[Freesurfer] Freesurfer Website Ports

[Swearingen, Hannah]

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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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Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

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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 ()
escribió:

> 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 ()
> 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 (<
>> dgr...@mgh.harvard.edu>) 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?
> 

[Freesurfer] "ERROR: crypt() returned null with 4-line file"

[Cook, Philip]

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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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Re: [Freesurfer] quantification of volume of perivascular spaces

[Douglas N. Greve]

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

On 3/31/2021 5:54 AM, Antonín Škoch wrote:


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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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Re: [Freesurfer] Talairach Failed: Distorted T1

[Douglas N. Greve]

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:


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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   0.9788    90.4171
                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] Subthalamic nucleus volume

[Douglas N. Greve]

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:


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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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Re: [Freesurfer] ERROR: Cannot find stats file

[Douglas N. Greve]

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


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


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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] Problem with freesurfer measures

[Douglas N. Greve]

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 
(mailto:dgr...@mgh.harvard.edu>>) 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
(mailto:dgr...@mgh.harvard.edu>>) 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:


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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
(mailto: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:


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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
(mailto:bfis...@mgh.harvard.edu>>) 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

mailto: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
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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Re: [Freesurfer] functional to anatomical registration question

[Douglas N. Greve]

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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Re: [Freesurfer] Running recon-all with FLAIR

[Douglas N. Greve]

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 Szabó wrote:


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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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Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

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:


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Hi Douglas,

Just following up on this. Thanks!

On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins 
mailto:jordan.mull...@email.ucr.edu>> 
wrote:


Yes! Results attached.

On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
mailto:dgr...@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:


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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
mailto:dgr...@mgh.harvard.edu>> wrote:

This problem is documented (along with a fix) on our
release notes
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https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes




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
mailto: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:


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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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from "secure-web.cisco.com" claiming to be*

http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

.
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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http://ucrkindlab.com




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[Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

[Bahar Hazal Yalçınkaya]

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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 Yalçınkaya
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