[Freesurfer] dcmunpack

[O'Dor, Sarah,PHD]

Good afternoon,
Quick question about unpacking:
The instructions I have from a previous staff member said to do this:
In folder where files are going, type: unpacksdcmdir -src  
-targ . -scanonly scanout.txt

So what I submit is:
unpacksdcmdir -src 
/cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 -targ . 
-scanonly scanout.txt

When I do that, it just makes the files:
dicomdir.sumfile  scanout.txt  unpack.log

I’m trying to use the dcmunpack command instead. From following the template on 
the website, I’ve been trying the following commands:
[pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src 
/cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 -index-out 
dcm.index.dat

{lots of other content here, so let’s skip to….}
dcmunpack done

[pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src 
/cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 -index-in 
dcm.index.dat -targ .
ERROR: need input runs

How should I specify input runs?
Thanks,
Sarah

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Re: [Freesurfer] Fwd: Error

[Douglas N. Greve]

not sure what is going on. It received a kill signal (the 9 mentioned at 
the end). This often means that it was killed externally. Does this 
happen repeatedly? Does this happen on other subjects? How much memory 
did you allocate to your virtual box?


On 9/23/2022 1:04 AM, Ahmad Khan wrote:


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Dear Free Surfer Development Team.

I am using the recon -all command to compute the volume of different 
regions of the brain. I am running the free surfer version 
freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 
installed on a virtual box. I am getting the following errors and the 
log file is also attached with this email.

*ERROR: mri_ca_register with non-zero status 137*
Your timely response would be highly appreciated.

Best Regards
 Dr. Ahmad Raza Khan
(Ramalingaswami Fellow)
Center of Bio-Medical Research (CBMR)
SGPGI Campus, Raibareli Road
Lucknow-226014, UP, INDIA

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Re: [Freesurfer] dcmunpack

[Douglas N. Greve]

Sam way as with unpacksdcmdir, ie, by specifying  -run run subdir format 
stemname

Another way it to use the -auto-runseq format , eg -auto-runseq mgz
this will output all the runs preprending the run number and protocol name
If you are using 7.3.X, then you can also add --dcm2niix which will 
speed things up a lot



On 9/23/2022 8:26 AM, O'Dor, Sarah,PHD wrote:


Good afternoon,

Quick question about unpacking:

The instructions I have from a previous staff member said to do this:

In folder where files are going, type: unpacksdcmdir -src scans> -targ . -scanonly scanout.txt


So what I submit is:

unpacksdcmdir -src 
/cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 
-targ . -scanonly scanout.txt


When I do that, it just makes the files:

dicomdir.sumfile scanout.txt  unpack.log

I’m trying to use the dcmunpack command instead. From following the 
template on the website, I’ve been trying the following commands:


[pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src 
/cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 
-index-out dcm.index.dat


{lots of other content here, so let’s skip to….}

dcmunpack done

[pandas:Pandas57UC] (nmr-stable6-env) dcmunpack -src 
/cluster/archive/338/siemens/Prisma_fit-67026-20220208-132737-000260 
-index-in dcm.index.dat -targ .


ERROR: need input runs

How should I specify input runs?

Thanks,

Sarah


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Re: [Freesurfer] Running v7 with recon-all v6 files

[Douglas N. Greve]

yes, it is ok

On 9/22/2022 8:36 AM, Alexandra Brouillard wrote:


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Hi

I ran recon-all on an external server using the version 6. I recently 
downloaded the v6 on my Mac v12.6. I was able to set a home directory 
but get a ‘*permission denied*’ error when typing ‘$FREESURFER_HOME’ 
(but have the permissions/sudo). I also can’t open Freeview: by double 
clicking on the app, the GUI crashes, or by typing ‘freeview’ in the 
terminal I get a PETSC error.


According to some previous forum threads, I’m thinking of downloading 
the v7 but would like to validate that it’s OK when using recon-all v6 
files.


Thank you for your support,

Alexandra


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Re: [Freesurfer] SAMSEG - modification of the template files

[Douglas N. Greve]

On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote:


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Would providing better manual segmentations of those structures of 
interest help you in building better solutions?
I can work with the segmentation that is produced now, but I am 
interested in improving the results for extracerebral tissues using 
multimodal imaging and better manual segmentations.
The samseg authors used 20 subjects and did not find that increasing 
that helped all that much (at least on dice scores)
Can you shed some light on the steps required for creating the current 
atlas?
Unfortunately not. The atlas creation software was the lowest priority 
of the samseg authors, so it is not easy to run. I myself find it 
extremely challenging to create new atlases, so I can't support helping 
others do that. We're trying to get it more streamlined (for you and for 
us:)



thanks,

Mikolaj

On Wed, Sep 21, 2022 at 4:01 PM Douglas N. Greve 
 wrote:


by template I'm assuming you mean the atlas. There is not an easy
way to create a new atlas or modify the existing one (though we
are developing methods to do both). For the eyes, you could
probably just write something to look at the column index in the
eyes. If it is less than 128, then set it to left otherwise right.

On 9/21/2022 6:01 AM, Mikolaj Pawlak wrote:


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Dear Freesurfers,
I have been using samseg for a while and like it a lot. Thank you
for this tool. How do you modify the template for this tool? Is
there a guideline for this?
I would like to divide Fluid_Inside_Eyes label to left and right
and improve the bone information in the template. What is the
procedure?
thanks,
Mikolaj Pawlak

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[Freesurfer] (no subject)

[fsbuild]

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Sorry if this is a repeat email from last night, but signal 9 can mean you ran 
out of memory.  You should try allocating more memory to the VM..
You could also try running the latest freesufer version = 7.3.2 which is 
compiled for Ubuntu 20 and you can get 
from, https://secure-web.cisco.com/1qqb_N_CupmU2BzFF50PfaJo-Ylza_cis45qmQBTenmkrXglOcw75L9OBJZfdg7SWOK4yX327ERVQq3TcnjfDY-zE8olnmEbtkd788oiLKZneQIW6H2TVGrsF8mEFcJYwK4drVTafYRiHTOlHn_1IKMmG3l4x_h_ML8WHcJHPmIOmJkxfAHbTNsv4ssfExbecvmXcbbsKrDdvX4Ge5xwhFZkps2dqStX8R4ZCTLlu1Gft1E3046HexFK4JOVgvS82mwBvr2tuPQzn1DoWDYu3CKDcxS5nhK6rU8tlooCNscJ9KGyLrHLAjD9fCEp-TNKZ0ACgA1jJbxVHTWPmRLxiVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer_ubuntu20-7.3.2_amd64.deb
  I would uninstall 7.1.1 if you are going to try 7.3.2, but a different 
version won’t make a difference if you are running short on available RAM.
- R.

On Sep 23, 2022, at 09:50, Douglas N. Greve  
wrote:not sure what is going on. It received a kill signal (the 9 mentioned at 
the end). This often means that it was killed externally. Does this happen 
repeatedly? Does this happen on other subjects? How much memory did you 
allocate to your virtual box?On 9/23/2022 1:04 AM, Ahmad Khan 
wrote:External Email - Use 
Caution Dear Free Surfer 
Development Team.I am using the recon -all command to compute the volume of 
different regions of the brain. I am running the free surfer version 
freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 installed on a 
virtual box. I am getting the following errors and the log file is also 
attached with this email. ERROR: mri_ca_register with non-zero status 
137Your timely response would be highly appreciated.Best Regards Dr. Ahmad 
Raza Khan(Ramalingaswami Fellow)Center of Bio-Medical Research (CBMR)SGPGI 
Campus, Raibareli RoadLucknow-226014, UP, 
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[Freesurfer] Help with group analysis

[fernanda rohrsetzer]

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Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the error
always appears (print below). There are 3 groups ( risk_group) that I would
like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
and I would like to control for sex, age and total brain measure. Please,
if anyone can help me understand what I'm doing wrong, I'd really
appreciate it.
The FSG file is attached
Thank you.


w0_group.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals
and experts in the field about the issue below.

Thank you for your kindness.

Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then
normalize white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection we realize that the
algorithm has been developed to correct bias field correction in T1 not
clear if it works on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be
applied on T1 images? I would like to send a "recon-all.log" file that
includes the processing steps of FLAIR. Is there any link I can use to
upload the file. It gets rejected every time I send it due to size
limitations.

We appreciate any feedback about the proper way to correct FLAIR images for
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB

On Wed, Sep 21, 2022 at 10:18 AM James Brown  wrote:

> Dear Freesurfer experts,
> In order to normalize white matter intensity of T1 images and correct for
> bias field. We do the following steps:
> mri_convert T1.nii.gz T1.mgz
> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
> mri_convert T1_norm.mgz T1_norm.nii.gz
>
> We would like to apply bias field correction on FLAIR images then
> normalize white matter intensity.
> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
> Reviewing documents about N4biasfieldcorrection we realize that the
> algorithm has been developed to correct bias field correction in T1 not
> clear if it works on FLAIR images.
>
> Are the steps above valid for normalizing FLAIR images or can it only be
> applied on T1 images? I would like to send a "recon-all.log" file that
> includes the processing steps of FLAIR. Is there any link I can use to
> upload the file. It gets rejected every time I send it due to size
> limitations.
>
> We appreciate any feedback about the proper way to correct FLAIR images
> for bias fields and normalize white matter intensity in FLAIR images.
>
> Thank you
> JamesB
>
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Re: [Freesurfer] White matter normalization of FLAIR images

[Fischl, Bruce R.,PHD]

Hi JamesB

there is T2/FLAIR normalization in recon-all if you process it through there. 
You can look for "nonmax_suppress" if you want to find the command line

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of James Brown 

Sent: Friday, September 23, 2022 2:06 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] White matter normalization of FLAIR images


External Email - Use Caution

Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals and 
experts in the field about the issue below.

Thank you for your kindness.

Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for bias 
field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then normalize 
white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected. 
Reviewing documents about N4biasfieldcorrection we realize that the algorithm 
has been developed to correct bias field correction in T1 not clear if it works 
on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be 
applied on T1 images? I would like to send a "recon-all.log" file that includes 
the processing steps of FLAIR. Is there any link I can use to upload the file. 
It gets rejected every time I send it due to size limitations.

We appreciate any feedback about the proper way to correct FLAIR images for 
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB

On Wed, Sep 21, 2022 at 10:18 AM James Brown 
mailto:jb1979...@gmail.com>> wrote:
Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for bias 
field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then normalize 
white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected. 
Reviewing documents about N4biasfieldcorrection we realize that the algorithm 
has been developed to correct bias field correction in T1 not clear if it works 
on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be 
applied on T1 images? I would like to send a "recon-all.log" file that includes 
the processing steps of FLAIR. Is there any link I can use to upload the file. 
It gets rejected every time I send it due to size limitations.

We appreciate any feedback about the proper way to correct FLAIR images for 
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB
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Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

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Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the following
command line is reported in the "recon-all.log":

/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
FLAIR.nii.gz -s test

When I search for normalization of flair, I only find how Freesurfer
normalized T1.
I searched for "nonmax_suppress" and it is not in the log file. I am just
wondering what I am doing wrong. Thanks again for any highlights about the
correct method to normalize FLAIR

Sincerely,



Hi JamesB

there is T2/FLAIR normalization in recon-all if you process it through
there. You can look for "nonmax_suppress" if you want to find the command
line

cheers
Bruce

On Fri, Sep 23, 2022 at 2:06 PM James Brown  wrote:

> Dear Freesurfer experts,
> We appreciate any advice or guidance from your community of professionals
> and experts in the field about the issue below.
>
> Thank you for your kindness.
>
> Dear Freesurfer experts,
> In order to normalize white matter intensity of T1 images and correct for
> bias field. We do the following steps:
> mri_convert T1.nii.gz T1.mgz
> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
> mri_convert T1_norm.mgz T1_norm.nii.gz
>
> We would like to apply bias field correction on FLAIR images then
> normalize white matter intensity.
> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
> Reviewing documents about N4biasfieldcorrection we realize that the
> algorithm has been developed to correct bias field correction in T1 not
> clear if it works on FLAIR images.
>
> Are the steps above valid for normalizing FLAIR images or can it only be
> applied on T1 images? I would like to send a "recon-all.log" file that
> includes the processing steps of FLAIR. Is there any link I can use to
> upload the file. It gets rejected every time I send it due to size
> limitations.
>
> We appreciate any feedback about the proper way to correct FLAIR images
> for bias fields and normalize white matter intensity in FLAIR images.
>
> Thank you
> JamesB
>
> On Wed, Sep 21, 2022 at 10:18 AM James Brown  wrote:
>
>> Dear Freesurfer experts,
>> In order to normalize white matter intensity of T1 images and correct for
>> bias field. We do the following steps:
>> mri_convert T1.nii.gz T1.mgz
>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>
>> We would like to apply bias field correction on FLAIR images then
>> normalize white matter intensity.
>> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>> Reviewing documents about N4biasfieldcorrection we realize that the
>> algorithm has been developed to correct bias field correction in T1 not
>> clear if it works on FLAIR images.
>>
>> Are the steps above valid for normalizing FLAIR images or can it only be
>> applied on T1 images? I would like to send a "recon-all.log" file that
>> includes the processing steps of FLAIR. Is there any link I can use to
>> upload the file. It gets rejected every time I send it due to size
>> limitations.
>>
>> We appreciate any feedback about the proper way to correct FLAIR images
>> for bias fields and normalize white matter intensity in FLAIR images.
>>
>> Thank you
>> JamesB
>>
>
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Re: [Freesurfer] White matter normalization of FLAIR images

[Fischl, Bruce R.,PHD]

I think you need to add something like -FLAIRpial or -T2pial so it uses it (in 
which case it will first normalize it), but hopefully someone else can confirm

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of James Brown 

Sent: Friday, September 23, 2022 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] White matter normalization of FLAIR images


External Email - Use Caution

Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the following 
command line is reported in the "recon-all.log":

/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair 
FLAIR.nii.gz -s test

When I search for normalization of flair, I only find how Freesurfer normalized 
T1.
I searched for "nonmax_suppress" and it is not in the log file. I am just 
wondering what I am doing wrong. Thanks again for any highlights about the 
correct method to normalize FLAIR

Sincerely,



Hi JamesB

there is T2/FLAIR normalization in recon-all if you process it through there. 
You can look for "nonmax_suppress" if you want to find the command line

cheers
Bruce

On Fri, Sep 23, 2022 at 2:06 PM James Brown 
mailto:jb1979...@gmail.com>> wrote:
Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals and 
experts in the field about the issue below.

Thank you for your kindness.

Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for bias 
field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then normalize 
white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected. 
Reviewing documents about N4biasfieldcorrection we realize that the algorithm 
has been developed to correct bias field correction in T1 not clear if it works 
on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be 
applied on T1 images? I would like to send a "recon-all.log" file that includes 
the processing steps of FLAIR. Is there any link I can use to upload the file. 
It gets rejected every time I send it due to size limitations.

We appreciate any feedback about the proper way to correct FLAIR images for 
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB

On Wed, Sep 21, 2022 at 10:18 AM James Brown 
mailto:jb1979...@gmail.com>> wrote:
Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for bias 
field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then normalize 
white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected. 
Reviewing documents about N4biasfieldcorrection we realize that the algorithm 
has been developed to correct bias field correction in T1 not clear if it works 
on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be 
applied on T1 images? I would like to send a "recon-all.log" file that includes 
the processing steps of FLAIR. Is there any link I can use to upload the file. 
It gets rejected every time I send it due to size limitations.

We appreciate any feedback about the proper way to correct FLAIR images for 
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB
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contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] Sclimbic segmentation error

[bar gen]

External Email - Use Caution

Hi all,

I am receiving this error when trying to run sclimbic module.


 mri_sclimbic_seg --i /Users/mdbargen/Documents/control-T1  --o
/Users/mdbargen/Documents/control-limbic  --conform


Segmenting image 1/68

Loaded input image from
/Users/barisgenc/Documents/Kontrol-T1/Acar_Ebru-T1.nii.gz

Traceback (most recent call last):

  File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 1048, in 

main()

  File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 312, in main

segmenter.process_files(**params)

  File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 577, in process_files

post, seg, vox_counts, volumes, mean_probs = self.segment(image)

  File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 497, in segment

conformed = self.preprocess(image)

  File "/Applications/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg",
line 469, in preprocess

print('The input image has resolution (%4.2f,%4.2f,%4.2f) mm, but
1mm-isotropic input is required.\n'

TypeError: only size-1 arrays can be converted to Python scalars


How can i solve this?
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contains patient information, please contact the Mass General Brigham 
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