On 5 Apr 2021, at 17:00, freesurfer-request@nmr.mgh.harvard.edu wrote:

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Today's Topics:

  1. Dicom Tag Problem Reconall (Banu Femir)
  2. mri_vol2surf empty output (Karan Desai)
  3. mri_gtmpvc error Checking tissue type ERROR:
     CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya)
  4. Re: make_average_subject error (Douglas N. Greve)
  5. Re: Running recon-all with FLAIR (Douglas N. Greve)
  6. Re: functional to anatomical registration question
     (Douglas N. Greve)
  7. Re: Problem with freesurfer measures (Douglas N. Greve)
  8. Re: ERROR: Cannot find stats file (Douglas N. Greve)
  9. Re: Subthalamic nucleus volume (Douglas N. Greve)
10. Re: Talairach Failed: Distorted T1 (Douglas N. Greve)
11. Re: quantification of volume of perivascular spaces
     (Douglas N. Greve)
12. "ERROR: crypt() returned null with 4-line file" (Cook, Philip)
13. Re: Problem with freesurfer measures (Alberto Del Cerro Leon)

----------------------------------------------------------------------

Message: 1
Date: Sun, 4 Apr 2021 22:57:57 +0300
From: Banu Femir <banu.femir@gmail.com>
Subject: [Freesurfer] Dicom Tag Problem Reconall
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CANuRgTpGaqjYJVd9V+n3-82ASsx0uP=S=3dH5ksxoxda34S3gA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

Dear Freesurfer Developers,

I'm trying to analyze a set of MRI data that I got via CD. Dicom files did
not have .dcm extension, so I used a program and they turned into a .dcm
image.

My reconall run for around 2 hours, after I got an error:

Counting frames
nframes = 481
nslices = 1
ndcmfiles = 481
PE Dir = UNKNOWN (dicom read)
Loading pixel data
JPEG compressed, decompressing
cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow
fsdcmdecompress --i
/home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o
/tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >&
/tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out
ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for more
details
Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019
x86_64 x86_64 x86_64 GNU/Linux

Before that, I got many Warnings about imagenumber, tag serial number,
seriesnumber, tag, ect. In case you want I can share the whole log file. I
am wondering if there was sth wrong with my .dcm format. If yes, how I can
solve this problem? It seems like there was sth wrong with tags, but I
really cannot solve the problem.

Many thanks!
Have a nice and healthy week!
Banu
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Message: 2
Date: Mon, 5 Apr 2021 04:09:07 +0000
From: Karan Desai <karan.desai@duke.edu>
Subject: [Freesurfer] mri_vol2surf empty output
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM6PR05MB40096B471BBB697482E1939E9C779@DM6PR05MB4009.namprd05.prod.outlook.com>

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Hi FS Forum,

I am posting because after using the command mri_vol2surf to downsample
my scans to fsaverage4, I ended up with empty files when viewed in Freeview.
This is the command that I ran generally:

mri_vol2surf --src bold_preproc.nii.gz --out lh.imagename.nii.gz --regheader
sub-01 --trgsubject fsaverage4 -hemi lh

I am assuming there are some tags that I may be missing which are leading me to
output with empty nii.gz files. The input bold preprocessed files are viewed
normally in Freeview, but the output is empty.

Thank you in advance.

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Message: 3
Date: Mon, 5 Apr 2021 12:43:18 +0200
From: Bahar Hazal Yal??nkaya <baharhazalyalcinkaya@gmail.com>
Subject: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR:
CheckSegTissueType() tissue type for seg
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAGZFL9cpgOZFDSYndyJg0T4=dbd8Fvk5TwHUJGLYUQg+363SCw@mail.gmail.com>
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Hello Freesurfer"s Developers,

I am trying to follow *PetSurfer* (
https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwSGz7RCQalhqGZJFfIT2Ob3QQETtldwxv9y8xYVYGSkRdQ_GjplqWAGkIFRP1S40sf8UfJTbg-jdroEwAQvGW-9HmP1fatTZ8h3DhbPvM4MaRIdn-gicol4f85-JI5PjVoycwQ5z0q2oYvFmz9DuRwGJZg7EiKqmfCLYhXNUOPOwhpm1kKKikeaQrRAVCr4-WbYz4Z0GXBVuflZqXa84PEzxVj0uL51CZ_xoDuhu3DA/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 Yal??nkaya
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Message: 4
Date: Mon, 5 Apr 2021 09:43:06 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <957177a6-1c79-0149-4cbd-1a16122cd203@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

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.mullins@email.ucr.edu <mailto:jordan.mullins@email.ucr.edu>>
wrote:

   Yes! Results attached.

   On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
   <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> 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
       <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> 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:

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           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
           <dgreve@mgh.harvard.edu <mailto:dgreve@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:

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               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
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               <http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqGjdSamQfU6_udvX8lNDAGu6fMmZJqlcAAuJtuijJsAYfi7M55moSpWy1McHpeqmMGAqqWT-7M-IStYk9Qs2pOnTfoJznpdLsEgVASogVifdHzPfK1t3pQowp_WCXSDaaHhTDzz7qCl-DUbTHTPKKgBhR1NruBOW9_7sIsS86UbWXqE7CaL5hUOQNwrRGh4iX37y5CgC4I9HuJDYQNG_3fPAfLJmyVuWMB5QC4E_jw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F>.
               I did this, but continue to get the same error. I'm
               working with Freesurver Version 6.0.0 and MacOS Big
               Sur Version 11.2.3. I've attached the recon-all.log
               below, but please let me know if you need
               additional information.

               Any insight on this would be appreciated! Thank you!

               Jordan

               --
               *Jordan L. Mullins, B.A.*
               Doctoral Student, Department of Psychology
               University of California, Riverside
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           --
           *Jordan L. Mullins, B.A.*
           Doctoral Student, Department of Psychology
           University of California, Riverside
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       --
       *Jordan L. Mullins, B.A.*
       Doctoral Student, Department of Psychology
       University of California, Riverside
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   --
   *Jordan L. Mullins, B.A.*
   Doctoral Student, Department of Psychology
   University of California, Riverside
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--
*Jordan L. Mullins, B.A.*
Doctoral Student, Department of Psychology
University of California, Riverside
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Message: 5
Date: Mon, 5 Apr 2021 09:45:47 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Running recon-all with FLAIR
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <26935515-0e6a-2960-9fe4-e7fb16ebf265@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Try this
cd subject/mri
mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta
You can run with multiple threads by adding --threads N
where N is the number of threads

On 3/29/2021 5:18 PM, Edina Szab? wrote:

????????External Email - Use Caution

Dear All,

We are running recon-all on the latest version of FreeSurfer (v7.1.1).
We are using both T1 and FLAIR images to better define the pial
surfaces, but when we run the recommended command line (recon-all
-subject subjectname -i /path/to/input_volume -FLAIR
/path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very
underestimated (?.pial.FLAIR ? and the aseg volume is based on these
surfaces), and we get better results without the FLAIR.
It seems that FreeSurfer mis-registers the FLAIR to the T1 during the
process. Is there a separate step we should do to register FLAIR to T1?

Thank?you,
Edina

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Message: 6
Date: Mon, 5 Apr 2021 09:48:22 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] functional to anatomical registration
question
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <067c4ed5-b664-87a3-722b-45b9da81ab95@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You can add --aparc+aseg (hit 'c' to toggle on and off), alternatively
You can use tkregsiterfv (same command arguments) but add -aparc+aseg
-seg-outline
You will need to use the lta registration file (not the .dat)

On 3/29/2021 6:13 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurferers,

I have a question and I appreciate it much if you could please reply.
I need to know how to check *subcortical*?functional to anatomical
registration. I know for checking the cortical registration I can use
the below command:

tkregister2 --s $subj --mov ?template.nii.gz ?--surf --reg
init.register.dof6.dat

Could you please tell me what command should I use to check the
registration in subcortex?

Thanks
MOna

*Zahra (Mona) Nasiriavanaki, M.D.*
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General?Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129

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Message: 7
Date: Mon, 5 Apr 2021 09:49:45 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with freesurfer measures
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <70cde94b-a8f5-3504-72ca-bd43a4f9c384@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

What are your command lines?

On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:

????????External Email - Use Caution

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
(<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribi?:

   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
   (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribi?:

       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
       (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>)
       escribi?:

           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
           (<BFISCHL@mgh.harvard.edu
           <mailto:BFISCHL@mgh.harvard.edu>>) escribi?:

               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-bounces@nmr.mgh.harvard.edu
               <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
               <freesurfer-bounces@nmr.mgh.harvard.edu
               <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
               *On Behalf Of *Alberto Del Cerro Leon
               *Sent:* Monday, March 8, 2021 7:02 AM
               *To:* Freesurfer support list
               <freesurfer@nmr.mgh.harvard.edu
               <mailto:freesurfer@nmr.mgh.harvard.edu>>
               *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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Message: 8
Date: Mon, 5 Apr 2021 09:51:34 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] ERROR: Cannot find stats file
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5220512d-4f0c-44e3-63a3-3c2c5e3f4894@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1254"

Does that file exist? If not, have you run the amygdalar nuclei
segmentation?

On 3/30/2021 3:00 PM, atacan zeybek wrote:

????????External Email - Use Caution

????????External Email - Use Caution

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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Message: 9
Date: Mon, 5 Apr 2021 09:54:24 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Subthalamic nucleus volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <2737d6a7-618b-cd97-b4a2-fe29f4c1ce49@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

If you want the volume in the native space, then why not just register
your volume to mni space, then map the label back to the individual? You
could probably do that all with FSL (or SPM). BTW, the "volume" you get
is not at all likely to be accurate. It will just reflect the
registration in that area.

On 3/30/2021 4:28 PM, T. Pansuwan wrote:

????????External Email - Use Caution

????????External Email - Use Caution

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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Message: 10
Date: Mon, 5 Apr 2021 09:56:13 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Talairach Failed: Distorted T1
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6037d9f2-eadc-f756-db09-01ef43e60f2f@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Correct. You can measure the volume of the brainstem and add it on. Eg,
mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat

On 3/30/2021 7:03 PM, Harkey, Thomas Jarrott wrote:

????????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-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgreve@mgh.harvard.edu>
*Sent:* Thursday, March 25, 2021 9:48 PM
*To:* freesurfer@nmr.mgh.harvard.edu <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, 1.000000
? ? ? ? ? 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: 0.000000
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
? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? ? 1.0000

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 ? 0.9788 ? ?90.4171
? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? ? 1.0000

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022
------------------------------------------------------------------------
*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu>
*Sent:* Thursday, March 25, 2021 9:11 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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*

*TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>*

------------------------------------------------------------------------
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Message: 11
Date: Mon, 5 Apr 2021 09:57:27 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] quantification of volume of perivascular
spaces
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <183d083f-5146-90e2-85c1-5b58d7526c30@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

It might work, but I doubt it has been tested.

On 3/31/2021 5:54 AM, Anton?n ?koch wrote:

????????External Email - Use Caution

Dear experts,

We would like to quantify volume of brain perivascular spaces.
Ideally longitudinally - i.e. to study the dynamics of perivascular
spaces in multiple measurement of the same subject.

Is it possible to use samseg for this?

Do you think, that --lesion flag in samseg would work estimation of
perivascular spaces? Or other setting of samseg will be better option?

Or, would you rather recommend other tools?

Any idea/comment will be greatly appreciated.

Regards,

Antonin Skoch

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Message: 12
Date: Mon, 5 Apr 2021 15:41:22 +0000
From: "Cook, Philip" <cookpa@pennmedicine.upenn.edu>
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file"
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BL0PR04MB5028D2F00940DA4CE992E424E67A9@BL0PR04MB5028.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

       External Email - Use Caution

Dear FreeSurfer developers,

I have also encountered the error that Katja Zoner reported in

https://secure-web.cisco.com/1HqVP4_2gCSsHuuEFWzIN0yTWdDhhIeKNpc8cqD9BfBOmmKgsS9FIE4BKco1FPCE5Anq994ZwqQIsH-u2071nrJlW0a_AaHRcLWJn3XuQgUjRiMEp2BpE0gI8eF8s8ikJXS3BqmyQAUgeKlcpib4mDD1S8E5UXh2JD2sXO-AbxxBDu9bQNKF7rf0lHDkDNfYjGSc8DunjxMCM05q_bkGDOiO-2GdCV_NpBoID8eaQZnvykADMJvFpXiqJDCGjMz27Qf6gJexxyJqD-dYrRp6waA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg69509.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

https://secure-web.cisco.com/1-z_qWpPYjwD6UccsUQP4XQEVo4YMH5WkF2I0eRZ2Z2G-7Y-JnshMWuVhJZRyY0wfjmrZSyrmDTgQdj8O3GxncnrQ9AmpeIZGVXTqsBAcmX4Akup4RNxjeeoGse6bLy7yCNdP6FVB4ITMiUxFHnihZ2QuHIacEPmNLw7ffxyzQj5q7xb5umpROXZPIM3JXy_CRpxqY4C0jW5lndQ7MTP8JG5k8TxqDQDDzAWwmM80_qobm3N-fykZlBXA8zPcd64E2ednYIz2DS7cZpFNtQrhkA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg54981.html

https://secure-web.cisco.com/1D8Zt97JISxcqWsV-6sX9O6GUs5X59E2NOYaxNQqkDBr8tOgbGrQnC9a2mf-tNs_Fych5ae4pGNCU1oJZP4QbtDo2Kqh3uYCrInZ5_i0oPnfgk1byC79h8O7xrTu44C0O_zATfdd5JdOnS3S8k3i7P8_4rcS2PeZLL6IfNh61kZIFJHY4y5RvwC4cpRazga8DWUU-EaznxbicQkee-raOBRj3DULH-QkNgzsXVTBcUtT0FkgE1YLXmOjoSuFN5AOD4Vun7Krv0Reds-4RXTuzqA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57637.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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Message: 13
Date: Mon, 5 Apr 2021 17:47:03 +0200
From: Alberto Del Cerro Leon <bertocerron@gmail.com>
Subject: Re: [Freesurfer] Problem with freesurfer measures
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAKXUO47yYhA=k9JK9dbfr_q05dz=1d+nznp-TT8dSaiTmZkD6A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

To obtain de stats from mri_anatomical stats i used
*>>mris_anatomical_stats -a
/usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f*
*/usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats
-b 218 rh*
In another hand, the workflow to obatian the stats from mri_segstats was:

*mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask

--o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz **--annot myAAL*
*>>**mri_segstats --seg
/usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz* *--ctab
/home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum
/usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats *
*-**-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0
--brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in
/usr/local/freesurfer/subjects/218/mri/norm.mgz*
*--in-intensity-name norm --in-intensity-units MR --subject 218
--surf-wm-vol --etiv*

El lun, 5 abr 2021 a las 15:50, Douglas N. Greve (<dgreve@mgh.harvard.edu>)
escribi?:

What are your command lines?

On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:

       External Email - Use Caution
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 (<dgreve@mgh.harvard.edu>)
escribi?:

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 (<
dgreve@mgh.harvard.edu>) escribi?:

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 (<
dgreve@mgh.harvard.edu>) escribi?:

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 (<BFISCHL@mgh.harvard.edu>)
escribi?:

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-bounces@nmr.mgh.harvard.edu <
freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del
Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*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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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc_oWbeIxdBjn0a4ewo9DlEK_n-LjuwWtI4RxcKWU-yqzXa3st3yjrX10XajoHKJeVldQTiodHCNkahvwy3fU5mJR4RqHtQWdlxfMKiBQRTRFYaPVPkC0U3VSPuTe_zXkBpNk0hUjeaBouPTJgAmklTHg0YnJ9sGaCsslcxUtJs64ox6q5AccOiFDTlqoIPTl0dXDTwdkN0Iodg_9LRx7qHyOyuZp1vqc81IDslbXOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5OfMoayKhs_3KQu2Of-pNFnkKv4aCDH5bgpGDz9VcW-tGQIUIAt172I-tNHanxfB2OHj9nNbVaEInREVZwtxJM_jFMf0lLIXT5gJHIRKX0q_RgpAUoygww/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

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https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc_oWbeIxdBjn0a4ewo9DlEK_n-LjuwWtI4RxcKWU-yqzXa3st3yjrX10XajoHKJeVldQTiodHCNkahvwy3fU5mJR4RqHtQWdlxfMKiBQRTRFYaPVPkC0U3VSPuTe_zXkBpNk0hUjeaBouPTJgAmklTHg0YnJ9sGaCsslcxUtJs64ox6q5AccOiFDTlqoIPTl0dXDTwdkN0Iodg_9LRx7qHyOyuZp1vqc81IDslbXOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
<https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5OfMoayKhs_3KQu2Of-pNFnkKv4aCDH5bgpGDz9VcW-tGQIUIAt172I-tNHanxfB2OHj9nNbVaEInREVZwtxJM_jFMf0lLIXT5gJHIRKX0q_RgpAUoygww/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc_oWbeIxdBjn0a4ewo9DlEK_n-LjuwWtI4RxcKWU-yqzXa3st3yjrX10XajoHKJeVldQTiodHCNkahvwy3fU5mJR4RqHtQWdlxfMKiBQRTRFYaPVPkC0U3VSPuTe_zXkBpNk0hUjeaBouPTJgAmklTHg0YnJ9sGaCsslcxUtJs64ox6q5AccOiFDTlqoIPTl0dXDTwdkN0Iodg_9LRx7qHyOyuZp1vqc81IDslbXOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9QEXcl20ViD3v1z-M2EnYwrZWMYqvtsknqADt-sYTrwIi7-QQnkSVceOtdB-0S8AqEDBMmBNsG-4S2GSEk6U4J7musJNzSul2W-jtDPz_Gupshs5I_p0kVxymhPFs0JhDHOTXcRJvuk_gwZ1iVHbS1CPyCBxZY4G0CD0ZIROVbMetqm06qRdFq44Lgy3eMw5itYXU1rBjP-rWv68qNDS4AXSn0w_4gXtoaLB1YULbQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

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https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc_oWbeIxdBjn0a4ewo9DlEK_n-LjuwWtI4RxcKWU-yqzXa3st3yjrX10XajoHKJeVldQTiodHCNkahvwy3fU5mJR4RqHtQWdlxfMKiBQRTRFYaPVPkC0U3VSPuTe_zXkBpNk0hUjeaBouPTJgAmklTHg0YnJ9sGaCsslcxUtJs64ox6q5AccOiFDTlqoIPTl0dXDTwdkN0Iodg_9LRx7qHyOyuZp1vqc81IDslbXOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
<https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9QEXcl20ViD3v1z-M2EnYwrZWMYqvtsknqADt-sYTrwIi7-QQnkSVceOtdB-0S8AqEDBMmBNsG-4S2GSEk6U4J7musJNzSul2W-jtDPz_Gupshs5I_p0kVxymhPFs0JhDHOTXcRJvuk_gwZ1iVHbS1CPyCBxZY4G0CD0ZIROVbMetqm06qRdFq44Lgy3eMw5itYXU1rBjP-rWv68qNDS4AXSn0w_4gXtoaLB1YULbQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

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https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc_oWbeIxdBjn0a4ewo9DlEK_n-LjuwWtI4RxcKWU-yqzXa3st3yjrX10XajoHKJeVldQTiodHCNkahvwy3fU5mJR4RqHtQWdlxfMKiBQRTRFYaPVPkC0U3VSPuTe_zXkBpNk0hUjeaBouPTJgAmklTHg0YnJ9sGaCsslcxUtJs64ox6q5AccOiFDTlqoIPTl0dXDTwdkN0Iodg_9LRx7qHyOyuZp1vqc81IDslbXOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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End of Freesurfer Digest, Vol 206, Issue 5
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