External Email - Use Caution        


Dear Douglas, 

I think my previous reply got lost… 

Could you possibly elaborate more on how this method will only reflect the registration in that area instead of volume? I got this method from freesurfer tutorial on obtaining custom anatomical ROI analysis.And do you have any suggestion on an alternative method to accurately obtain sub thalamic nucleus volume?


Note: these were our original messages 

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


Best wishes,
Tanrada




On 15 Apr 2021, at 15:10, freesurfer-request@nmr.mgh.harvard.edu wrote:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. Re: Skull stripping with T2 (Douglas N. Greve)
  2. Re: Regarding xhemi comparison of hemispheres of the same
     subject (Douglas N. Greve)
  3. Re: Decompressed problem during reconall (Douglas N. Greve)
  4. Re: Freesurfer Digest, Vol 206, Issue 6 (Douglas N. Greve)
  5. Re: Surface registration problem (Douglas N. Greve)
  6. Re: aparc+aseg to native space issue (Douglas N. Greve)
  7. Re: mkcontrast2 typo in 7.1.1 (Douglas N. Greve)
  8. Re: mri_segstats to report empty and non-empty segmentation
     (Douglas N. Greve)
  9. Re: Subthalamic nucleus volume (Douglas N. Greve)
     (Douglas N. Greve)


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

Message: 1
Date: Thu, 15 Apr 2021 09:49:23 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Skull stripping with T2
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <cedcfba5-f488-2cb9-87eb-f8e778e5384d@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

It looks like you are running a T2 through recon-all, which won't work.
recon-all only takes T1-weighted. You can run it through samseg, eg,
samseg --i T2_age_reg_bias.nii.gz --o samseg
You can then binarize the seg.mgz to get everything inside the skull

On 4/7/2021 2:17 PM, Rohan Bareja wrote:

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

Hello,

I am doing skull stripping with free surfer v6.0, and have tried
various watershed cut-offs to do skull stripping on T2 scans. But, it
removes a lot of brain portion.

Here are my commands:

mri_convert
/Applications/freesurfer/subjects/patient_20_t2/mri/T2_age_reg_bias.nii.gz
/Applications/freesurfer/subjects/patient_20_t2/mri/001.mgz

recon-all -s patient_20_t2 -autorecon1

## to be used only when increasing or decreasing threshold of skull
stripping.
recon-all -skullstrip -wsthresh 25 -clean-bm -s patient_12_t2

Is there any way that I can improve?upon this and get better results
if I am missing something?

Thanks,
Rohan

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

Message: 2
Date: Thu, 15 Apr 2021 09:52:11 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Regarding xhemi comparison of hemispheres of
the same subject
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9da0b8dc-1a16-ba96-42f4-74425e2a62a8@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Yes, I think you should be able to do that. It would be something like
mris_apply_reg --sval rh.thickness --tval rh-on-lh.thickness.mgz --streg
xhemi/surf/lh.fsaverage_sym surf/lh.fsaverage_sym


On 4/7/2021 4:55 PM, Ghassemieh, A. (Anna) wrote:

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

Dear all,


I'm currently working on comparing left with right hemisphere
activation for individual subjects and using version 7.1.1.

Since it is on an individual level, we would like to register the left
hemisphere of each subject to their mirrored right hemisphere (or vice
versa).


When looking at the way this is described in the wiki (*MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
<https://secure-web.cisco.com/1b80Mej4E9rovgmSCJq2Tz2wDNVe2geAoqeHRggKKORugGs8glJnoq6QJA3t5WFGFIlwv6QL1UANERB57fTBtyYD_BdRICx6iGWbeFI91zQ4Z6c3HcepV2JmTQMy4No1lYaeXpFs84XoBjk-zLWXsB0t_yxIjkx8irMyHNjtXeiC7uTbvLcRb8P9aIOXI5G1DsMEhTCDXpYzwC2_RW8fmNjqWdX4RBfPfAMNWZJLXQCeJ422IpL_9yOEk9soPIrwLTUxEvMTNNkFwIzyFcRbs3w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FXhemi>),
we started to wonder the following:

It is suggested to register to the symmetrical template for each
subject. However, it is unclear to us why this is necessary since
there is already a matched registration via the spherical reg file for
each subject. Does anyone know if it is possible to use this for the
purpose somehow instead?

Kind regards!


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

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

Message: 3
Date: Thu, 15 Apr 2021 09:53:45 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Decompressed problem during reconall
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <af2c561b-8677-a404-49a0-399ac5741163@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Can you send the log file of the run using the nifti as input? The file
you attached is for? dicom input.

On 4/8/2021 8:39 AM, Banu Femir wrote:

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

Dear FreeSurfer Developers,

I've a problem that cannot solve for the last week. I am using virtual
box, FS7 on my windows. I run reconall for Bert and checked that it is
working.I have an MRI scan of sepstic patients that I got via CD,
these are DICOM files but does not end with .dcm.

When I try to run reconall, for dcm images I got the following error
(the longer version is in the attachment)

........
Loading pixel data
JPEG compressed, decompressing
cd /home/developer/Documents/7.1.0-1/subjects/sepsis2
fsdcmdecompress --i
/home/developer/Documents/7.1.0-1/subjects/D_000001/F_000001 --o
/tmp/developer.tmp.decompressed.dcm.0oOV4x --jpeg >&
/tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out
ERROR: 512, see
/tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out for more details
Command exited with non-zero status 1
@#@FSTIME ?2021:04:08:08:29:16 mri_convert N 2 e 1.97 S 1.19 U 0.60 P
91% M 9200 F 2 R 999 W 0 c 174 w 356 I 32240 O 0 L 0.55 0.33 0.41
@#@FSLOADPOST 2021:04:08:08:29:18 mri_convert N 2 0.55 0.33 0.41
Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu
May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sepsis2 exited with ERRORS at Thu Apr ?8 08:29:18 EDT 202


I converted files to nii, this time I decided to run reconall on nii
images, it took more time but again failed on talairach transform.

I tried to run on different shells but ended up with the same problem.
Is it related with my MRI data or computer, how can I understand that?

Many thanks!
Banu

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

Message: 4
Date: Thu, 15 Apr 2021 09:57:15 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 206, Issue 6
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <a56fd629-7aef-0f74-1622-629b3acf070d@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

What do you get if you run:
cd
/home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri
UpdateNeeded ../surf/autodet.gw.stats.lh.dat brain.finalsurfs.mgz wm.mgz
../surf/lh.orig.premesh



On 4/8/2021 5:59 PM, zalewk wrote:

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


Hi Doug,

Sorry for the late reply, and thanks for all your help. Attached is
the text file of the output. This was testing autorecon-pial, but the
bug is the same no matter if it's autorecon2-wm, autorecon3, or any
place it hits the "if ( $ud" statement.

Best,
Kody

   Run it with -debug as the first option, capture the output, and
   send it
   to us.
   On 4/1/2021 8:29 PM, zalewk wrote:

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

Hi Freesurfer team,

My lab recently switched over from FS6 to FS7 and I think I've
encountered a bug with recon-all.
I'm running subjects stepwise and editing them, running
   recon-all with
the -autorecon2 and -autorecon3 flags initially are no problem,
   they
run fine.? Trying to re-run them or use the -autorecon2-wm,
-autorecon-pial etc. flags lead to crashing at certain parts of the
program. The error message I get is "if: expression syntax".
   Digging
into the code, it seems to crash when it hits a line of code
   "if($ud
|| $ForceUpdate)". The syntax superficially looks right (I don't
   know
tcsh), checking the variables it seems like $ForceUpdate is
   never set,
but removing it from recon-all doesn't fix the problem.
It seems the $ud variable is for checking if updates are needed
   for a
set of volumes passed to the program. I don't know why that
   would be a
problematic argument, removing that part seems to fix it, but this
also seems like an important variable and I don't know enough about
tcsh to understand why it works after removing it. Can one of the
folks who wrote the recon-all script help me out? I'm running the
commands step-wise as a work-around, but that is much less
   convenient.

Best,


------------------------------------------------------------------------
*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
freesurfer-request@nmr.mgh.harvard.edu
<freesurfer-request@nmr.mgh.harvard.edu>
*Sent:* Tuesday, April 6, 2021 6:41 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Freesurfer Digest, Vol 206, Issue 6
Send Freesurfer mailing list submissions to
??????? freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
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You can reach the person managing the list at
??????? freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

?? 1. Freesurfer Website Ports (Swearingen, Hannah)
?? 2. mris_average_surface fails (?????????)
?? 3. Re: 2mm thick image for hippocampal segmentation. (Ramesh Babu)
?? 4. Re: fMRIPrep BOLD Output (Douglas N. Greve)
?? 5. Re: mri_glmfit error (Douglas N. Greve)
?? 6. Re: Regarding recon all (Douglas N. Greve)
?? 7. Re: retaining label ids (Douglas N. Greve)
?? 8. Re: recon-all bug (Douglas N. Greve)
?? 9. Re: mris_label2annot - make all command exiting with errors
????? (Douglas N. Greve)
? 10. Re: recon-all bug (Douglas N. Greve)
? 11. Re: Dicom Tag Problem Reconall (Douglas N. Greve)
? 12. unsubscribe (Coleman, Katherine)
? 13. Re: mri_gtmpvc error Checking tissue type ERROR:
????? CheckSegTissueType() tissue type for seg (Douglas N. Greve)
? 14. Re: Problem with freesurfer measures (Douglas N. Greve)
? 15. Re: Freesurfer Website Ports (Douglas N. Greve)
? 16. Re: mris_average_surface fails (Douglas N. Greve)
? 17. Re: 2mm thick image for hippocampal segmentation.
????? (Douglas N. Greve)
? 18. Freesurfer Versions - Zeros in the Cortex (Daniel Gutstein)
? 19. Re: mri_gtmpvc error Checking tissue type ERROR:
????? CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya)


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

Message: 1
Date: Mon, 5 Apr 2021 15:20:31 -0400
From: "Swearingen, Hannah" <hannah_swearingen1@brown.edu>
Subject: [Freesurfer] Freesurfer Website Ports
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAG+grQp1wJ8ywX0StrT4VJO38JYtwfxivTNvdH3KwQrhtwiRGw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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

Hi,

I am setting up an Access Control List for an isolated VLAN in which my
center's neuroimaging computing workstations will be connected to our
hospital's network for data back-up.

We want to be able to connect to Freesurfer's website while connected to
the VLAN, and we need to supply which ports the website accesses. I used
nmap to scan and see which ports are open, and I found this:

PORT??? STATE? 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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------------------------------

Message: 2
Date: Tue, 6 Apr 2021 19:39:40 +0900
From: ????????? <m-bakhit@fmu.ac.jp>
Subject: [Freesurfer] mris_average_surface fails
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D78D558F-CE86-441D-B824-2D90D22E1749@fmu.ac.jp>
Content-Type: text/plain; charset="us-ascii"

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

Hi,
I am trying to make an average subject but when the process reaches
mris_average_surface it fails as seen below.
My command was as follow:
make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03
spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
Can you please guide me to solve this issue.

Thanks

Mudathir

###########################################
#@# Making average lh.white surface ---------------------
Tue Apr? 6 19:23:39 JST 2021
/Applications/freesurfer/subjects/avgsubject
mris_make_average_surface -i 7 -o white -sdir-out
/Applications/freesurfer/subjects lh white sphere.reg avgsubject
spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
reading vertex positions from white...
---------------------------------------------------
hemi??????????? = lh
avg_surf_name?? = white
canon_surf_name = sphere.reg
out_sname?????? = avgsubject
xform?????????? = talairach.xfm
---------------------------------------------------


Is a directory
Is a directory
ERROR: creating directory /
ERROR: creating directory
/Applications/freesurfer/subjects/avgsubject/surf
mris_average_surface failed
ERROR: make_average_surface
#################################################








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

Message: 3
Date: Tue, 6 Apr 2021 17:40:29 +0530
From: Ramesh Babu <mgrameshbabu2013@gmail.com>
Subject: Re: [Freesurfer] 2mm thick image for hippocampal
??????? segmentation.
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAHRhR0BLJv7Du65i1x0DKkUe1Nm_jxcJauUpkBXQ-JrSQ4ybqg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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

Dear Eugenio and Philipp,

Thank you very much for your suggestions. Could you please give more input
on "acquire the T1WI double and average it after coregistration, this
increases the SNR".

Should aquire twise the same sequence with 1x1x2 voxel dimension?

Thanks
Ramesh


On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., <
JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

That all sounds right, thanks a lot Philipp!





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)


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*From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Saemann,
Philipp" <saemann@psych.mpg.de>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, April 2, 2021 at 03:51
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, Umesh
Rurdrapatna <umeshrs@gmail.com>
*Subject: *Re: [Freesurfer] 2mm thick image for hippocampal
segmentation.



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

Hi,



I try to answer but Eugenio may also add comments. Several points
that are
important:

- 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can
manage.

- Post-aquisition reslicing to a higher resolution does not really
increase the information content. Internally the algorithm works at
a much
higher resolution, anyway.

- If possible, switch to 3 Tesla.

- If possible and this is a prospective study, add a coronal T2
image and
use the bi-channel option. See papers of Iglesias et al. on this.

- What you could also do on a 1.5 T is acquire the T1WI double and
average
it after coregistration, this increases the SNR.

- Generally, isometric resolutions are good due to the symmetry, of
course.

- Also on 1.5 T, you may go bit below 1 mm with good head
immobilization,
and a longer scanning time. BRAVO in general is a good T1 option.



Best,

Philipp


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

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu <
freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu <
mgrameshbabu2013@gmail.com>
*Gesendet:* Freitag, 2. April 2021 09:29
*An:* Freesurfer support list; Umesh Rurdrapatna
*Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal
segmentation.



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

Dear experts,

Sorry for reposting. I am expecting some response from experts, so
that I
can proceed with confidence.

For our project work, we are looking for hippocampal and its
subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO
sequence with
1x1x1 resolution, 256x256x160 dimension with 8* flip angle which
produced
images with a lot of noise. Then we tried the same sequence with 1x1x2
resolution, and 256x256x80 FOV, which produced a clean image without
noise.
When we reformatted the images, it produces 0.5x0.5x1 resolution with
512x512x172 dimension.



Is this sequence good for hippocampal volume estimation and subfield
segmentation (also for whole-brain VBM analysis)?

Could you please suggest to me a correct sequence, if need to be
changed?



Regards

Ramesh
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Freesurfer mailing list
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------------------------------

Message: 4
Date: Tue, 6 Apr 2021 09:11:52 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] fMRIPrep BOLD Output
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0b7e2dda-5e83-a588-7aef-1d029775f75c@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Did you check that the bold is really in register with the anat? You can
do this with
tkregisterfv --mov bold_preproc.nii.gz? --s sub-01--reg deleteme.lta
--surfs


On 3/31/2021 10:49 AM, Karan Desai wrote:

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

Hi FS Forum,

I am following up on this post because after using 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--srcbold_preproc.nii.gz?--outlh.imagename.nii.gz--regheadersub-01--trgsubject
fsaverage4 -hemilh

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.
------------------------------------------------------------------------
*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 18, 2021 9:43 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] fMRIPrep BOLD Output
sounds like you need mri_vol2surf (use --projfrac 0.5)

On 3/18/2021 11:38 AM, Karan Desai wrote:

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

Hi Freesurfer List,

I am running fMRIPrep and getting the first two FS output files (aseg
and aparcaseg seen above in the screenshot), but not the actual file
I need which is the one where it is resampled to the mesh. I have run
fMRIPrep and have those two files except the actual BOLD series
resampled to the surface mesh. Is there?a FS command that can be used
to do that one step?

Best,
Karan

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

Message: 5
Date: Tue, 6 Apr 2021 09:14:36 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0f19df0b-fbd4-19ea-3903-28775075232b@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

The format is not correct. It should be
Input SubjectID Class
You have SubjectID in there twice

On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote:

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

Hello FS experts,

I attempted to execute? mri_glmfit on my structural?data through the
following command -

mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd
dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir
lh.volume.glmdir

But it gives me an error (attached below) indicating?a formatting
problem in my FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to
debug it.

Could someone please help me resolve it?
Thanks for your time.

/Regards,/
/Ishi Tandon/
/B.Tech + M.Tech - Cognitive Neuroscience/
/Amity University, Rajasthan/



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

Message: 6
Date: Tue, 6 Apr 2021 09:15:04 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Regarding recon all
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0b627188-d0c3-e1ce-1955-d078f696ba1f@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Include the flag -cw256 with recon-all!

On 4/1/2021 1:52 AM, Amar Shukla wrote:

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

Dear Team,

Actually I am trying to test my own data in recon all , but i have
taken only one subject for recon. It shows me this error.

ERROR! FOV=408.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************

Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar
20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

--
With Regards,
Amar Shukla
Assistant Professor,
M tech AI ANN(2014-2016),
Centre Of Information Technology,
UPES
Contact :+91 897 977 8016

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

Message: 7
Date: Tue, 6 Apr 2021 09:15:56 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] retaining label ids
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1acc0845-8087-77ec-c427-ffe427378093@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I don't understand, please elaborate

On 4/1/2021 2:00 PM, miracle ozzoude wrote:

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

Hello Experts,

I did like to extract wm whilst retaining the label ids. I tried
mri_extract_labels but it didn't work.

Any help?would be appreciated.

Many?thanks,
Paul

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

Message: 8
Date: Tue, 6 Apr 2021 09:17:12 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all bug
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <ccd97428-0587-d4cc-88fa-e54f632ea16d@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Run it with -debug as the first option, capture the output, and send it
to us.

On 4/1/2021 8:29 PM, zalewk wrote:

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

Hi Freesurfer team,

My lab recently switched over from FS6 to FS7 and I think I've
encountered a bug with recon-all.
I'm running subjects stepwise and editing them, running recon-all with
the -autorecon2 and -autorecon3 flags initially are no problem, they
run fine.? Trying to re-run them or use the -autorecon2-wm,
-autorecon-pial etc. flags lead to crashing at certain parts of the
program. The error message I get is "if: expression syntax". Digging
into the code, it seems to crash when it hits a line of code "if($ud
|| $ForceUpdate)". The syntax superficially looks right (I don't know
tcsh), checking the variables it seems like $ForceUpdate is never set,
but removing it from recon-all doesn't fix the problem.
It seems the $ud variable is for checking if updates are needed for a
set of volumes passed to the program. I don't know why that would be a
problematic argument, removing that part seems to fix it, but this
also seems like an important variable and I don't know enough about
tcsh to understand why it works after removing it. Can one of the
folks who wrote the recon-all script help me out? I'm running the
commands step-wise as a work-around, but that is much less convenient.

Best,
Kody Zalewski

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

Message: 9
Date: Tue, 6 Apr 2021 09:18:35 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_label2annot - make all command exiting
??????? with errors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0a8872e7-1d93-c58a-4973-d8e161500d05@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

The "-make" functionality does not work in V7. We should have disabled
that flag

On 4/2/2021 3:41 AM, Marion DURTESTE wrote:

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

Dear?FreeSurfer developers,

When running*recon-all -make all *after correcting a few errors from
the recon-all output, it exits with an error.?This occurs when the
mris_label2annot command is called.

Loading

/Users/mariondurteste/Documents/PhD/FreeSurfer/ReconstructedAfterQC/ToDo/ALA076_1/surf/lh.orig
1 1376057 FG1
2 16711935 FG2
ERROR: lh.FG2.mpm.vpnl.label, n=580, vertex 119494 out of range

If we rerun the -make all command a second time it then finishes
without errors.?Do you know why this is ?

?? * FREESURFER version:?freesurfer-darwin-macOS-7.1.1-20200811-8b40551
?? * Platform: macOS BigSur 11.2.2

Thanks for your help !
Marion D


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

Message: 10
Date: Tue, 6 Apr 2021 09:19:41 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all bug
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <8ac90e23-495c-4067-424d-f7632644fae1@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

So the problem is that there are spaces in the path? That will probably
cause a lot of FS to fail

On 4/2/2021 11:30 PM, zalewk wrote:

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

Hi freesurfer team,

I've tried running recon-all as mentioned before with the -xf flag
under different conditions.
As far as I can tell, any line using the UpdateNeeded function. e.g.:
"set ud = `UpdateNeeded $thickness $pial $white`" fails with the
following if statement because the variable $ud includes paths as
strings in it instead of a 0/1 integer. Setting it to a 1 or 0
beforehand also seems to solve the problem. The function UpdateNeeded
only seems to return an integer as an exit status, so I'm not sure why
there are path strings in it causing it to fail.
If I print out the $ud variable before it fails and the result is:
"/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER
/subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1"
It returns the exit status of 1 preceded by the path of the subject's
mri directory, just "mri", "mri_FREESURFER" and the subject's stats
directory (all subjects in this particular study have the suffix
"_FREESURFER"). It prints this out these strings no matter the
variables as .mgz file names, or number of variables passed to the
UpdateNeeded function. I still don't have a clue what would cause this
behavior. The UpdateNeeded function seems to work fine and as intended
as far as I can tell, so I still don't know why these paths/strings
are being added and causing it to crash.

Best,
Kody Zalewski

???? Message: 3
???? Date: Fri, 02 Apr 2021 03:49:02 +0200
???? From: fsbuild <fsbuild@contbay.com>
???? Subject: Re: [Freesurfer] recon-all bug
???? To: freesurfer@nmr.mgh.harvard.edu
???? Cc: cmacd@neurosurgery.washington.edu
???? Message-ID: <1617328142.6066780ef2824@trashmail.com>
???? Content-Type: text/plain; charset="utf-8"

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

???? Hello Kody,
???? One thing you could try to get more information printed about what
???? is going on is to edit the very first line in the recon-all script
???? to be:
???? #! /bin/tcsh -xf
???? ? instead of
???? #! /bin/tcsh -f
???? Adding the x option will echo each line in the script as it?s run
???? with the variable values expanded, and seeing that output could
???? help with debugging.

???? - R.

???? On Apr 1, 2021, at 20:29, zalewk &lt;zalewk@uw.edu&gt;
wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External
???? Email - Use
Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi
???? Freesurfer team,&nbsp;My lab recently switched over from FS6 to
???? FS7 and I think I've encountered a bug with recon-all..&nbsp;I'm
???? running subjects stepwise and editing them, running recon-all with
???? the -autorecon2 and -autorecon3 flags initially are no problem,
???? they run fine.&nbsp; Trying to re-run them or use the
???? -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at
???? certain parts of the program. The error message I get is "if:
???? expression syntax". Digging into the code, it seems to crash when
???? it hits a line of code "if($ud || $ForceUpdate)". The syntax
???? superficially looks right (I don't know tcsh), checking the
???? variables it seems like $ForceUpdate is never set, but removing it
???? from recon-all doesn't fix the problem.&nbsp;&nbsp;It seems the
???? $ud variable is for checking if updates are !
???? ?needed fo
???? ?r a set of volumes passed to the program. I don't know why that
???? would be a problematic argument, removing that part seems to fix
???? it, but this also seems like an important variable and I don't
???? know enough about tcsh to understand why it works after removing
???? it. Can one of the folks who wrote the recon-all script help me
???? out? I'm running the commands step-wise as a work-around, but that
???? is much less convenient.&nbsp;Best,&nbsp;Kody
Zalewski_______________________________________________Freesurfer
???? mailing

listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?


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

Message: 11
Date: Tue, 6 Apr 2021 09:22:33 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Dicom Tag Problem Reconall
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <bcd0a4ad-aa63-ba67-79a1-45f74cd4faf0@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Can you send /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ?
If that is not there any more, run it again and send the newly created
file

On 4/4/2021 3:57 PM, Banu Femir wrote:

????????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: 12
Date: Tue, 6 Apr 2021 13:22:57 +0000
From: "Coleman, Katherine" <kcoleman0@bwh.harvard.edu>
Subject: [Freesurfer] unsubscribe
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <218EBD99-160A-4937-B1A6-D7EDEF09AA39@bwh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"

Hello,

Please remove me from the free surfer forum mailing list.

Thank you,
Katherine

Katherine Coleman, MS
Research Assistant II
Mood Trajectories and Outcomes Laboratory
Department of Psychiatry

[cid:image001.jpg@01D6CE33.2A446E30]

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

Message: 13
Date: Tue, 6 Apr 2021 09:25:59 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR:
??????? CheckSegTissueType() tissue type for seg
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <014bcfc7-3d2b-0314-24f2-8d7280900b66@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

You will need to create a new color table. This is not hard, but not
easy either. First, there should be a color table already there. I'm not
sure what that will be like; it might have your segments in it, it might
not. It might be easier to run gtmseg with the standard options and look
at the color table, then try to replicate it with your segmentation

On 4/5/2021 6:43 AM, Bahar Hazal Yal??nkaya wrote:

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

Hello Freesurfer"s Developers,

I am trying to follow */PetSurfer/* (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be*
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<https://secure-web.cisco.com/1w-20YuJbRV4WuZCKwBm5cwzjrDf_VgyVOkZEOk6P7qaWL3Gg_xLuQRHvaCrhEes_g3GDPaJSaA-i1SzRrAPfk-PDKmM3cB5xfIdEt1W4fBJfr3wkvPF-PGr0hC89sNBBWNtIgZ5yvk-ok3N0j9HkSxM_TJ11uWtvE4sxxJ70doT0te8mkgOjCqqYnRfrUuSI8ZoZI2zmRG0KsqDih6ry2iO-TTxWTgstDUZKbyZ6Nwl2A7af15wzHIfYlb1-uvGRz0vjPr7KKH6nyirFUrL1wQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>


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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-annotSchaefer2018_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: 14
Date: Tue, 6 Apr 2021 09:28:21 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with freesurfer measures
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <bee9db6e-332d-d5d6-fe10-0e8697f03490@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

It is normal that those give different results. I would expect them to
be extremely close to each other, so small that the difference does not
matter. But if you had to take one, I'd take the output of
mris_anatomical_stats

On 4/5/2021 11:47 AM, Alberto Del Cerro Leon wrote:

????????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 <mailto:dgreve@mgh.harvard.edu
<mailto: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 <mailto: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
<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
<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
<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
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
<freesurfer-bounces@nmr.mgh.harvard.edu
????????????????????
<mailto: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
<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: 15
Date: Tue, 6 Apr 2021 09:29:20 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Website Ports
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1d438758-e598-6101-209b-5b14bd1ec83a@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

why do you need to connect to the web site? that is not needed to run FS

On 4/5/2021 3:20 PM, Swearingen, Hannah wrote:

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

Hi,

I am setting up an Access Control List for an isolated VLAN in which
my center's neuroimaging computing workstations will be connected to
our hospital's network for data back-up.

We want to be able to connect to Freesurfer's?website while connected
to the VLAN, and we need to supply which ports the website accesses. I
used nmap to scan and see which ports are open, and I found this:

PORT ? STATE? 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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------------------------------

Message: 16
Date: Tue, 6 Apr 2021 09:30:17 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_average_surface fails
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <a6bc5f6a-0e93-3d9b-3070-2d16d56f648e@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

Do you have write permissions to

/Applications/freesurfer/subjects

Of not on a mac

On 4/6/2021 6:39 AM, ????????? wrote:
????????? External Email - Use Caution

Hi,
I am trying to make an average subject but when the process reaches
mris_average_surface it fails as seen below.
My command was as follow:
make_average_subject --out avgsubject --subjects spl_01 spl_02
spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
Can you please guide me to solve this issue.

Thanks

Mudathir

###########################################
#@# Making average lh.white surface ---------------------
Tue Apr? 6 19:23:39 JST 2021
/Applications/freesurfer/subjects/avgsubject
mris_make_average_surface -i 7 -o white -sdir-out
/Applications/freesurfer/subjects lh white sphere.reg avgsubject
spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
reading vertex positions from white...
---------------------------------------------------
hemi??????????? = lh
avg_surf_name?? = white
canon_surf_name = sphere.reg
out_sname?????? = avgsubject
xform?????????? = talairach.xfm
---------------------------------------------------


Is a directory
Is a directory
ERROR: creating directory /
ERROR: creating directory
/Applications/freesurfer/subjects/avgsubject/surf
mris_average_surface failed
ERROR: make_average_surface
#################################################






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

Message: 17
Date: Tue, 6 Apr 2021 09:33:30 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] 2mm thick image for hippocampal
??????? segmentation.
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <715750d4-45f9-180c-d2ae-e0a485e61ffc@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Twice the same image at 1x1x1, then use mri_robust_template to register
and average them together

On 4/6/2021 8:10 AM, Ramesh Babu wrote:

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

Dear Eugenio and Philipp,

Thank you very much for your suggestions. Could you please give more
input on "acquire the T1WI double and average it after coregistration,
this increases the SNR".

Should aquire twise the same sequence with 1x1x2 voxel dimension?

Thanks
Ramesh


On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E.,
<JIGLESIASGONZALEZ@mgh.harvard.edu
<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu
<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>>> wrote:

???? That all sounds right, thanks a lot Philipp!

???? Juan Eugenio Iglesias

???? Senior research fellow

???? CMIC (UCL), MGH (HMS) and CSAIL (MIT)

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????
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???? *From: *<freesurfer-bounces@nmr.mgh.harvard.edu
???? <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> on behalf of
???? "Saemann, Philipp" <saemann@psych.mpg.de
???? <mailto:saemann@psych.mpg.de <mailto:saemann@psych.mpg.de>>>
???? *Reply-To: *Freesurfer support list
???? <freesurfer@nmr.mgh.harvard.edu
???? <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>>
???? *Date: *Friday, April 2, 2021 at 03:51
???? *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
???? <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>>, Umesh Rurdrapatna
???? <umeshrs@gmail.com <mailto:umeshrs@gmail.com
<mailto:umeshrs@gmail.com>>>
???? *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal
???? segmentation.

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

???? Hi,

???? I try to answer but Eugenio may also add comments. Several points
???? that are important:

???? -?1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm
???? can manage.

???? - Post-aquisition reslicing to a higher resolution does not really
???? increase the information content. Internally the algorithm works
???? at a much higher resolution, anyway.

???? - If possible, switch to 3 Tesla.

???? - If possible and this is a prospective study, add a coronal T2
???? image and use the bi-channel option. See papers of Iglesias et al.
???? on this.

???? - What you could also?do on a?1.5 T is acquire the T1WI double and
???? average it after coregistration, this increases the SNR.

???? - Generally, isometric resolutions are good due to the symmetry,
???? of course.

???? - Also on 1.5 T, you may go bit below 1 mm with good head
???? immobilization, and a longer scanning time. BRAVO in general is a
???? good T1 option.

???? Best,

???? Philipp

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

???? *Von:*freesurfer-bounces@nmr.mgh.harvard.edu
???? <mailto: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
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> im Auftrag von
???? Ramesh Babu <mgrameshbabu2013@gmail.com
???? <mailto:mgrameshbabu2013@gmail.com
<mailto:mgrameshbabu2013@gmail.com>>>
???? *Gesendet:* Freitag, 2. April 2021 09:29
???? *An:* Freesurfer support list; Umesh Rurdrapatna
???? *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal
???? segmentation.

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

???? Dear experts,

???? Sorry for reposting. I am expecting some response from experts, so
???? that I can proceed with confidence.

???? For our project work, we are looking for hippocampal??and its
???? subfield?volumes. Using GE 1.5T scanner, we?tried a 3D BRAVO
???? sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip
???? angle which produced images with a lot of noise. Then we tried the
???? same sequence?with 1x1x2 resolution, and 256x256x80 FOV, which
???? produced a clean image without?noise. When we reformatted?the
???? images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension.

???? Is this sequence good for hippocampal volume estimation and
???? subfield segmentation (also for whole-brain VBM analysis)?

???? Could you please suggest to me a correct sequence, if need to be
???? changed?

???? Regards

???? Ramesh

???? _______________________________________________
???? Freesurfer mailing list
???? Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 18
Date: Tue, 6 Apr 2021 13:38:37 +0000
From: Daniel Gutstein <daniel.gutstein@northwestern.edu>
Subject: [Freesurfer] Freesurfer Versions - Zeros in the Cortex
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2F5F4F23-A758-4F12-B303-EBD66FEF346F@northwestern.edu>
Content-Type: text/plain; charset="utf-8"

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

Hello,

We are looking at the vertex-wise thickness measures for participants
within the fsaverage space. There are a number of indices within the
cortex that have thickness values of 0 in the thickness.fsaverage.mgh
surface files. In FreeSurfer version 5.1, those same indices no longer
have thickness 0 in the corresponding rh and lh fwhm smoothed
thickness surface files due to the smoothing effect. However, in
versions 6 and 7.1.1, the indices with 0 values remain 0 even in the
fwhm smoothed files. Do you know why it was chosen that smoothing
should have no impact on zeros in the later versions of FreeSurfer?
Also, if we are interested in impacting the zeros from the later
versions, is there a methodology which you would recommend?

Thanks,

Daniel
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------------------------------

Message: 19
Date: Tue, 6 Apr 2021 15:41:36 +0200
From: Bahar Hazal Yal??nkaya <baharhazalyalcinkaya@gmail.com>
Subject: Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR:
??????? CheckSegTissueType() tissue type for seg
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGZFL9eVvG1+FhoUqK24DG=ahiMfYhQ2AGA5UbzfXDHZKA056g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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

Thanks for response, color table and annotations are there "--ctx-annot
Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab
Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an
error, you can see at attachments. (Also I can see 258 Head
segmentation in *gtmseg.ctab
*file) also mri_coreg is working well (see also attachments). The problem
is the "*mri_gtmpvc*" command where it fails while checking tissue types
more precisely it complains about Head segmentation.

I run with standard options. I checked everything I can think of, each
file
and image seems to be similar but still could not find a proper solution.
Is there anything specific I need to check?

Thanks in advance,
Kind regards



On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve <dgreve@mgh.harvard.edu>
wrote:

You will need to create a new color table. This is not hard, but not
easy
either. First, there should be a color table already there. I'm not sure
what that will be like; it might have your segments in it, it might
not. It
might be easier to run gtmseg with the standard options and look at the
color table, then try to replicate it with your segmentation

On 4/5/2021 6:43 AM, Bahar Hazal Yal??nkaya wrote:

???????? External Email - Use Caution
Hello Freesurfer"s Developers,

I am trying to follow *PetSurfer* (*MailScanner has detected a possible
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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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--
Ph.D. Bahar Hazal Yal??nkaya
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Message: 5
Date: Thu, 15 Apr 2021 10:01:38 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface registration problem
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <87b2dec1-21cb-c4f0-4ff5-e1d6d49284c9@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

This means that the source or target of the registration is not the same
as what is in the registration file. Did the subject folder change? You
can always delete the registration and rerun, and it will register to
the new target

On 4/9/2021 10:58 AM, Manenti, Giorgio wrote:
        External Email - Use Caution

Dear Experts,

I?m encountering a problem when running the preproc-sess on my functional data. When using the  flag -surface subject hemi i am getting ":ERROR: source volume is neither source nor target of the registration?.
The source is a template.nii file present in the bold folders, while the destination file is the mri/orig.mgz from the ?subject? folder (after Longitudinal recon-all).

I am not sure if the problem could be connected with the mc-sess,stc-sess or topup (where i need to crop out 1 slice to get an even volume) steps, that i?m running before preproc-sess, or if i?m missing an extra flag.

Here the command i?m running:
preproc-sess -s f10_sess01new -fsd bold -i my_hifi_images -nostc -nomc -surface hum_15721.long.long010 lhrh -mni305 -fwhm 4 -per-run


Many thanks for your time and support,
Best Regards

Giorgio

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Message: 6
Date: Thu, 15 Apr 2021 10:04:21 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] aparc+aseg to native space issue
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <90cf6e25-0f0a-3354-622a-bf6c326cabb3@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

What are the voxel sizes in the native space? It may be that if it were
shifted one voxel over, it would be shifted too far in the other direction.

On 4/12/2021 10:42 AM, Larson, Kathleen E wrote:

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

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

Hi again,

I realized that it may be helpful if I include some images to show
what I mean when I say ?slightly offset?. In the image attached are 2
T1w images overlayed with the right WM thresholded from the aparc+aseg
image. On the left is the native space, and the right is in FS space.
You can see a slight shift in the segmentation on the left compared to
the native space on the right. (I?m using the thresholded WM from the
aparc+aseg because it?s easier to see the offset than with the entire
segmentation).

Please let me know if you have any suggestions for how to correct this!

Katie Larson

*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Larson, Kathleen E
*Sent:* Wednesday, April 7, 2021 4:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] aparc+aseg to native space issue

Hi,

I am having an issue converting the aparc+aseg segmentation into the
native space. I have tried using both of the following commands:

mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o
aparc+aseg_native.mgz --regheader

mri_vol2vol --mov aparc+aseg.mgz --targ rawavg.mgz --regheader
--nearest --o aparc+aseg_native.mgz

In both cases, the output segmentation in native space is slightly
offset along the x axis (given x,y,z coordinates). In fact,
mri_label2vol is offset in the opposite direction as mri_vol2vol. All
outputs have the same origin as the original native space, so I am
wondering if it?s a problem with the interpolation. Do you have any
advice for how to fix this issue?

Thank you!

Kathleen Larson (she/her)

Medical Image Computing Lab (MedICL)

Biomedical Engineering | Ph.D. Candidate

Vanderbilt University


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Message: 7
Date: Thu, 15 Apr 2021 10:06:50 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mkcontrast2 typo in 7.1.1
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <a500afd4-5383-a3f2-e1f2-c99b147fdedd@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

Thanks, I just fixed it and pushed the change. Should be in the next
version.

On 4/12/2021 3:05 PM, Ben Singer wrote:
        External Email - Use Caution

On line 106:

if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then

there should be a "$" before the "UseOctave" to make the line read:

if($FS_MKCON_USE_BIN == 0 && $UseOctave == 0) then

Apologies if this has been already corrected, I didn't come across
this in an archive search.

It looks like this bug originated in July 2018, and is the reason for
a few 2019 and  one or two 2020 posts complaining of "MATLAB: variable
undefined" errors.

Below here is just some more background info about what sort of errors
might result, and why setting the MATLAB variable to the matlab
executable works around the problem, but causes a new problem with the
mex command.

The conditional is always false before the fix-- so the MATLAB
variable is never set to whatever fsfast's "getmatlab" function
assigns to it, in the body of the conditional. So this could be the
source of several "MATLAB: Undefined variable" errors reported on this
list.

If one sets the MATLAB environment variable to the "R20xx/bin/matlab"
executable , one can work around this problem. But-- the Matlab "mex"
command uses the MATLAB variable, and expects it to be set to the
Matlab root directory in order to determine the machine architecture
for your host (type "mex" at the shell prompt when MATLAB is set to
the matlab executable, to see the error message.) Setting the MATLAB
variable the way the "mex" command expects would then result in
"/path/to/R20xx: permission denied" errors when running
mkcontrast-related scripts. Sorry for the wordiness. Bottom line is
dollar sign.

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

Message: 8
Date: Thu, 15 Apr 2021 10:09:23 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_segstats to report empty and non-empty
segmentation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <2110d774-d5c7-de45-5803-6769f09ef7f9@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Try adding --empty

On 4/12/2021 4:58 PM, miracle ozzoude wrote:

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

Hello Experts,

I am using mri_segstats with the --ctab flag to extract dti and suvr
values from a white matter hyperintensities parcellation. Running
mri_segstats on the image and parcellation with --ctab only reports on
non-empty segmentations. I want it to also report on the empty
segmentations.

Is there a flag or any other freesurfer commands that i can use?

Summary: I want mri_segstats to report on non-empty and empty
segmentations, not just the former.

Cheers.
||
|cmdline mri_segstats --seg wmh_lobar.nii.gz --i
subj_rescaled_wholecere_PET2T1_smooth.nii.gz --sum
SUVR_WMH_lobar.stats --ctab WMColorLUT.ctab --pv norm.mgz|
|Loading wmh_lobar.nii.gz|
|INFO: using NIfTI-1 qform|
|Loading subj_rescaled_wholecere_PET2T1_smooth.nii.gz|
|Loading norm.mgz|
|Voxel Volume is 1 mm^3|
|Generating list of segmentation ids|
|Found 13 segmentations|
|Computing statistics for each segmentation||Reporting on 11
segmentations|
|Using PrintSegStat|
|mri_segstats done|

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Message: 9
Date: Thu, 15 Apr 2021 10:10:26 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Subthalamic nucleus volume (Douglas N.
Greve)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <372a67f2-828f-f654-12f1-0cb0cef42f62@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Sorry, which email is this referring to?

On 4/12/2021 5:58 PM, T. Pansuwan wrote:

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

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

Dear Douglas,

Thank you for your reply.

Could you possibly elaborate more on how this method will only reflect
the registration in that area instead of volume? I got this method
from freesurfer tutorial on obtaining custom anatomical ROI analysis.
And do you have any suggestion on an alternative method to accurately
obtain sub thalamic nucleus volume?

Best wishes,
Tanrada





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

Send Freesurfer mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


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>

Content-Type: text/plain; charset="iso-8859-1"

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

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>
Content-Type: text/plain; charset="utf-8"

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

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
???????????*MailScanner has detected a possible fraud attempt from
???????????"secure-web.cisco.com" claiming to be*
???????????https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
???????????<https://secure-web.cisco.com/1-guBCff1jWC1GKEt4a1kTf7-FWdC1pS-TRdvmtUoD4S5H1J9YevmGvFyfqiToxhlWyLk9yd2FL9ynWWyw9qrc4GMYipR_nQh2TsGzvrJem91qDSlnoJGUp3ytyyvEyT2e5q0-T2Fe_vnxBPOY0VICsRivaAxfyjEStvnGMVSnIqi0A2H-XZ1L8c6qkEpahiB8VCJNBXV1NivRiX6xTWyRasWhu0yxn3-RD6-RLySEjmUaCVHSjs3m1Zl3XCSNcbhISIuIENnF2bSSgZiJSOpGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>


???????????On 3/16/2021 3:39 PM, Jordan Mullins wrote:

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

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

???????????On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve
???????????<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:

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

???????????????Hello,

???????????????I am trying to create an average subject from a set
???????????????of subjects, but keep getting an error that says
???????????????"mghRead(mri/norm.mgz, -1): could not open file".
???????????????I've read that several others have solved this
???????????????issue by installing the patch available at
???????????????*MailScanner has detected a possible fraud attempt
???????????????from "secure-web.cisco.com" claiming to be*
???????????????http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
???????????????<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
???????????????*MailScanner has detected a possible fraud attempt
???????????????from "secure-web.cisco.com" claiming to be*
???????????????http://ucrkindlab.com
???????????????<http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwHVpzdDUXsf8sRfvrwwkKf_KCQA4CYMRZs_am6IcPJO32Jd2eKl8shUDgQlOekTOscmE92Qtz70DWtJSOKxC8By5T4JuwEig2QC0e1ectPTPZjOGXa_t8ycn5bPjuoIWCqI8uXn86bmPqLVHkPzX-YRnSkCSbiIVsQ8zLNZ4ZNr58YvZl22BNeoGzuyye1eQfd_y4ENFJHQxgCNS7c9JXTBAX_N76Z_PQM9TFwvJPA/http%3A%2F%2Fucrkindlab.com>


???????????????_______________________________________________
???????????????Freesurfer mailing list
???????????????Freesurfer@nmr.mgh.harvard.edu
?<mailto:Freesurfer@nmr.mgh.harvard.edu>
???????????????*MailScanner has detected a possible fraud attempt
???????????????from "secure-web.cisco.com" claiming to be*
???????????????https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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???????????????_______________________________________________
???????????????Freesurfer mailing list
???????????????Freesurfer@nmr.mgh.harvard.edu
???????????????<mailto:Freesurfer@nmr.mgh.harvard.edu>
???????????????*MailScanner has detected a possible fraud attempt
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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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If you are not the intended recipient, please contact the sender by
reply e-mail and destroy all copies of the original message.

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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>
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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
(<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:

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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 (<
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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