date:20210406

Re: [Freesurfer] mris_average_surface fails

2021-04-06 Thread バキット・ムダシル

External Email - Use Caution

I Think I have a permission. I ran chmod -R u+rwX to make sure, but the error 
was the same. Can you confirm from below please?

\mudathirbakhit$ ls -l $FREESURFER_HOME/
total 568
drwxr-xr-x   39 mudathirbakhit  admin   1248 Mar 18 20:24 6.0.0
-rwxr-xr-x1 mudathirbakhit  wheel   3240 Aug 12  2020 ASegStatsLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel  47514 Aug 12  2020 DefectLUT.txt
-rwxr-xr-x@   1 mudathirbakhit  wheel  89181 Aug 12  2020 FreeSurferColorLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel  18152 Aug 12  2020 FreeSurferEnv.csh
-rwxr-xr-x1 mudathirbakhit  wheel  18223 Aug 12  2020 FreeSurferEnv.sh
drwxrwxr-x@   3 mudathirbakhit  wheel 96 Mar 16 13:11 Freeview.app
drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 10:06 Freeview_backup.app
-rwxr-xr-x@   1 mudathirbakhit  wheel  28381 Aug 12  2020 SegmentNoLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel   1358 Aug 12  2020 SetUpFreeSurfer.csh
-rwxr-xr-x1 mudathirbakhit  wheel   1350 Aug 12  2020 SetUpFreeSurfer.sh
-rwxr-xr-x@   1 mudathirbakhit  wheel   4104 Aug 12  2020 
Simple_surface_labels2009.txt
-rwxr-xr-x1 mudathirbakhit  wheel  25476 Aug 12  2020 WMParcStatsLUT.txt
-rw-r--r--@   1 mudathirbakhit  staff   2718 Apr  1 14:13 aparc+aseg.txt
drwxr-xr-x  126 mudathirbakhit  wheel   4032 Apr  7 07:22 average
drwxr-xr-x  766 mudathirbakhit  wheel  24512 Mar 17 10:06 bin
-rwxr-xr-x1 mudathirbakhit  wheel 47 Aug 12  2020 build-stamp.txt
drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 19:35 color
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 diffusion
drwxr-xr-x   37 mudathirbakhit  wheel   1184 Aug 12  2020 docs
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 etc
drwxr-xr-x5 mudathirbakhit  wheel160 Aug 12  2020 fsafd
drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 fsfast
drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 lib
-rw-r--r--@   1 mudathirbakhit  wheel 55 Feb 17 09:40 license.txt
drwxr-xr-x  185 mudathirbakhit  wheel   5920 Apr  7 07:22 matlab
drwxr-xr-x   11 mudathirbakhit  wheel352 Apr  7 07:22 mni
-rw-r--r--@   1 mudathirbakhit  staff641 Apr  6 16:13 par.txt
drwxr-xr-x8 mudathirbakhit  wheel256 Apr  7 07:22 python
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 sessions
-rwxr-xr-x1 mudathirbakhit  wheel134 Aug 12  2020 sources.csh
-rwxr-xr-x1 mudathirbakhit  wheel132 Aug 12  2020 sources.sh
drwxr-xr-x+  42 mudathirbakhit  wheel   1344 Apr  7 09:37 subjects
-rwxr-xr-x1 mudathirbakhit  wheel   1681 Aug 12  2020 tkmeditParcColorsCMA
drwxr-xr-x   38 mudathirbakhit  wheel   1216 Apr  7 07:22 trctrain
-rwxr-xr-x1 mudathirbakhit  wheel972 Aug 12  2020 uninstall.sh

> On Apr 6, 2021, at 22:30, Douglas N. Greve  wrote:
> 
> Do you have write permissions to
> 
> /Applications/freesurfer/subjects
> 
> Of not on a mac
> 
> On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
>> External Email - Use Caution
>> 
>> Hi,
>> I am trying to make an average subject but when the process reaches 
>> mris_average_surface it fails as seen below.
>> My command was as follow:
>> make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 
>> spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
>> Can you please guide me to solve this issue.
>> 
>> Thanks
>> 
>> Mudathir
>> 
>> ###
>> #@# Making average lh.white surface -
>> Tue Apr  6 19:23:39 JST 2021
>> /Applications/freesurfer/subjects/avgsubject
>> mris_make_average_surface -i 7 -o white -sdir-out 
>> /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 
>> spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
>> reading vertex positions from white...
>> ---
>> hemi= lh
>> avg_surf_name   = white
>> canon_surf_name = sphere.reg
>> out_sname   = avgsubject
>> xform   = talairach.xfm
>> ---
>> 
>> 
>> Is a directory
>> Is a directory
>> ERROR: creating directory /
>> ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf
>> mris_average_surface failed
>> ERROR: make_average_surface
>> #
>> 
>> 
>> 
>> 
>> 
>> 
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Re: [Freesurfer] Talairach Failed: Distorted T1

2021-04-06 Thread Harkey, Thomas Jarrott

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Douglas,
Thanks again. Is this value in the brainstem.dat file accurate or is it subject 
to the same limitation in that the value will depend on the field of view of 
volume acquisition?
In other words, is it valid to add this number to the brain to obtain total 
brain volume?
Kind regards,
Thomas Harkey
UAMS College of Medicine M3

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Harkey, Thomas Jarrott 

Sent: Tuesday, March 30, 2021 6:03 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Talairach Failed: Distorted T1


External Email - Use Caution

Douglas,
Thank you for your help. Another question. The FreeSurfer wiki states that for 
version 5.2 and later, the brainstem is not included in the global measures of 
volume because the amount of brainstem changes depending upon the field of view 
of the volume acquisition.
We are interested in the obtaining the volume of the entire brain using the 
BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the 
brainstem and therefore underestimates total brain volume? Is there a way to 
correct for this?
Kind regards,
Thomas Harkey
UAMS College of Medicine M3


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:48 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

That is an axial scan that only covers 25mm of the brain inferior-superior. 
This is not whole brain coverage, which is causing the problem

On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Douglas,
Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz
  type: MGH
dimensions: 384 x 384 x 25
   voxel sizes: 0.598958, 0.598958, 1.00
  type: SHORT (4)
   fov: 230.000
   dof: 1
xstart: -115.0, xend: 115.0
ystart: -115.0, yend: 115.0
zstart: -12.5, zend: 12.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.9841, y_r =  -0.0087, z_r =  -0.1777, c_r =15.3722
  : x_a =   0.0272, y_a =  -0.9944, z_a =  -0.1022, c_a =14.0701
  : x_s =  -0.1758, y_s =  -0.1054, z_s =   0.9788, c_s =   -75.3479

talairach xfm :
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
   -0.5894  -0.0052  -0.1777   131.7540
0.0163  -0.5956  -0.1022   126.5760
   -0.1053  -0.0631   0.9788   -55.2497
0.   0.   0. 1.

voxel-to-ras determinant 0.358751

ras to voxel transform:
   -1.6429   0.0454  -0.2935   194.5030
   -0.0144  -1.6602  -0.1759   202.3262
   -0.1777  -0.1022   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

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

 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

It looks like something is wrong with your input. For starters, the voxel size 
looks huge. Run
mri_info subject/mri/orig/001.mgz
and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After 
running recon-all on this patient, the Talairach failed according to the .log 
file. No stats were calculated but loading the orig.mgz file into FreeView 
looks like this (see image attached). This DICOM file was successfully uploaded 
into other programs.

How can I fix this error?

Kind regards,

--

Thomas Harkey
University of Arkansas for Medical Sciences

College of Medicine, Class of 2022
501-553-6318

tjhar...@uams.edu




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Re: [Freesurfer] make_average_subject error

2021-04-06 Thread Jordan Mullins

External Email - Use Caution

The patch (see text below) only directed me to replace a file in the
freesurfer/gcc/lib directory, which I did. Do I also need to replace the
make_average_subject and mri_aparc2aseg files in my freesurfer bin?

*To patch the existing 6.0.0 release you may need administrator privileges
to do the following:*

*1) Remove your existing Freeview.app application bundle by sending it to
the trash (and then emtying the trash).*
*   You can also do this from the terminal by cd'ing to the top level
./freesurfer subdirectory and then doing,*
*   "rm -rf Freeview.app". *

*2) Copy the new Freeview.app.zip to where your old Freeview.app was
located aund uncompress it (so it becomes*
*   the replacement Freeview.app in your current freesrufer installation).*

*3) Remove ./freesurfer/lib/gcc/lib/libgomp.1.dylib from your existing
freesurfer installation.*

*4) Copy the ./freesurfer/lib/gcc/lib/libgomp.1.dylib from the patch
archive to /freesurfer/lib/gcc/lib in your current*
*   freesurfer installtion.*

*5) Try running the Freeview.app and loading a volume with it.*

On Mon, Apr 5, 2021 at 6:43 AM Douglas N. Greve 
wrote:

> It looks like you are still using the old make_average_subject as the time
> stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you confirm that
> those are really the patches?
>
> On 3/29/2021 12:52 PM, Jordan Mullins wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Just following up on this. Thanks!
>
> On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins <
> jordan.mull...@email.ucr.edu> wrote:
>
>> Yes! Results attached.
>>
>> On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve 
>> wrote:
>>
>>>
>>> Can you run
>>> ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
>>> $FREESURFER_HOME/bin/make_average_subject
>>> and send the result?
>>>
>>> Also, the result of
>>> which mri_aparc2aseg
>>> which make_average_subject
>>>
>>>
>>>
>>> On 3/17/2021 8:36 PM, Jordan Mullins wrote:
>>>
>>> External Email - Use Caution
>>> Yes, I had seen that report and had downloaded the patch, but still got
>>> the same error. Are there any other steps I can take?
>>>
>>> On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
>>> wrote:
>>>
 This problem is documented (along with a fix) on our release notes
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 On 3/16/2021 3:39 PM, Jordan Mullins wrote:

 External Email - Use Caution
 Yes, I used the make_average_subject command. I've attached a text file
 below of the command line and terminal output from my attempt to average
 two subjects. I get the same error when I try this with the full sample.

 On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve <
 dgr...@mgh.harvard.edu> wrote:

> What command are you using? make_average_subject? Send the command
> line and terminal output
>
> On 3/10/2021 3:53 PM, Jordan Mullins wrote:
>
> External Email - Use Caution
> Hello,
>
> I am trying to create an average subject from a set of subjects, but
> keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open
> file". I've read that several others have solved this issue by installing
> the patch available at *MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
> http://secure-web.cisco.com/1hZOnX5ZyoNBvuPdU7nwHA01_Q0xGjVvb4LN7phnE7_ESZ8rlXaERJDxY96UzmyuwC-RaiRyN5fUK56kcL4mnUlm5wRSpqUjYxJvn4e8mWUu-Cblpy06eO_7VgzY8yojF9sBrwaMsU5cnF5xojFZ3eMoKwywaYIwHhY_Inj5DsyRaUeR_Qc8Sbl0eMicp9bG2jt2Puz052S8D1yk3a_W51SNv0Q3rQ6VMjIgJrtuRldI1ELgyBFJRMM8RUUcNNxzPKhmC6n_vtnnpg2htaQi3Lg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F
> .
>

Re: [Freesurfer] Freesurfer Website Ports

2021-04-06 Thread fsbuild

External Email - Use Caution

Hello Hannah,
While the freesurfer group does not control the port(s) numbers exposed on the 
public facing web servers that host the freesurfer web pages, I’ve been told by 
IT that you should not need to access the ftp port and you should only need to 
setup the VPN to allow outgoing connections to port 443 on 
surfer.nmr.mgh.harvard.edu 

- R.

On Apr 6, 2021, at 10:45, Swearingen, Hannah 
hannah_swearing...@brown.edu 
wrote:External Email - Use 
CautionWe are wanting to 
connect to the site in the need of support from the freesurfer website (i.e. 
the manual pages) while behindour closed system.On Tue, Apr 6, 2021 at 
9:29 AM Douglas N. Greve dgr...@mgh.harvard.edu wrote:why do you need 
to connect to the web site? that is not needed to run FSOn 4/5/2021 3:20 PM, 
Swearingen, Hannah 
wrote:External Email - Use 
CautionHi,I am setting up an 
Access Control List for an isolated VLAN in which my center's neuroimaging 
computing workstations will be connected to our hospital's network for data 
back-up.We want to be able to connect to Freesurfer'swebsite while 
connected to the VLAN, and we need to supply which ports the website accesses. 
I used nmap to scan and see which ports are open, and I found this:PORT 
 STATE SERVICE21/tcp open  ftp80/tcp open  
http443/tcp open  httpsOur hospital's IT is unsure if the FTP port can be 
opened without a security breach, and they are wonderingif we will still 
be able to access the website without the 21/FTP port opened?Can anyone provide 
me with that 
information?Thanks,Hannah--___
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Re: [Freesurfer] recon-all transformations: raw nii to T1.mgz

2021-04-06 Thread Fischl, Bruce

Hi Noam

You can always use the -rl  switch in mri_convert (rl == "reslice 
like"). So for example

mri_convert -rl rawavg.mgz orig.mgz orig_back_to_raw.mgz

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam
Sent: Tuesday, April 6, 2021 2:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Perlman, Or 
Subject: [Freesurfer] recon-all transformations: raw nii to T1.mgz

Hello,
I was running recon-all on a raw T1 image with the following properties:
dimensions: 126 x 144 x 88
voxel sizes: 1.78, 1.78, 1.78
Orientation: PSL

Besides the raw T1, I have other nii files with the same dimensions and 
orientation that I want to visualize on top of the recon-all output T1.mgz.
How can I run the same transformations (and reslicing) that were used in 
recon-all (from my raw nii file to T1.mgz) on the other nii files?

Thanks!
Noam
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[Freesurfer] recon-all transformations: raw nii to T1.mgz

2021-04-06 Thread Peled, Noam

Hello,
I was running recon-all on a raw T1 image with the following properties:
dimensions: 126 x 144 x 88
voxel sizes: 1.78, 1.78, 1.78
Orientation: PSL

Besides the raw T1, I have other nii files with the same dimensions and 
orientation that I want to visualize on top of the recon-all output T1.mgz.
How can I run the same transformations (and reslicing) that were used in 
recon-all (from my raw nii file to T1.mgz) on the other nii files?

Thanks!
Noam
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[Freesurfer] Postdoc opportunity - fMRI and EEG in childhood leukemia

2021-04-06 Thread Mark Wagshul

External Email - Use Caution

Postdoctoral Fellow position available at Albert Einstein College of Medicine
in NYC

The departments of Neuroscience (Dr. Elyse Sussman) and Radiology (Dr. Mark
Wagshul) at the Albert Einstein College of Medicine in New York City are
seeking a full-time postdoctoral research associate to work on an NIH-funded
project exploring the neural bases of chemotherapy-induced cognitive deficits
(chemobrain) in survivors of childhood leukemia. The project employs both
EEG-based and fMRI-based methods to elucidate the cognitive pathways driving
chemo-related cognitive dysfunction in children ages 5 - 12 years. The position
is available starting June 2021; candidates are expected to be able to commit
to join for the duration of the project through March 2025.
Successful candidates for the position will have a PhD in physics, biomedical
engineering, neuroscience or a related discipline, a strong background in
either cognitive neuroscience or MRI physics, expertise in image and EEG data
processing, as well as data and statistical analysis. Programming experience
should include the commonly used packages for image and EEG processing, such as
C++, Matlab, and FSL. The candidate should have significant experience in
event-related potential (ERP) data collection and analysis methods and/or
imaging in a clinical setting and a strong background in the development and/or
application of novel methods for human brain imaging, such as DTI / fMRI /
structural MRI data analyses. Candidates with experience only in EEG-based or
fMRI-based methods will be considered if they can demonstrate through
experience or letters of reference that they are able to quickly and
independently master new techniques and methods of analysis. The candidate will
allocate equal amounts of time to the EEG and MRI labs. Prior experience with
auditory-based ERP/fMRI is not necessary, but candidates with such experience
will be given preference. A strong work ethic, excellent organizational and
communication skills, and ability to work independently is expected. Previous
experience working with child populations is a plus. The candidate will be
expected to be involved in all aspects of the project, including EEG, image and
data analysis, statistical analysis, as well as interfacing with the clinical
team. Competitive salary and benefits will be offered based on qualifications.
The Gruss MRRC is located on the main campus of the Albert Einstein College of
Medicine in Bronx, NY. The Center has a multinuclear 3.0 Tesla Whole Body
Philips Elition human system and a 9.4 T Direct Drive Varian animal system.
Image processing facilities including a computing cluster, multiple Linux
workstations and PCs with imaging and general software installed. Please visit
our website for more details
(http://secure-web.cisco.com/1GGPHY7tcK4iQ7uhuzlRsC2wStBZnZ-wk-MUQxbdrTpcNFZfopkAgCV6l94mG38U29AiQwndux16mYidTjQSGg68emyseFhnD3AeEhqD0vjJtxPHBSyhu0d3EEyjx96X230qfm97u9VFLIQpR7-ZWOcuzNreM9qvOQS6rt_12gB4P0McvhxcG6D6HOd1u3hz4_OXofSHd4LZ0LUR30EdeFuBeyv6os68kuWEeO8HxjmbtYADeBmY4t-ejnEJNNddridOCZO9N4HLpM7WvzbqxpQ/http%3A%2F%2Fwww.einsteinmed.org%2Fcenters%2Fgruss-magnetic-resonance-research%2F).
The Albert Einstein College of Medicine is a leading academic institution, with
over $170M in NIH funding. The candidate will have access to state-of-the-art
brain imaging (MRI, EEG) and computing facilities. Einstein is one of the
nation's premier institutions for medical education, basic research and
clinical investigation. It is home to some 2,000 faculty members, 750 M.D.
students, 350 Ph.D. students attending the Sue Golding Graduate Division -
including 125 in the combined M.D./Ph.D. program - and 325 postdoctoral
investigators training at our Belfer Institute for Advanced Biomedical Studies.
More than 7,000 Einstein alumni are among the nation's foremost clinicians,
biomedical scientists and medical educators.
Interested candidates should send their CV, a brief statement of their research
interests and career goals, and the names and phone numbers of three references
to:
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(elyse.suss...@einsteinmed.org). Review of applications will begin immediately
and continue until the position is filled.
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Action Employer. All qualified applicants will receive consideration for
employment without regard to race, color, religion, sex, sexual orientation,
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professional experience, have prepared them to contribute to our commitment to
diversity and excellence, and the communities we serve.

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Re: [Freesurfer] Cortical surface analysis

2021-04-06 Thread Fischl, Bruce

Hi Ornaith

The mapping uses the vertex index. That is, the vertex index is stored in the 
flatmap, so you should always be able to recover it, then look up the location 
of that vertex on any other surface (of the same hemisphere/subject)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 6, 2021 2:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cortical surface analysis


External Email - Use Caution
Hello FreeSurfer developers,

Thanks a lot for your help.  I have initialised the pialxyz the way you 
suggested and made the flatmap in MatLab using the read_patch function 
(screenshots attached).  I still don't understand how to convert between the 
two.  For example how to see what point (x,y,z) on the pial surface corresponds 
to what (x,y) point on the flatmap.

Thanks a lot for your help.

Kind Regards,
Ornaith



On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:

External Email - Use Caution
Hello Freesurfer developers,

I am new to Freesurfer and I'm hoping that someone can help me.

My goal is to be able to visualise electrodes contacts that are on lying on the 
cortical surface on a flat map and a spherical map.

I've run recon-all and created the flatmap.

I'm using Matlab to achieve this and I've loaded the information with the lines

lhsphere = 
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D');

1. I want to be able to access the coordinates and show the electrons on the 
flat map/ sphere and I was wondering how to do this?  I understand that the 
vertex ID number is what relates the coordinates in the original image to these 
surfaces.  I am wondering how to access the vertex ID numbers ?  At the moment 
I think that I only have access to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into an mgz 
file using mri_surf2surf, eg
mri_surf2surf  --hemi lh   --sval-xyz white --tval lh.white.xyz.mgz   --s 
yoursubject
You can then get the xyz of a given vertex by reading
whitexyz = MRIread('lh.white.xyz.mgz');



2. Additionally, I was wondering if there is a way to display the surface 
images through Matlab?  What would be the best way to show the surface with the 
electrons overlaid on it?
I know there are ways, but I don't know their details


The version of Freesurfer and the platform that I'm using is outlined below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)

I really appreciate any help with this as I'm really stuck.

Thanks in advance for any help.

Kind Regards,
Ornaith O'Reilly


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Re: [Freesurfer] Cortical surface analysis

2021-04-06 Thread Ornaith O Reilly

External Email - Use Caution

Hello FreeSurfer developers,

Thanks a lot for your help.  I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached).  I still don't understand how to convert between
the two.  For example how to see what point (x,y,z) on the pial surface
corresponds to what (x,y) point on the flatmap.

Thanks a lot for your help.

Kind Regards,
Ornaith




On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve 
wrote:

>
>
> On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
>
> External Email - Use Caution
> Hello Freesurfer developers,
>
> I am new to Freesurfer and I'm hoping that someone can help me.
>
> My goal is to be able to visualise electrodes contacts that are on lying
> on the cortical surface on a flat map and a spherical map.
>
> I've run recon-all and created the flatmap.
>
> I'm using Matlab to achieve this and I've loaded the information with the
> lines
>
> lhsphere = fs_read_surf(
> '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
> lhflatpatch=fs_read_patch(
> '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D'
> );
>
> 1. I want to be able to access the coordinates and show the electrons on
> the flat map/ sphere and I was wondering how to do this?  I understand that
> the vertex ID number is what relates the coordinates in the original image
> to these surfaces.  I am wondering how to access the vertex ID numbers ?
> At the moment I think that I only have access to the vertex coordinates and
> the vertex faces.
>
> The easiest way to do this is probably to map the white or pial xyz into
> an mgz file using mri_surf2surf, eg
> mri_surf2surf  --hemi lh   --sval-xyz white --tval lh.white.xyz.mgz   --s
> yoursubject
> You can then get the xyz of a given vertex by reading
> whitexyz = MRIread('lh.white.xyz.mgz');
>
>
> 2. Additionally, I was wondering if there is a way to display the surface
> images through Matlab?  What would be the best way to show the surface with
> the electrons overlaid on it?
>
> I know there are ways, but I don't know their details
>
>
> The version of Freesurfer and the platform that I'm using is outlined
> below:
> 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
> 2) Platform: macOS High Sierra 10.13.6 (17G7024)
>
> I really appreciate any help with this as I'm really stuck.
>
> Thanks in advance for any help.
>
> Kind Regards,
> Ornaith O'Reilly
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Re: [Freesurfer] "ERROR: crypt() returned null with 4-line file"

2021-04-06 Thread 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

2021-04-06 Thread 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/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] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

2021-04-06 Thread Bahar Hazal Yalçınkaya

External Email - Use Caution

Thank you Douglas, I tried quickly via correcting my gtmseg.ctab output
with standardized for gtmseg only for tissue types, it runs without error,
I will create a new look up table and try further.

Thanks again,
Kind regards.

On Tue, Apr 6, 2021 at 3:53 PM Douglas N. Greve 
wrote:

> gtmseg will not give an error, but the color table that gtmseg outputs
> will not be right and needs to be fixed.
>
> On 4/6/2021 9:41 AM, Bahar Hazal Yalçınkaya wrote:
>
> External Email - Use Caution
> Thanks for response, color table and annotations are there "--ctx-annot
> Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
> Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an
> error, you can see at attachments. (Also I can see 258 Head segmentation in 
> *gtmseg.ctab
> *file) also mri_coreg is working well (see also attachments). The problem
> is the "*mri_gtmpvc*" command where it fails while checking tissue types
> more precisely it complains about Head segmentation.
>
> I run with standard options. I checked everything I can think of, each
> file and image seems to be similar but still could not find a proper
> solution. Is there anything specific I need to check?
> Thanks in advance,
> Kind regards
>
> On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve 
> wrote:
>
>> You will need to create a new color table. This is not hard, but not easy
>> either. First, there should be a color table already there. I'm not sure
>> what that will be like; it might have your segments in it, it might not. It
>> might be easier to run gtmseg with the standard options and look at the
>> color table, then try to replicate it with your segmentation
>>
>> On 4/5/2021 6:43 AM, Bahar Hazal Yalçınkaya wrote:
>>
>> External Email - Use Caution
>> Hello Freesurfer"s Developers,
>>
>> I am trying to follow *PetSurfer* (*MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1B2HO1KM0jnhlHMvubnOYbXX6eMhgWiZ6pFbmY8cJ2rCR2zh7VM-XMlmpKiWAzd5tpEcw6RAupdohvdRKmcJoaAgzRSY1dmGSjgmtdT6CARZGIoZpbZtWPP6y1VMM1fKmi4Psm_C57Invn3aAGEGE0zFpdyHGoW22HTxO2OCOQfY1hc_50vWrBdP468EQW9X5TzK4SepUR_s94d7KIzuv7hfNO_WUMrR3z8qtqTjb0jNNcQDGNKZ5HpdLi9nOSFrkv-V_F731T7DiDbbsXdd1Mw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
>> )
>> to apply PVC to Pet images.
>> Default pipeline is working however, whenever i try to use another atlas,
>> Schaefer parcellation, mri_gtmpvc command I get following error:
>>
>> WARNING: LTAconcat(): inverting LTA 1 to match geometry
>>
>> Replacing 18
>>
>> Pruning ctab
>>
>> tissue type schema
>>
>> Checking tissue type
>>
>> ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral
>> not set
>>
>> Failed tissue type check
>>
>> I have searched to list several people who have issued similar errors but
>> unfortunately i could not find any solution that works for me. Below you
>> can find commands I used:
>>
>> $ gtmseg --s subject --o gtmseg.mgz --ctx-annot
>> Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
>> Schaefer2018_400Parcels_7Networks_order_LUT.txt
>> $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta
>> $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta
>> --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx
>> .01 --km-ref 8 47 --o gtmpvc.output
>> Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258
>> Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258
>> Head-ExtraCerebral in the list.
>> I will be happy to hear from you.
>> Kind regards.
>> --
>> Ph.D. Bahar Hazal Yalçınkaya
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1bpF6vIi1TzZFN2hZ0kddt70_T6WpYlp2YZzHb5NmkZ84_1QPYWHPFG_xAVTFs0DyiO447A3zVtvA1ojS8Z8JosjVW8f3y0vj30YJkXv-aHu9fuTxZbXYw3yLNG_KcGHo4zuQVTUWWLdS1gC-8ruqQFYpqPr1xcicpcyTesO93J5fcSWFiwz4clzLYUFYIqTZloMS8RZXIBq8rdi8YpSJspibOvtmsyOKwwu0yTASPYGmgQhVxjSWyuVCfdVWPQ8xe0DtRPiILA2jkIQaxvO4aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>>

Re: [Freesurfer] Freesurfer Website Ports

2021-04-06 Thread Swearingen, Hannah

External Email - Use Caution

We are wanting to connect to the site in the need of support from the
freesurfer website (i.e. the manual pages) while behind our closed system.

On Tue, Apr 6, 2021 at 9:29 AM Douglas N. Greve 
wrote:

> why do you need to connect to the web site? that is not needed to run FS
>
> On 4/5/2021 3:20 PM, Swearingen, Hannah wrote:
>
> External Email - Use Caution
> Hi,
>
> I am setting up an Access Control List for an isolated VLAN in which my
> center's neuroimaging computing workstations will be connected to our
> hospital's network for data back-up.
>
> We want to be able to connect to Freesurfer's website while connected to
> the VLAN, and we need to supply which ports the website accesses. I used
> nmap to scan and see which ports are open, and I found this:
>
> PORTSTATE  SERVICE
>
> 21/tcp  open   ftp
>
> 80/tcp  open   http
>
> 443/tcp open   https
>
>
>
> Our hospital's IT is unsure if the FTP port can be opened without a
> security breach, and they are wondering if we will still be able to access
> the website without the 21/FTP port opened?
>
>
> Can anyone provide me with that information?
>
>
> Thanks,
>
> Hannah
>
> --
>
>
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>
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-- 
Hannah Swearingen
hannah.swearin...@va.gov
hannah_swearing...@brown.edu 
401-273-7100 x14449
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Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

2021-04-06 Thread Ramesh Babu

External Email - Use Caution

Dear Douglas

Thank you very much for your suggestions.

Regards
Ramesh

On Tue, 6 Apr, 2021, 7:03 PM Douglas N. Greve, 
wrote:

> Twice the same image at 1x1x1, then use mri_robust_template to register
> and average them together
>
> On 4/6/2021 8:10 AM, Ramesh Babu wrote:
>
> External Email - Use Caution
> Dear Eugenio and Philipp,
>
> Thank you very much for your suggestions. Could you please give more input
> on "acquire the T1WI double and average it after coregistration, this
> increases the SNR".
>
> Should aquire twise the same sequence with 1x1x2 voxel dimension?
>
> Thanks
> Ramesh
>
>
> On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
>> That all sounds right, thanks a lot Philipp!
>>
>>
>>
>>
>>
>> Juan Eugenio Iglesias
>>
>> Senior research fellow
>>
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>>
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>> *From: * on behalf of "Saemann,
>> Philipp" 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Friday, April 2, 2021 at 03:51
>> *To: *Freesurfer support list , Umesh
>> Rurdrapatna 
>> *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi,
>>
>>
>>
>> I try to answer but Eugenio may also add comments. Several points that
>> are important:
>>
>> - 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can
>> manage.
>>
>> - Post-aquisition reslicing to a higher resolution does not really
>> increase the information content. Internally the algorithm works at a much
>> higher resolution, anyway.
>>
>> - If possible, switch to 3 Tesla.
>>
>> - If possible and this is a prospective study, add a coronal T2 image and
>> use the bi-channel option. See papers of Iglesias et al. on this.
>>
>> - What you could also do on a 1.5 T is acquire the T1WI double and
>> average it after coregistration, this increases the SNR.
>>
>> - Generally, isometric resolutions are good due to the symmetry, of
>> course.
>>
>> - Also on 1.5 T, you may go bit below 1 mm with good head immobilization,
>> and a longer scanning time. BRAVO in general is a good T1 option.
>>
>>
>>
>> Best,
>>
>> Philipp
>>
>>
>> --
>>
>> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu <
>> mgrameshbabu2...@gmail.com>
>> *Gesendet:* Freitag, 2. April 2021 09:29
>> *An:* Freesurfer support list; Umesh Rurdrapatna
>> *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Dear experts,
>>
>> Sorry for reposting. I am expecting some response from experts, so that I
>> can proceed with confidence.
>>
>> For our project work, we are looking for hippocampal  and its
>> subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with
>> 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced
>> images with a lot of noise. Then we tried the same sequence with 1x1x2
>> resolution, and 256x256x80 FOV, which produced a clean image without noise.
>> When we reformatted the images, it produces 0.5x0.5x1 resolution with
>> 512x512x172 dimension.
>>
>>
>>
>> Is this sequence good for hippocampal volume estimation and subfield
>> segmentation (also for whole-brain VBM analysis)?
>>
>> Could you please suggest to me a correct sequence, if need to be changed?
>>
>>
>>
>> Regards
>>
>> Ramesh
>> ___
>> Freesurfer mailing list
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