it actually downloaded correctly. Did the initial command finish with errors? 
And what’s the output of running:

ls -l $FREESURFER_HOME/bin/fs_install_mcr

best
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Georgia Kapizioni 

Date: Monday, February 8, 2021 at 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Matlab version 2012b installation problem

External Email - Use Caution
Dear Freesurfer experts,

I am trying to install Matlab version 2012b but a message appears: command not 
found.

Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x
Then I typed: fs_install_mcr R2012b and I receive: command not found.
My FS version is 6 and I have already install Matlab2016_b on my Mac.

Could you please help me resolve this issue?
Thank you in advance,
Georgia

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Re: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release

[Hoopes, Andrew]

The issue only exists in v6
Andrew

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

Date: Monday, February 8, 2021 at 9:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: costanza.bianca.par...@gmail.com 
Subject: Re: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 
Release

External Email - Use Caution
I have another library change you can try for freesurfer 6.  I will send it to 
your private email shortly.


- R.


On Feb 8, 2021, at 06:14, Costanza Parodi  
wrote:

External Email - Use Caution

no difference has been detected  in the files but the same error comes up.

 Error opening file dyld: lazy symbol binding failed: Symbol not found: 
___emutls_get_address
  Referenced from: 
/Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: 
/Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib
  Expected in: /usr/lib/libSystem.B.dylib


I would like to avoid disabling the SIP. Any other suggestions? Does the v7 
have the same bug?


On 6 Feb 2021, at 00:15, fsbuild 
mailto:fsbu...@contbay.com>> wrote:

If you followed the directions for the 6.0.0 patch, then you replaced the copy 
of libgomp.1.dylib inside the freesurfer application bundle with the updated 
version from the patch archive under,

./Freeview.app/Contents/Frameworks/libgomp.1.dylib

But there is another copy of libgomp under,

./lib/gcc/lib/libgomp.1.dylib

In the original 6.0.0 download, those 2 copies of libgomp are identical (or 
unpatched).

So you could try using the patched version of libgomp.1.dylib to replace the 
copy under ./lib/gcc/lib as well.

You could move it aside and replace it with something like,

$ sudo cd /freesurfer/lib/gcc/lib
$ sudo mv  libgomp.1.dylib  OLD_libgomp.1.dylib
$ sudo cp -p  -f  ../.../../Freeview.app/Contents/Frameworks/libgomp.1.dylib  .
$ sudo diff  libgomp.1.dylib  
../../../Freeview.app/Contents/Frameworks/libgomp.1.dylib
… no diff results should be reported ...

Then try running your command again.

- R.

On Feb 5, 2021, at 12:37, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

Yes, this probably has to do with SIP being enabled, which blocks libraries 
stored in /usr. This was a pretty common issue that people had with v6. You can 
try disabling SIP via MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x<http://secure-web.cisco.com/1tMo1B0Wev-AXmkf1seEjPbNhnfyxVDZnKjJOUZYe6-x5PHuinA4gCSlCb0JH0ey7YeEOp-964nB7hgiDIipWL3vfhYsC-oGkftqJW9NOit7OaiJ9Go-L6QrBZ3Q8PpRfpnIC8cVZWrbX4y4Efb3KKIyTHM60JP7QvcyM4UGuidKdOQaDNbbrGMb5bV0_f2IFFBaML5hrm8o26BZX515Cghx-xo9JudVGKYRaoB138MClzfpP8-WHM0Ljn9JEzvOG6NEz87ctVVVfCwdf8NP8aA/http%3A%2F%2Fosxdaily.com%2F2015%2F10%2F05%2Fdisable-rootless-system-integrity-protection-mac-os-x>

best
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Costanza Parodi 
mailto:costanza.bianca.par...@gmail.com>>
Date: Friday, February 5, 2021 at 9:30 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 
Release
External Email - Use Caution
Hello Freesurfer Developers,

I was attempting to use the mri_cvs_register command ( mri_cvs_register -- mov 
subjid  -- mni) and I received this error:

asegfname aseg
Using m3z type morph files.
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/.../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Abort

I resolved the issue by downloading the Freeview_6.0.0_MacOS patch, but a new 
error came up :

 Error opening file dyld: lazy symbol binding failed: Symbol not found: 
___emutls_get_address
  Referenced from: 
/Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: 
/Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib
  Expected in: /usr/lib/libSystem.B.dylib

I did not find similar errors in the archive. Should I disable SIP? Could you 
help me trouble-shoot this error?
My freesurfer is installed on an external hard disk and I am processing my 
subjects on my Mac desktop.

1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
2) MacOs High Sierra version 10.13.6
3)Darwin MacBook-Air.local

Re: [Freesurfer] Recommendation for FreeSurfer BIDS derivatives?

[Hoopes, Andrew]

Hi Francois, just responded on github.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Francois Tadel, Mr 
[Affiliate] 
Date: Friday, February 5, 2021 at 6:17 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recommendation for FreeSurfer BIDS derivatives?
External Email - Use Caution

Hello

In the BIDS-examples, we're trying to figure out whether we should use:
1) derivatives/freesurfer/sub-01/ses-01/ or
2) derivatives/freesurfer/sub-01_ses-01/ ?

According to the FreeSurfer wiki, option #2 is recommended:
https://secure-web.cisco.com/1sCCtE6LTMa-49XUNxEx--YIegNS1bF7eTcXR_u4FqKST748y_V5ly1fxDQwFv6ksaO7Jn-SlZQ0HdGkehXdZmjvkDAhOi5PZ2a0fd8uL2KjFVW-DNjOesHeGPNtSmyA_TW7sPqWaEPVNUtSSCf4PBUHcaXYU-mRSD6Sa3SfqPqq_S16pKHtCMQorzEUgmqKXHC2AyVN0A6GFQymWaqX2slzbl_2WrpYoEnz8o1nCUpO8PrRlphml8_YqgdAfdrczYeEiQg9BtqybNp8DiCcL7g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBIDS
But since the last time this page was edited was in 2018, we were
wondering if this info is still up-to-date.

Could someone comment directly on this pending PR?
https://secure-web.cisco.com/1tQpQxw5ftUz9Yde9DKP1YMlGQWO1XQjNCa6L7RxMhdB2qoVTBY42vzPC_mIneqnKW7X031gw4xQLAb1rzoNhkYJSZ66X6op6JBuUs-C1S204d2j4QKQ7NzG0TGL4dalb4mBjDek2pX_pDJYahDQ3E2m4UN_PD91qUSMCMQKVcLJRHbmGI9WSTmt-lFQiu06T-IobHgROjeP_iuhxBgleCFZGtbbPb_LGDh-2MdHSjHVHBn_PCVeA5YCxPwk2ajr13GkwtfIdq-3_QcN4JJKeJw/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-examples%23233

Thanks!
Francois


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Re: [Freesurfer] Issue with the hypothalamic segmentation

[Hoopes, Andrew]

Honestly, I’m not really sure how to fix this. This isn’t reproducible, and it 
appears to be an issue with your system libraries. I don’t know how much we can 
do about it on our side. Have you reached out to your sys admin, and do you 
observe this issue elsewhere? It seems like this is commonly observed when 
running perl as well. Rob, any ideas?

Here is the Debian bug report:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=951880

Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mackenzie Langan 

Date: Friday, February 5, 2021 at 9:35 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution


On Feb 3, 2021, at 1:14 PM, Mackenzie Langan  
wrote:

Yes, so I tried both installing missing libraries and removing some outdated 
ones to no effect.



This was the result of mri_convert --help: mri_convert:



mri_convert: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not 
found (required by mri_convert)



On Feb 3, 2021, at 1:04 PM, Hoopes, Andrew  wrote:
Thanks. Can you run something like `mri_convert --help` to check if this is an 
issue with all the FS binaries? It seems like this is a known ubuntu bug:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://ubuntuforums.org/showthread.php?t=2438576<https://secure-web.cisco.com/1EEQYsHuLSmuHK07k0q90qymHo8_e1c-uc0erfhedd7Tc7qLT6kDUz-dxPo7Rce_PIHAmHSF7u4KUQU2X3cAY5lu7d2WDDYS1qFnfSO7JcDrr4JubBL7Zg9OOE4GKnC3aMc7M8yhOE7gXoUiZxtHBWhqpOJeL2w6uAPJ0etBovLXjaa6wFhtAdlYKEp-DJQRSOfRJoW-TvVcZkK_a0BINTKDEAVuqb0oiMR12BWpLgxqko3d3le6lBdNu2VnT3vrXcXGAuMTEXYCN0QBZTpzgiw/https%3A%2F%2Fubuntuforums.org%2Fshowthread.php%3Ft%3D2438576>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://askubuntu.com/questions/1254845/upgrade-from-19-10-to-20-04-fails<https://secure-web.cisco.com/1Kg6s6YYtcmG6yo2nNy72n8QrhfAtozluBCAdoyrEvjTBz5qAZ6XIHd3fRL8BRCQDx39OkxHKjdjCAl-qvHnzEwlZjASQUSWddBIJLaFLlqJ4Sz7_kQw25zed9faPXbMYRCnBc1h1EAlw9w3MeN-7_E-bCHSY_bpWywhyBaRCixtLinsX5T8_i2obEU7tXMhNvoUTA_0pVh3mhCdATJA1GgXhd3hb6m7s7U039vR4TX4crDkLikd4jYFzDxa3w0VaXKI_5IUjp21MENlSOmM2SQ/https%3A%2F%2Faskubuntu.com%2Fquestions%2F1254845%2Fupgrade-from-19-10-to-20-04-fails>

It might require updating some libraries on your end, but it’d be nice to see 
if this is a global issue first.
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Langan, Mackenzie 

Date: Wednesday, February 3, 2021 at 11:46 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution
Hi Andrew
We are running Ubuntu 19.10 on our computer and as for Freesurfer were we tried 
to run this on freesurfer 7 and the development version but both produced this 
error. (freesurfer 7: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297 
Freesurfer DEV: freesurfer-linux-centos8_x86_64-dev-20201109-2e16dca)

-Mackenzie

On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Mackenzie,

Can you let us know what OS and version you’re running this on?

Thanks,
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Langan, Mackenzie 
mailto:mackenzie.lan...@icahn.mssm.edu>>
Date: Wednesday, February 3, 2021 at 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution
Good Morning,

I have been trying to run the hypothalamic segmentation and get the following 
error:


aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ 
mri_segment_hypothalamic_subunits --s S05486

Traceback (most recent call last):

  File 
"/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 10, in 

import freesurfer as fs

  File 
"/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", 
line 8, in 

from . import bindings

ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not 
found (required by 
/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/bindings.cpython-36m-x86_64-linux-gnu.so<http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F>)





We installed the development version of freesurfer to see if that would work to 
run this, but that didn't wo

Re: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release

[Hoopes, Andrew]

Yes, this probably has to do with SIP being enabled, which blocks libraries 
stored in /usr. This was a pretty common issue that people had with v6. You can 
try disabling SIP via 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Costanza Parodi 

Date: Friday, February 5, 2021 at 9:30 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 
Release

External Email - Use Caution
Hello Freesurfer Developers,

I was attempting to use the mri_cvs_register command ( mri_cvs_register -- mov 
subjid  -- mni) and I received this error:

asegfname aseg
Using m3z type morph files.
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Abort


I resolved the issue by downloading the Freeview_6.0.0_MacOS patch, but a new 
error came up :

 Error opening file dyld: lazy symbol binding failed: Symbol not found: 
___emutls_get_address
  Referenced from: 
/Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: 
/Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib
  Expected in: /usr/lib/libSystem.B.dylib

I did not find similar errors in the archive. Should I disable SIP? Could you 
help me trouble-shoot this error?
My freesurfer is installed on an external hard disk and I am processing my 
subjects on my Mac desktop.

1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
2) MacOs High Sierra version 10.13.6
3)Darwin MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 18 
21:21:34 PDT 2020; root:xnu-4570.71.82.5~1/RELEASE_X86_64 x86_64
4)Xquartz 2.7.11





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Re: [Freesurfer] Issue with the hypothalamic segmentation

[Hoopes, Andrew]

Thanks. Can you run something like `mri_convert --help` to check if this is an 
issue with all the FS binaries? It seems like this is a known ubuntu bug:

https://ubuntuforums.org/showthread.php?t=2438576
https://askubuntu.com/questions/1254845/upgrade-from-19-10-to-20-04-fails

It might require updating some libraries on your end, but it’d be nice to see 
if this is a global issue first.
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Langan, Mackenzie 

Date: Wednesday, February 3, 2021 at 11:46 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution
Hi Andrew
We are running Ubuntu 19.10 on our computer and as for Freesurfer were we tried 
to run this on freesurfer 7 and the development version but both produced this 
error. (freesurfer 7: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297 
Freesurfer DEV: freesurfer-linux-centos8_x86_64-dev-20201109-2e16dca)

-Mackenzie

On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Mackenzie,

Can you let us know what OS and version you’re running this on?

Thanks,
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Langan, Mackenzie 
mailto:mackenzie.lan...@icahn.mssm.edu>>
Date: Wednesday, February 3, 2021 at 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution
Good Morning,

I have been trying to run the hypothalamic segmentation and get the following 
error:


aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ 
mri_segment_hypothalamic_subunits --s S05486

Traceback (most recent call last):

  File 
"/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 10, in 

import freesurfer as fs

  File 
"/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", 
line 8, in 

from . import bindings

ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not 
found (required by 
/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/bindings.cpython-36m-x86_64-linux-gnu.so<http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F>)





We installed the development version of freesurfer to see if that would work to 
run this, but that didn't work. We then installed XCRYPT_2.0 but still got the 
same error. We have two versions of python on our machine which we amended to 
fix the problem, but still get the same error. I am at a loss as to what I 
should try next to implement this. Any help would be great. Thanks







Best,

Mackenzie
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Re: [Freesurfer] Issue with the hypothalamic segmentation

[Hoopes, Andrew]

Hi Mackenzie,

Can you let us know what OS and version you’re running this on?

Thanks,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Langan, Mackenzie 

Date: Wednesday, February 3, 2021 at 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution
Good Morning,

I have been trying to run the hypothalamic segmentation and get the following 
error:


aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ 
mri_segment_hypothalamic_subunits --s S05486

Traceback (most recent call last):

  File 
"/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 10, in 

import freesurfer as fs

  File 
"/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", 
line 8, in 

from . import bindings

ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not 
found (required by 
/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/bindings.cpython-36m-x86_64-linux-gnu.so)





We installed the development version of freesurfer to see if that would work to 
run this, but that didn't work. We then installed XCRYPT_2.0 but still got the 
same error. We have two versions of python on our machine which we amended to 
fix the problem, but still get the same error. I am at a loss as to what I 
should try next to implement this. Any help would be great. Thanks







Best,

Mackenzie
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Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

[Hoopes, Andrew]

Hi Alex,

After sourcing the dev distribution, can you run:

fspython -m pip install h5py==2.10.0

This is an unfortunate bug with older versions of keras and newer versions of 
h5py, but we’ll be upgrading our internal scripts soon to deal with this. 
Thanks for point this out - I’ll put a note in the dev TF-install instructions.

As for dealing with multiple FS versions, just install them in different 
directories. Something like:

/path/to/freesurfer/6.0.0
/path/to/freesurfer/7.1.1
/path/to/freesurfer/dev
etc…

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lab of Autism and 
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 

Date: Tuesday, February 2, 2021 at 1:08 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

External Email - Use Caution
Thank you for your help!

I have tested the hypothalamus segmentation on the development version of FS, 
and this was the error output that I got (see below). How should I proceed to 
fix this?

:~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2

Using 1 thread

2021-02-02 12:19:04.878273: I 
tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports 
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-02-02 12:19:04.899000: I 
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 
295000 Hz
2021-02-02 12:19:04.899178: I tensorflow/compiler/xla/service/service.cc:150] 
XLA service 0x20b88f0 executing computations on platform Host. Devices:
2021-02-02 12:19:04.899215: I tensorflow/compiler/xla/service/service.cc:158]   
StreamExecutor device (0): , 
processing 1/1
Traceback (most recent call last):
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 1464, in 
main()
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 91, in main
threads=args.threads
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 165, in predict
net = build_model(path_model, model_input_shape, len(label_list))
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 579, in build_model
net.load_weights(model_file, by_name=True)
  File 
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py",
 line 1514, in load_weights
saving.load_weights_from_hdf5_group_by_name(f, self.layers)
  File 
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py",
 line 839, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'

Also, what's the best way for me to run a second version of Freesurfer on the 
same computer? I used a virtualbox, but is there a way to run it outside of 
that?

Thank you so much for the help and stay safe,
Alex



On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
It is not in version 7. You'll have to download a development version of FS to 
run it.
On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of 
Autism and Developmental Neuroscience wrote:

External Email - Use Caution
Dear Freesurfer experts,

I am having some trouble getting the hypothalamus segmentation recognized on 
the command line for FreeSurfer 7.1.0. Is it even available for this version? 
If not, will it work on the 6.0 or the 7.1.1 version?

Thanks and stay safe!

All the best,
Alex



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Re: [Freesurfer] FW: FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

[Hoopes, Andrew]

Hi Flavia,

At the moment, freesurfer needs access to /tmp in order to cache temporary 
processing files. Can you reach out to your system admin as to why you don’t 
have write access to /tmp, and perhaps they will grant you access?

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Thursday, January 28, 2021 at 10:41 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] FW: FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Andrew,

This is the output:

-bash-4.2$   touch /tmp/mytempfile && rm -f /tmp/mytempfile
touch: cannot touch ‘/tmp/mytempfile’: Permission denied

Yes, I am running it through the High Performance Computing (HPC) cluster. Is 
there a way to work around this kind of permission problem?

Many thanks for your help.
Best,
Flavia


From:  on behalf of "Hoopes, Andrew" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 22:05
To: Freesurfer support list 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Okay, maybe it’s a permission error. How about the output of the following?

touch /tmp/mytempfile && rm -f /tmp/mytempfile

Also, are you running recon-all on a cluster?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 1:56 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Andrew,
Many thanks for your reply. This is what I get if I ls/temp:

-bash-4.2$ ls /tmp
hsperfdata_gc520
hsperfdata_rf1116
hsperfdata_scliffor
pbs.3000969.pbs
systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-gKdDDc
systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-ZujPj0
systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-sX44ZN
systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-ukGmwH

What would you recommend doing?

Thank you.
Best,
Flavia


From:  on behalf of "Hoopes, Andrew" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 17:32
To: Freesurfer support list 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Hi Flavia,
Do you have access to /tmp on your system? Can you `ls /tmp`?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 11:29 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Douglas,
Here is the result:

-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
-rw-rw 1 floreto rds-000730 925609 Jan 17 04:02 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot

Thank you.
Best,
Flavia


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 16:25
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Sorry, that first one should have been
ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
left off the "t"
On 1/26/2021 10:55 AM, Loreto, Flavia wrote:

External Email - Use Caution
Dear Douglas,
Thanks for your reply. Please see below the results of those commands:


-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno

ls: cannot access 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno: No 
such file or directory

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label

drwxrws--- 2 floreto rds-000730 4096 Jan 17 04:47 
/rds/general/project/imperialapc/live/freesurfer/APC001/label

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001

drwxrws--- 10 floreto rds-000730 4096 Jan 17 12:46 
/rds/general/project/imperialapc/live/freesurfer/APC001

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer

drwxrws--- 3 floreto rds-000730 4096 Jan 16 20:33 
/rds/general/project/imperialapc/live/freesurfer

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live

drwxrws--- 11 root rds-000730 8192 Jan 18 13:06 
/rds/general/project/imperialapc/live

Thank you.
Best,
Flavia


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 26 January 2021 at 15:30
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Sub

Re: [Freesurfer] Java / Matlab Runtime error

[Hoopes, Andrew]

Hi Ali,

Can you please remove the MCR directory and install it using the instructions 
found at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime? I think this 
will fix the issue.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Snedden, Ali 

Date: Wednesday, January 27, 2021 at 11:46 AM
To: Freesurfer support list 
Subject: [Freesurfer] Java / Matlab Runtime error

External Email - Use Caution
Hello,

I’m helping a user run freesurfer/7.1.0 on CentOS 8.1.  They initially 
encountered an error due to the missing Matlab Compiler Runtime (MCR).  I 
downloaded the package and installed it in the location suggested by the error 
message :


LINUX:



cd /gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download

curl 
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bLinux.tar.gz";
 -o "runtime2014b.tar.gz"

tar xvf runtime2014b.tar.gz

After installing the MCR, I had to change all the subdirectories’ in MCRv84 to 
755 permissions so our user could access it.   When trying to run 
`segmentHA_T1.sh`, she gets the error :


[user@computer-name Subjects]$ export 
FS_LICENSE=/gpfs0/home1/group/lab/Software/FreeSurfer/license.txt

[user@computer-name Subjects]$ export 
SUBJECTS_DIR=/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects

[user@computer-name Subjects]$ cd 
/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects

[user@computer-name Subjects]$ segmentHA_T1.sh subject1

#

#@# Hippocampal Subfields processing (T1) left Wed Jan 27 10:53:02 EST 2021

--

Setting up environment variables

---

LD_LIBRARY_PATH is 
.:/lib64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//runtime/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//bin/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/os/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/lib:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/zlib/1.2.11-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib64:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib

Error using checkRequiredMCRProducts (line 25)

Java exception occurred:

java.lang.NullPointerException

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)

at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)



Error in deployrc (line 9)







Error in matlabrc (line 238)









Command exited with non-zero status 255

@#@FSTIME  2021:01:27:10:53:02 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 35.91 S 0.42 U 2.80 P 8% M 184232 F 0 R 52021 W 0 c 11 w 7851 I 0 O 84128 
L 0.02 0.06 0.08

@#@FSLOADPOST 2021:01:27:10:53:38 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 0.35 0.15 0.11

Linux computer-name 4.18.0-147.el8.x86_64 #1 SMP Wed Dec 4 21:51:45 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux



T1 hippocampal subfields exited with ERRORS at Wed Jan 27 10:53:38 EST 2021



For more details, see the log file 
/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects/subject1/scripts/hippocampal-subfields-T1.log

In the archive, it seems that this has been encountered before 
(here
 and 
there

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

[Hoopes, Andrew]

Okay, maybe it’s a permission error. How about the output of the following?

touch /tmp/mytempfile && rm -f /tmp/mytempfile

Also, are you running recon-all on a cluster?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 1:56 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Andrew,
Many thanks for your reply. This is what I get if I ls/temp:

-bash-4.2$ ls /tmp
hsperfdata_gc520
hsperfdata_rf1116
hsperfdata_scliffor
pbs.3000969.pbs
systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-gKdDDc
systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-ZujPj0
systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-sX44ZN
systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-ukGmwH

What would you recommend doing?

Thank you.
Best,
Flavia


From:  on behalf of "Hoopes, Andrew" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 17:32
To: Freesurfer support list 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Hi Flavia,
Do you have access to /tmp on your system? Can you `ls /tmp`?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 11:29 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Douglas,
Here is the result:

-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
-rw-rw 1 floreto rds-000730 925609 Jan 17 04:02 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot

Thank you.
Best,
Flavia


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 16:25
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Sorry, that first one should have been
ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
left off the "t"
On 1/26/2021 10:55 AM, Loreto, Flavia wrote:

External Email - Use Caution
Dear Douglas,
Thanks for your reply. Please see below the results of those commands:


-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno

ls: cannot access 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno: No 
such file or directory

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label

drwxrws--- 2 floreto rds-000730 4096 Jan 17 04:47 
/rds/general/project/imperialapc/live/freesurfer/APC001/label

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001

drwxrws--- 10 floreto rds-000730 4096 Jan 17 12:46 
/rds/general/project/imperialapc/live/freesurfer/APC001

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer

drwxrws--- 3 floreto rds-000730 4096 Jan 16 20:33 
/rds/general/project/imperialapc/live/freesurfer

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live

drwxrws--- 11 root rds-000730 8192 Jan 18 13:06 
/rds/general/project/imperialapc/live

Thank you.
Best,
Flavia


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 26 January 2021 at 15:30
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

This email from dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu> 
originates from outside Imperial. Do not click on links and attachments unless 
you recognise the sender. If you trust the sender, add them to your safe 
senders 
list<https://secure-web.cisco.com/1k8uIv8n4Mfbh8DZmvx7sJwGsuor3hXZNK6Wfb-oxGwnrHdkEWkFdoBjerEQqhLHERzXndHTA208ZU1hOWKU8hY9OtYeeKup69Tl-_eHk0uPQd497hf_o1XF2MxlZoW3TvLPemjJu69vqXzVdzg0nyL7mk3Ga1zlbBDIn9ow-ZNYUIh4JNkJ7FClq6fsmFIC2V4ikEJvYaYP-vD3yi2WkHmB04KpQYFw_8da7ebu5eG7zWA4W9Y_l33xVgA4cGTuk3Kmv8_QrUUsjJue0l3lU1w/https%3A%2F%2Fspam.ic.ac.uk%2FSpamConsole%2FSenders.aspx>
 to disable email stamping for this address.


please send the result of
ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno
ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label
ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001
ls -ld /rds/general/project/imperialapc/live/freesurfer
ls -ld /rds/general/project/imperialapc/live



On 1/26/2021 7:50 AM, Loreto, Fla

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

[Hoopes, Andrew]

Hi Flavia,
Do you have access to /tmp on your system? Can you `ls /tmp`?
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loreto, Flavia 

Date: Tuesday, January 26, 2021 at 11:29 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

External Email - Use Caution
Hi Douglas,
Here is the result:

-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
-rw-rw 1 floreto rds-000730 925609 Jan 17 04:02 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot

Thank you.
Best,
Flavia


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 26 January 2021 at 16:25
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

Sorry, that first one should have been
ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
left off the "t"
On 1/26/2021 10:55 AM, Loreto, Flavia wrote:

External Email - Use Caution
Dear Douglas,
Thanks for your reply. Please see below the results of those commands:


-bash-4.2$ ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno

ls: cannot access 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno: No 
such file or directory

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label

drwxrws--- 2 floreto rds-000730 4096 Jan 17 04:47 
/rds/general/project/imperialapc/live/freesurfer/APC001/label

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001

drwxrws--- 10 floreto rds-000730 4096 Jan 17 12:46 
/rds/general/project/imperialapc/live/freesurfer/APC001

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer

drwxrws--- 3 floreto rds-000730 4096 Jan 16 20:33 
/rds/general/project/imperialapc/live/freesurfer

-bash-4.2$ ls -ld /rds/general/project/imperialapc/live

drwxrws--- 11 root rds-000730 8192 Jan 18 13:06 
/rds/general/project/imperialapc/live

Thank you.
Best,
Flavia


From: 

 on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 

Date: Tuesday, 26 January 2021 at 15:30
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not 
open file for writing

This email from dgr...@mgh.harvard.edu 
originates from outside Imperial. Do not click on links and attachments unless 
you recognise the sender. If you trust the sender, add them to your safe 
senders 
list
 to disable email stamping for this address.


please send the result of
ls -l 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno
ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label
ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001
ls -ld /rds/general/project/imperialapc/live/freesurfer
ls -ld /rds/general/project/imperialapc/live



On 1/26/2021 7:50 AM, Loreto, Flavia wrote:

External Email - Use Caution
Dear FreeSurfer Experts,

I am writing to kindly follow-up on my below query. Is there any chance you 
could assist me?

Thank you.
Kind regards,
Flavia


From: "f.lor...@imperial.ac.uk" 

Date: Monday, 18 January 2021 at 13:19
To: "Freesurfer@nmr.mgh.harvard.edu" 

Subject: Recon-all error: CTABWriteFileASCII; could not open file for writing

Dear FreeSurfer Experts,

Version: FreeSurfer 7.0
Platform: Bash remotely through High Performance Computing (HPC) on a MacOS 
Mojave

We are trying to run recon-all on T1 images but the job stops with the 
following error:

Reading annotation 
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 1000
error: Permission denied
error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.APC001.lh.176.ctab): could not 
open for writing

Could you please help us figuring out where is the problem? I am attaching the 
script we are running and the recon-all log for one of our analysed subjects.

Thank you

Re: [Freesurfer] Error Using samseg

[Hoopes, Andrew]

Hi Jesper,

It’s a memory error - how much do you have available? Also, what is the size of 
your input image? That array shape seems rather large.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jesper Folsted Kallehauge 

Date: Saturday, January 23, 2021 at 2:26 PM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: [Freesurfer] Error Using samseg

External Email - Use Caution
Dear All,

I have encounter an error when running samseg for a fraction of my subjects. I 
am very new to FreeSurfer so there is a good chance it is a rookie mistake. The 
error message I get is the following:

Traceback (most recent call last):
  File "/home/frog/freesurfer/python/scripts/run_samseg", line 166, in 
reg_only=args.reg_only
  File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", 
line 132, in segment
return self.postProcess()
  File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", 
line 239, in postProcess
posteriors, biasFields, nodePositions, _, _ = 
self.computeFinalSegmentation()
  File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", 
line 778, in computeFinalSegmentation
posteriors = self.gmm.getPosteriors(data, priors, self.classFractions)
  File "/home/frog/freesurfer/python/packages/freesurfer/samseg/GMM.py", line 
183, in getPosteriors
posteriors = posteriors / np.expand_dims(normalizer, 1)
MemoryError: Unable to allocate 7.15 GiB for an array with shape (21800066, 44) 
and data type float64

The it finishes without a segmentation. Does anyone know the solution to this 
issue ?

King regards
Jesper Kallehauge
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Re: [Freesurfer] mincRead error in recon-all

[Hoopes, Andrew]

Hi Michele,

Looks like the base error here is:
ncopen: filename "./tmp.mri_nu_correct.mni.6973/nu1.mnc": Not a netCDF file

My immediate guess is this is a version incompatibility. You mentioned that you 
reinstalled minc tools? How so and with what version? Also, what was the 
previous nu_correct error you were getting?

best,
Andrew

From:  on behalf of Michele Valotti 

Reply-To: FS Help 
Date: Monday, January 4, 2021 at 10:49 AM
To: FS Help 
Subject: [Freesurfer] mincRead error in recon-all


External Email - Use Caution
Dear Freesurfer Team,
I am trying to run recon-all on a test scan, but I am getting this error:

Error opening ./tmp.mri_nu_correct.mni.6973/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.6973/nu1.mnc

(logs attached)

I just reinstalled minc tools due to a nu_correct error I was getting, not sure 
if this could be a problem. I read on the mailing list that it could be a 
permission error but trying the suggested solutions did not solve the problem

runningls -l tmp.mri_nu_correct.mni.3787/nu1.mnc

returns   -rw-rw-r-- 1 michele michele 22990022 Jan  4 15:01 
tmp.mri_nu_correct.mni.3787/nu1.mnc

Any help is greatly appreciated
Thank you

Michele
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Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

[Hoopes, Andrew]

Hi Nárlon,

Unfortunately, this is a known bug with parallel processing in FS 7.1.1. A fix 
will make it into the next v7 patch. As you mentioned, this error occurs at 
random, so in the meantime, you can mitigate this by either:

- Rerunning recons until they don’t fail (not recommended)
- Rerunning these failing recons without the parallel flag enabled
- Patching your version of recon-all by commenting out or removing the 
following (line 4217) from $FREESURFER_HOME/bin/recon-all:
if($OMP_NUM_THREADS > 1) set cmd = ($cmd --parallel)

Hope that helps,
Andrew

From:  on behalf of "Boa Sorte Silva, 
Narlon" 
Reply-To: FS Help 
Date: Monday, December 14, 2020 at 7:31 PM
To: FS Help 
Subject: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!


External Email - Use Caution
Hi there,
Hope this finds you well

I have noticed the following error for some of my runs:


@# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020
/Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri
\n mris_volmask --aseg_name aseg.presurf --label_left_white 2 
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 
--save_ribbon --parallel BT_055_base \n
SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long
loading input data...
Running hemis in parallel
Processing left hemi
Processing right hemi
computing distance to right white surface
computing distance to left white surface
error: MatrixMultiply: m1 is null!
Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 
20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64

recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020


Here are details of the computer and FS version I am using:


  *   OS: macOS Mojave (10.14.4)
  *   FS: 7.1.1

It seems to happen at random, whenever I run recon-all on the same subject 
again, the error doesn’t occur. This is true for cross-sectional, base, and 
long processing steps in my machine. I have seen an email relating to this 
issue before, but I wasn’t able to access the attachment file which would fix 
the problem.

I was wondering if you guys would be able to help?


Thank you
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon

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Re: [Freesurfer] Error while requesting a license file {Disarmed}

[Hoopes, Andrew]

Hi Jan,

Thanks for pointing this out. We upgraded our server recently, and I think some 
files got moved around. Should be fixed now.

Best,
Andrew

From:  on behalf of "Sellner, Jan" 

Reply-To: FS Help 
Date: Tuesday, December 8, 2020 at 11:50 AM
To: FS Help 
Subject: [Freesurfer] Error while requesting a license file {Disarmed}


External Email - Use Caution

Dear FeeSurfer Developers,



I tried to obtain a valid license file for the FreeSurfer tool with this link:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/registration.html



Unfortunately, after completing the form, I got the following error message:

Not Found

The requested URL /cgi-bin/fslic.new was not found on this server.



Can you help me?



Thank you very much and best regards


Jan Sellner
Division of Medical Image Computing (E230)
PhD Student

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 223
69120 Heidelberg
Germany

j.sell...@dkfz-heidelberg.de
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich
VAT-ID: DE143293537
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Re: [Freesurfer] segmentHA_T1.sh failing {Disarmed}

[Hoopes, Andrew]

Hi Keith, what version of ubuntu are you using?

Best
Andrew

From: "Iglesias Gonzalez, Juan E." 
Date: Friday, December 4, 2020 at 4:42 PM
To: FS Help 
Cc: "Hoopes, Andrew" 
Subject: Re: [Freesurfer] segmentHA_T1.sh failing {Disarmed}

Dear Keith,
It is a license problem. The hippo/amygdala module relies on 
mri_robust_register for initialization, and this program is failing due to the 
aforementioned license problem. Once that has been fixed, the hippocampal 
module should be fine.
Regarding the license problem: I have no idea, but I am CCing Andrew Hoopes, 
who hopefully will be able to help.
Cheers,
/Eugenio


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



From:  on behalf of Keith Harenski 

Reply-To: Freesurfer support list 
Date: Friday, December 4, 2020 at 16:24
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T1.sh failing {Disarmed}


External Email - Use Caution
Hello,

I am getting a strange message when trying to run the amygdala and hippocampal 
sementations, even when attempting to run the script on someone who the script 
previously completed.

When it starts, the script immediately displays the following message:
error parsing license file, expected 4 values

The license error message further instructs libc requires a newly formatted 
license so I got a new one. The new one is identical to the original however 
and it has four entries - my email address, a five digit number, followed by 
two alphanumeric strings..

The script then seems to start, will run for about 30 seconds or so then stop 
again with the following message:
Error using segmentSubjectT1_autoEstimateAlveusML (line 533)
Fitting mesh to synthetic image resulted in no deformation
...
T1 hippocampal subfields exited with ERRORS at Thu Dec  3 15:56:32 MST 2020

I get slightly different errors when running on another subject, who like the 
one above, previously completed. For this subject the license error is more 
persistent:
error parsing license file, expected 4 values

I've attached the hippocampal-subfields-T1.log for the first subject as it 
contains the full output.
Thank you,
Keith
--
Keith Harenski
Mobile MRI Manager
Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory

The Mind Research Network
1101 Yale Blvd NE Albuquerque, NM 87106-4188
Office (Cell): 505.504.1338 | Fax: 505.272.8002
kharen...@mrn.org<mailto:kharen...@mrn.org> | MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
www.mrn.org<http://secure-web.cisco.com/1dteY9vqOnPkmed6Gi9ngcVDCP_LkM_NDWWJ44EjsUH1kpcdY7pTUt_OAitzF2jiVojEqlNmU6ChusO7dxvMmEwotJUObbbe7vs_DFHynWzqHzC3LWZf93olez5aVnSRCPR5TQoWwmBkjKr3XecflF6yGRSp8YtB-6q8n75jHWlh-Ia_WT6aJwFYFvv_tBlbcyp10DxHmwim-6ges_U8rNZSuQyymAV76fqRkx4n0WnPWCD30Z5D1QGMs_5OcL9GypONAcMJvHD-sd7CzPfMNLA/http%3A%2F%2Fwww.mrn.org>
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Re: [Freesurfer] error: MatrixMultiply: m1 is null

[Hoopes, Andrew]

Hi Noam,

Do the volumes look okay? I’m seeing a lot of ‘non-orthogonal axes’ warnings in 
the log. If that’s not the issue, this could be a bug that’s randomly occurring 
with parallel recons in v7. Although, I’ve never seen it fail during 
mri_convert. Can you try to rerun? It might succeed the second time. If not, 
can you send us the input scan and try again without the -parallel flag.

best
Andrew

From:  on behalf of "Peled, Noam" 

Reply-To: FS Help 
Date: Tuesday, November 24, 2020 at 10:10 PM
To: FS Help 
Subject: [Freesurfer] error: MatrixMultiply: m1 is null

Dear FreeSurfer community,
I encountered a recon-all error where I couldn’t find on the web.
The error message is: “error: MatrixMultiply: m1 is null!”. You can find the 
complete log attached.
I used the stable7.1.1 version.

Thanks,
Noam
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Re: [Freesurfer] License error on Windows Subsystem for Linux

[Hoopes, Andrew]

Thanks Lunhao, I will follow up with you temporarily off-list to test some 
things out.
Andrew

From:  on behalf of Shen Lunhao 

Reply-To: FS Help 
Date: Monday, November 23, 2020 at 1:27 AM
To: FS Help 
Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux


External Email - Use Caution
Hi Andrew,

The following is the information of four systems. System #3 and #4 are same 
configuration where license error occurred.
#1
#2
#3
#4
Core
Intel(R) Xeon(R) CPU E5-2620
Intel i7
AMD R9 5900X
AMD R9 5900X
Mem
32GB
16GB
32GB
32GB
Platform
Linux version 4.15.0-112-generic (buildd@lcy01-amd64-027) (gcc version 7.5.0 
(Ubuntu 7.5.0-3ubuntu1~18.04))
Window subsystem for linux(WSL2) + Ubuntu20.04
Window subsystem for linux(WSL2) + Ubuntu20.04
Window subsystem for linux(WSL2) + Ubuntu20.04
Worked
Worked
Didn’t work
Didn’t work
The freesurfer package I used is 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0which downloaded from 
freesurfer website. The license file was four lines type. Hope this information 
is helpful.

Thanks,
Lunhao


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Hoopes, Andrew 

Date: 2020年11月21日 1:19
Reply-To: Freesurfer support list 
Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux


Hi Lunhao,



Interesting. Can you provide some details on the configurations where this 
worked? Were you using the same linux subsystem and windows versions?



thanks

Andrew



From:  on behalf of Shen Lunhao 

Reply-To: FS Help 
Date: Friday, November 20, 2020 at 2:44 AM
To: FS Help 
Subject: [Freesurfer] License error on Windows Subsystem for Linux



External Email - Use Caution

Hello FreeSurfer Developers,



I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 
20.04), but I got license error message as described below:



--

ERROR: Invalid FreeSurfer license key found in license file 
/space/tools/freesurfer/5.3.0/license.txt

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

--



I tried with the same 5.3.0 packages and same license file on four different 
computers, and two of them work well with the other two got similar license 
error. Does anyone have any thoughts on how to trouble-shoot this one?



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2) Platform: Windows Subsystem for Linux (Ubuntu 20.04)

3) uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 
01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux


Best,
Lunhao


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Re: [Freesurfer] License error on Windows Subsystem for Linux

[Hoopes, Andrew]

Hi Lunhao,

Interesting. Can you provide some details on the configurations where this 
worked? Were you using the same linux subsystem and windows versions?

thanks
Andrew

From:  on behalf of Shen Lunhao 

Reply-To: FS Help 
Date: Friday, November 20, 2020 at 2:44 AM
To: FS Help 
Subject: [Freesurfer] License error on Windows Subsystem for Linux


External Email - Use Caution

Hello FreeSurfer Developers,



I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 
20.04), but I got license error message as described below:



--

ERROR: Invalid FreeSurfer license key found in license file 
/space/tools/freesurfer/5.3.0/license.txt

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

--



I tried with the same 5.3.0 packages and same license file on four different 
computers, and two of them work well with the other two got similar license 
error. Does anyone have any thoughts on how to trouble-shoot this one?



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2) Platform: Windows Subsystem for Linux (Ubuntu 20.04)

3) uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 
01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux


Best,
Lunhao

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Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Hoopes, Andrew]

Hi James,

Rsync is a very common unix command for syncing/copying across filesystems. 
There’s plenty of information about it online, and you can access the help text 
through `man rysnc`. This might be useful 
https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/

Best
Andrew

From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Tuesday, October 27, 2020 at 12:12 PM
To: FS Help 
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


External Email - Use Caution
Hi Andrew,

Thank you so much for your prompt response.

Our IT department was unfortunately a bit unfamiliar with these types of files.

We were not using rsync to move our files but instead just copying the files 
over through a file explorer.

Could you please point me in the right direction as to where I could access 
more information on rsync or moving data to a different location?

That would be super helpful!

Thank you again for your help.


Sincerely,

James Park




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


Hi James,



It sounds like your target filesystem does not support symlinks? The answer to 
your question depends on how you are actually copying data, and you should 
probably contact your IT about this, but if you’re using rsync to move recons, 
you can supply the --copy-links flag to transform symlinks into referent 
file/dir.



best,

Andrew



From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer 
Output to Secondary Location



External Email - Use Caution

Hello,



My name is James Park, and I had a question regarding some issues with 
Freesurfer.



We noticed that for the freesurfer recon-all output there were multiple aliases 
files such as surf/rh.white.K among others.

Unfortunately we have been unable to copy these types of files to secondary 
locations (i.e. a network server).



I have confirmed this is not an issue with the computer-network connection as I 
have been able to copy other alias file types to the network location.

I was wondering if there is any workaround for this issue?



This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.



Thank you for your help in advance.



Sincerely,

James Park



This e-mail message (including any attachments) is for the sole use of
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If you have received this message in error, please contact
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Re: [Freesurfer] Exited with errors, segmentation fault

[Hoopes, Andrew]

Hi Julia,

The -tp flags for the base creation require a subject ID as input, but you 
supplied a nifty file. That’s why it can’t find any subject files. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing.

Best,
Andrew

From:  on behalf of Julia Lam 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 7:29 PM
To: FS Help 
Subject: Re: [Freesurfer] Exited with errors, segmentation fault


External Email - Use Caution
Hi,
Thank you for your email. Sorry about that. Here they are.
Best regards,
Julia


> 27 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
>
> Hi Julia,
> I think you might have forgotten to attach the logs :)
> Andrew
>
> On 10/25/20, 11:55 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Julia Lam"  julia@mau.se> wrote:
>
>External Email - Use Caution
>
>Hi Andrew,
>Thank you for your reply. Updating freesurfer solved the problem. However, 
> when I ran step 2 in the longitudinal processing three subjects exited with 
> errors. I’ve attached the recon-all.log and recon-all.error. What can I do to 
> solve this problem?
>
>Thank you in advance.
>
>    Kind regards,
>Julia Lam
>
>> 20 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
>>
>> Hi Julia,
>>
>> This is a small bug that's been fixed in the 7.1.1 patch release. I would 
>> recommend updating freesurfer versions (there will be no differences in 
>> recon-all results).
>>
>> Best,
>> Andrew
>>
>> On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
>> Julia Lam" > julia@mau.se> wrote:
>>
>>   External Email - Use Caution
>>
>>   Hi,
>>   In one of 56 volumes, recon-all exited with errors (segmentation fault). I 
>> tried to rerun but received the same result. How can this be solved?
>>
>>   I’ve attached the recon-all.log and recon-all.error.
>>
>>   I am looking forward to your reply.
>>
>>   Kind regards,
>>   Julia Lam
>>
>>
>>
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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Re: [Freesurfer] Exited with errors, segmentation fault

[Hoopes, Andrew]

Hi Julia,
I think you might have forgotten to attach the logs :)
Andrew

On 10/25/20, 11:55 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Julia Lam"  wrote:

External Email - Use Caution

Hi Andrew,
Thank you for your reply. Updating freesurfer solved the problem. However, 
when I ran step 2 in the longitudinal processing three subjects exited with 
errors. I’ve attached the recon-all.log and recon-all.error. What can I do to 
solve this problem?

Thank you in advance.

Kind regards,
Julia Lam

> 20 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
> 
> Hi Julia,
> 
> This is a small bug that's been fixed in the 7.1.1 patch release. I would 
recommend updating freesurfer versions (there will be no differences in 
recon-all results).
> 
> Best,
> Andrew
> 
> On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Julia Lam"  wrote:
> 
>External Email - Use Caution
> 
>Hi,
>In one of 56 volumes, recon-all exited with errors (segmentation 
fault). I tried to rerun but received the same result. How can this be solved?
> 
>I’ve attached the recon-all.log and recon-all.error.   
> 
>I am looking forward to your reply.
> 
>Kind regards,
>Julia Lam
> 
> 
> 
> 
> 
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Re: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Hoopes, Andrew]

Hi James,

It sounds like your target filesystem does not support symlinks? The answer to 
your question depends on how you are actually copying data, and you should 
probably contact your IT about this, but if you’re using rsync to move recons, 
you can supply the --copy-links flag to transform symlinks into referent 
file/dir.

best,
Andrew

From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer 
Output to Secondary Location


External Email - Use Caution
Hello,

My name is James Park, and I had a question regarding some issues with 
Freesurfer.

We noticed that for the freesurfer recon-all output there were multiple aliases 
files such as surf/rh.white.K among others.
Unfortunately we have been unable to copy these types of files to secondary 
locations (i.e. a network server).

I have confirmed this is not an issue with the computer-network connection as I 
have been able to copy other alias file types to the network location.
I was wondering if there is any workaround for this issue?

This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

Thank you for your help in advance.

Sincerely,
James Park


This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
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Re: [Freesurfer] replace the vertex_label_index in .annot file

[Hoopes, Andrew]

Your best bet is using the FS matlab library to script annotation edits (see 
read_annotation.m and write_annotation.m). Otherwise, if you’re using 
freesurfer 6, you can use tksurfer to manually edit labels/annotations through 
the GUI (https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit).
Andrew


From:  on behalf of 1248742467 
<1248742...@qq.com>
Reply-To: FS Help 
Date: Monday, October 19, 2020 at 10:20 PM
To: FS Help 
Subject: [Freesurfer] replace the vertex_label_index in .annot file


External Email - Use Caution
hello,
Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id 
and vertex_label,
'

from freesurfer_surface import Surface
from freesurfer_surface import Label
from freesurfer_surface import Annotation


surface = Surface.read_triangular('rh.white')
surface.load_annotation_file('rh.aparc.a2009s.annot')
with open("rhlabels.txt","w") as f:
for vertex_index, vertex in enumerate(surface.vertices):
vertex_label_index = surface.annotation.vertex_label_index[vertex_index]
vertex_label = surface.annotation.labels[vertex_label_index]
#print(vertex_index, vertex, vertex_label)
#f.write("vertex_index:{}  vertexlabel:{} \n".format(vertex_index, 
vertex_label))
f.write("vertex_index:{} vertex_label:{}\n".format(vertex_index, 
vertex_label))
'
the output:vertex_index:0 vertexlabel:Label(name=S_precentral-sup-part, 
index=70, color=#1514c8)
and the label_index obtained after a certain algorithm was updated to replace 
the vertex_labe_index in rh.aparc.2009s.annot, and then load the result with 
freeview. But I don't know how to replace the vertex_label_index value in 
.annot?
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Re: [Freesurfer] Exited with errors, segmentation fault

[Hoopes, Andrew]

Hi Julia,

This is a small bug that's been fixed in the 7.1.1 patch release. I would 
recommend updating freesurfer versions (there will be no differences in 
recon-all results).

Best,
Andrew

On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Julia Lam"  wrote:

External Email - Use Caution

Hi,
In one of 56 volumes, recon-all exited with errors (segmentation fault). I 
tried to rerun but received the same result. How can this be solved?

I’ve attached the recon-all.log and recon-all.error.

I am looking forward to your reply.

Kind regards,
Julia Lam





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Re: [Freesurfer] Open the .annotation file with Notepad is garbled

[Hoopes, Andrew]

You can’t open an annotation as a plain text file – it’s a custom binary 
structure. You can visualize it on top of a surface in freeview. Something like:
freeview -f surf/lh.inflated:annot=label/lh.aparc.annot

From:  on behalf of 1248742467 
<1248742...@qq.com>
Reply-To: FS Help 
Date: Tuesday, October 13, 2020 at 8:42 AM
To: FS Help 
Subject: [Freesurfer] Open the .annotation file with Notepad is garbled


External Email - Use Caution
Hello, FreeSurfer
Why is it garbled when I open the .annotation file with Notepad? Is there any 
solution?
[cid:C964CF87@C8A79C62.0DA0855F.png]
Looking forward to your reply
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Re: [Freesurfer] Freesurfer 5.3.0 recon-all error

[Hoopes, Andrew]

Hi Michele,

Does $FREESURFER_HOME/mni/bin/nu_correct exist for you? This error usually 
indicates that you have not configured the freesurfer environment correctly. 
Have you sourced the SetUpFreeSurfer script?

Best,
Andrew

From:  on behalf of Michele Valotti 

Reply-To: FS Help 
Date: Wednesday, October 7, 2020 at 2:44 PM
To: FS Help 
Subject: Re: [Freesurfer] Freesurfer 5.3.0 recon-all error


External Email - Use Caution
Hi, thank you for getting back to me so quickly, I can confirm that it does not 
run through on any scan and I have tried to run the command as you suggested.
This is the error I am getting:

--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux ian-System-Product-Name 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 
10 12:50:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Wed  7 Oct 16:46:17 BST 2020
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.1081
/home/michele/spd_processing/freesurfer2016/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=7.92, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.22236e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 4.65661e-10, -1)
k_ras = (7.82893e-09, 1, -4.65661e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1081/nu0.mnc...


Iteration 1 Wed  7 Oct 16:46:18 BST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.1081/nu0.mnc 
./tmp.mri_nu_correct.mni.1081/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1081/0/ 
-iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct

I am assuming I am missing the MNI tools, so I have tried to download them from 
http://bic-mni.github.io/ but all the downloads failed, do you have a 
recommended way to download and install what I need to run my script?

Thank you again,
Michele

On Tue, 6 Oct 2020 at 15:59, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

My guess is it is a problem with the install of the MNI tools. Does it run all 
the way through on other subjects? What happens when you run this command?

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

On 10/6/2020 9:16 AM, Michele Valotti wrote:

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I am using freesurfer 5.3.0 (unfortunately this is the version I have to use) 
and I am encountering an error in the process. I have attached the 
recon-all.log file. Any pointers to identify the error would be very helpful,

Thank you,
Michele



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Re: [Freesurfer] recon-all 7.1.1

[Hoopes, Andrew]

Hi James, please ignore that step. In fact, adding those matlab paths to your 
default DYLD_LIBRARY_PATH will most likely mess up freesurfer binaries in your 
environment.
Andrew

From: James Hartzell 
Date: Tuesday, September 22, 2020 at 2:19 PM
To: "Hoopes, Andrew" 
Cc: FS Help 
Subject: Re: recon-all 7.1.1


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Hi Andrew
Thanks, that works just fine.
I'll see if I can figure out how to do the path append part--just something I'm 
not familiar with doing:
(On the target computer, append the following to your DYLD_LIBRARY_PATH 
environment variable:

/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.LPxBFTBS/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.LPxBFTBS/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.LPxBFTBS/install-target/v84/bin/maci64:)
Cheers
James

On Tue, Sep 22, 2020 at 6:43 PM Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi James,

If freesurfer was installed under root, you should prepend sudo to the command 
to make changes to the directory:

sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr R2014b

best
Andrew


From: James Hartzell mailto:james.hartz...@gmail.com>>
Date: Monday, September 21, 2020 at 10:49 AM
To: "Hoopes, Andrew" mailto:ahoo...@mgh.harvard.edu>>, 
FS Help mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: recon-all 7.1.1


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Hi Andrew

recon-all appears to have run successfully in 7.1.1, so thanks again for all 
the guidance.

I've just tried to install the matlab runtime for hipp, amyg, brainstem and 
thalamic segmentation,
as per
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

fs_install_mcr R2014b

the command finished, but indicated a problem with. final renaming requirement:
"On the target computer, append the following to your DYLD_LIBRARY_PATH 
environment variable:
/var/folders/kl/72rg80dd57ncd7nc638fwzmhgn/T/tmp.0al9EPfQ/install-target/v84/runtime/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmhgn/T/tmp.0al9EPfQ/install-target/v84/sys/os/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmhgn/T/tmp.0al9EPfQ/install-target/v84/bin/maci64:

(Sep 21, 2020 16:41:29) Exiting with status 0
(Sep 21, 2020 16:41:29) End - Successful.
Finished
mv: rename 
/var/folders/kl/72rg80dd57ncd7nc638fwzmhgn/T/tmp.0al9EPfQ/install-target/v84
 to /Applications/freesurfer/7.1.1/MCRv84: Permission denied

Also, if you could provide guidance for the append step, that would be great.

Cheers

James


On Sat, Sep 19, 2020 at 4:17 PM James Hartzell 
mailto:james.hartz...@gmail.com>> wrote:
Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1.
When I try to run the original patch you suggested I still get permissions 
problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer
/Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup
Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl 
https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all
 > recon-all
zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers
James



--
James Hartzell, PhD (2x)
Donostia-San Sebatián, Spain
Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
Center for Buddhist Studies, Columbia University, USA



--
James Hartzell, PhD (2x)
Donostia-San Sebatián, Spain
Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
Center for Buddhist Studies, Columbia University, USA

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--
James Hartzell, PhD (2x)
Donostia-San Sebatián, Spain
Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
Center for Buddhist Studies, Columbia University, USA

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