Re: [Freesurfer] Talairach Failed: Distorted T1

[Harkey, Thomas Jarrott]

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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:

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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:

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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] Abormally high foldind index

[Fischl, Bruce]

Hi Ellen

It is certainly possible. Have you looked at the surfaces for those subjects?

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ellen Ji
Sent: Tuesday, March 30, 2021 5:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Abormally high foldind index

External Email - Use Caution

Dear Experts,

While the majority of our subjects have a folding index between 5-30, there are 
a couple of *extreme* outliers in the thousands or even negative.

Could this hint that a particular part of recon-all failed and should be rerun?

Thank you for your interpretation and advice!

-Ellen

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[Freesurfer] Abormally high foldind index

[Ellen Ji]

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Dear Experts,

While the majority of our subjects have a folding index between 5-30, 
there are a couple of *extreme* outliers in the thousands or even negative.

Could this hint that a particular part of recon-all failed and should be 
rerun?

Thank you for your interpretation and advice!

-Ellen

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[Freesurfer] Subthalamic nucleus volume

[T. Pansuwan]

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Dear Freesurfer experts,

As part of my project, I would need to have subthalamic nucleus as one of my 
ROIs in which this is not available by Freesurfer. I found a probabilistic 
subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would 
convert this to fsaverage space. I have attempted:

mri_label2vol —reg $FREESURFER_HOME/average/mni152.register.dat —seg 
STN-maxprob-thr25-0.5mm.nii.gz —temp 
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz —o STN_mni152_in_mni305.nii.gz

But the location was much more dorsal than original,
1) I was wondering if there are alternative methods I should try and what could 
have been the problem?

At the end, I hope to obtain individual subject’s subthalamic nucleus volume,
2) I was wondering how to convert volume in fsaverage space to labels in 
fsaverage space so that I can convert the labels to native space?


Thank you so much!

Tanrada Pansuwan






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[Freesurfer] ERROR: Cannot find stats file

[atacan zeybek]

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Hello FreeSurfer Developers,

I'm attempting to create a text file of amygdalar nuclei of given subjects. I 
use this command:

asegstats2table --subjects 8070  8071  8077 
--statsfile=amygdalar-nuclei.lh.T1.v21.stats 
--tablefile=amygdalarnuclei.lh.T1.v21.txt –skip

And get an error like this:

ERROR: Cannot find stats file 
/home/atacan/Desktop/freesurfer/subjects/8070/stats/amygdalar-nuclei.lh.T1.v21.stats

Unfortunately I can't search the mail archives because I get an another error 
while loading the page.

Freesurfer version: CentOS 7 x86_64 (64b) tar archive
Platform: Ubuntu 20.04.2 LTS
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Re: [Freesurfer] [External] Re: "ERROR: crypt() returned null with 4-line file" when running via Singularity

[Zoner, Katja]

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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 
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`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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[Freesurfer] 2mm thick image for hippocampal segmentation.

[Ramesh Babu]

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Dear Experts,

For our project work, we particularly 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 for our project?

Regards
Ramesh
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Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

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Thanks a lot, It works!, now I have obtained values to ctx and wm volumes
for each area. However when I look at the gray matter volume values
calculated by mri_anatomical stats, the results are pretty similar to the
ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In
that case what measure will be more suitable?

El lun, 29 mar 2021 a las 5:22, Douglas N. Greve ()
escribió:

> You'll need to create your own color table by adding 3000 to the left hemi
> structures and 4000 to the right hemi structures. Look at the 3000s and
> 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>
> On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Douglas, i tried but when i look at the wmparc.mgz created by the
> code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names
> from FreeSurferColorLUT instead of the names in the colorLUT
> associated with myAAL.annot then the ROIs are disorganized. Could you help
> me with this problem?
>
> El jue, 25 mar 2021 a las 14:59, Douglas N. Greve ()
> escribió:
>
>> Look in recon-all.log to find the command that creates the wmparc.mgz.
>> Run that command changing the aparc annot to your annot and the output to a
>> new file name. Look in wmparc.stats; at the top will be an mri_segstats
>> command line. Copy that command line changing the file names as needed.
>>
>> On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> Thanks!, how can I obtain the white matter volume stats using my
>> annotation file?
>>
>> El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (<
>> dgr...@mgh.harvard.edu>) escribió:
>>
>>> I think they will give very similar results, but my guess is that #1 is
>>> a little better
>>>
>>> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>>>
>>> External Email - Use Caution
>>> I want to use the annotation file created by myself in fsaverage to
>>> calculate the anatomical stats, but i dont know what is the best workflow.
>>>
>>> 1. Convert the annotation file to each subject space using mri_sur2surf
>>> and using mri_anatomical_stats in each subject
>>> 2. Convert the surface of each subject to fsaverage space and use
>>> mri_segstats to obtain the data, in this case i dont know what surface i
>>> have to convert to fsaverage space to do it (i can see thickness
>>> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
>>> matter volume)
>>>
>>> Any idea?
>>>
>>> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
>>> escribió:
>>>
 Hi Alberto



1. And 4. Are not properties of single surfaces – they are computed
from the white and the pial. For 2 and 3 that is really up to you

 Cheers
 Bruce



 *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
 freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del
 Cerro Leon
 *Sent:* Monday, March 8, 2021 7:02 AM
 *To:* Freesurfer support list 
 *Subject:* [Freesurfer] Problem with freesurfer measures



 *External Email - Use Caution*

 Hello Freesurfer team, I am using an annotation file that i've created
 previously to obtain the measures of some ROIs. To do that i am using de
 commands mri_surf2surf and mri_segstats. I want to obtain the following
 measures:

 1. Gray and White Matter Volume

 2. Folding Index

 3. Curvature measures

 4. Thickness

 However I don't know what surface in the surf folder of each subject I
 have to use. Could u help me?
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