[Freesurfer] Unsupported Datatype

[Rachel Wagner]

External Email - Use Caution

Hello, I’m getting the following error, not sure how to resolve!

developer@developer-VirtualBox:~$ mri_convert 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz
mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz
reading from dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii...
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
error: No such file or directory
error: niiRead(): unsupported datatype 128 (with scl_slope = 0) in 
/home/developer/dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii


Thanks!
Rachel Wagner
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Re: [Freesurfer] aparcstats2table segmentation fault error

[fsbuild]

External Email - Use Caution

Difficult to enlarge your screenshots and read the text, but it looks like even 
though the output from the setup script displays the path to FREESSURFER_HOME, 
the script wrapper for the shell cannot verify that path actually exists. 
 And it looks like you are using a “dot” directory named “.local” in your 
path for FREESURFER_HOME which is usually reserved for hidden subdirs in the 
shell. I would not name any subdirectory to begin with a "dot" for normal 
use with the shell, so try

$ mv .local local
… reset FREESURFER_HOME, source the setup script again, and see if running the 
command works.
- R.
On Nov 15, 2022, at 19:59, Eric Yin eric@mail.utoronto.ca 
wrote:External Email - Use 
CautionHello!I’m trying 
to run the aparcstats2table function on a single participant and I cannot seem 
to get rid of the following segmentation fault error. I checked the forums and 
did not find anyone with the same 
problem.9ECE8F5D2E7645A5962B55E842687C47.pngI have tried a 
few different options. First, I read that aparcstats2table requires PATH to 
lead to python2, but this call would throw the error that freesurfer has not 
been sourced properly even though I sourced it manually. Please find my 
Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 
(Core).4E289904EB384B21861CA9E16B7DD234.pngThen I thought 
that it might be because freesurfer/7.2.0 requires a newer version of python, 
but it also did not work for python3 or 
python3.6.64B17BE84D1E4AFBBF7FFCE28ED15CD7..pngPlease let 
me know if I’m doing something wrong, or if anyone has run into a similar 
issue.Thank you for your 
time.___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] Original image and the mask file dimension mismatch

[priya padma]

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Hello Team,
I have a nifti file of dimension (256, 256, 156) but once I run the
freesurfer recon-all the subregions mask "*aparc.DKTatlas+aseg.mgz*" has a
dimension of (256,256,256) due to this I am unable to view the
segmentation overlaid on the original image in any dicom viewer.

May I know why freesurfer changes the dimension of the original image and
the mask ?
Is there any solution for this?

Any help will be highly appreciated.
Thank you.

-- 
Best Regards
Padma Priya
*AI Developer *

*PhenoMx, Inc.*
*pr...@phenomx.ai  | (+82)10-5405-2685*
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[Freesurfer] about using -norandomness flag with recon-all

[Xin Qi]

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Hello Freesurfer Team:

Because of ensuring that results are exactly the same from run to run,
norandomness flag is used with recon-all.

To better understand the randomness, we have a few questions listed below.

1. Which algorithms inside the recon-all use the seeded random number?
And what randomness is about?
2. Is there a way to use a seed value to ensure the same data can be
reproduced?
3. Whether we are compromising anything by going with the non-random option?

Thank you very much for your time and looking forward to hearing from you.

Best regards
Xin
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Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

[Wang, Ruopeng]

You can run this command to clear the settings of freeview only:

rm ~/.config/Massachusetts\ General\ Hospital/freeview.conf

Ruopeng

On Nov 15, 2022, at 5:05 PM, Dierker, Donna 
mailto:do...@wustl.edu>> wrote:


External Email - Use Caution

This happens to me when I control-C in the terminal to quit freeview, instead 
of clicking the X in the upper right corner.
Doing this works for me:

rm -rf ~/.config/Massachusetts?General?Hospital

But this would blow away settings for other apps you might have that write to 
that subdir.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Drucker, Daniel 
mailto:ddruc...@mclean.harvard.edu>>
Date: Tuesday, November 15, 2022 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1
* External Email - Caution *
Hi,

If I do:
$ freeview -v myfile.nii.gz

If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview 
window pops up, the loading bar gets to 99%, then then nothing else happens. 
I'm not sure what to do to debug this further.



--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

[Dierker, Donna]

External Email - Use Caution

This happens to me when I control-C in the terminal to quit freeview, instead 
of clicking the X in the upper right corner.

Doing this works for me:



rm -rf ~/.config/Massachusetts?General?Hospital

But this would blow away settings for other apps you might have that write to 
that subdir.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Drucker, Daniel 

Date: Tuesday, November 15, 2022 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1
* External Email - Caution *
Hi,

If I do:
$ freeview -v myfile.nii.gz

If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview 
window pops up, the loading bar gets to 99%, then then nothing else happens. 
I'm not sure what to do to debug this further.



--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] Pial surfaces include cerebellum - unable to fix with manual edits

[Fischl, Bruce R.,PHD]

Hi Tommi

If you point us at the location of the data (and we have access) we will take a 
look

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Raij, Tommi A.
Sent: Monday, November 14, 2022 11:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Pial surfaces include cerebellum - unable to fix with 
manual edits

Dear Surfers,

I have a case where recon-all labels cerebellum as cerebral white matter 
(aparc+aseg.mgz) and the pial surfaces therefore include the cerebellum. The 
error has been resistant to attempts to fix the situation with manual edits to 
$SUBJECT/mri/brain.finalsurfs.mgz and re-running autorecon3 (with or without 
autorecon2).

Specifically:

Without manual edits, recon-all hangs at the stage:
...
CORRECTING DEFECT 0 (vertices=34440, convex hull=821, v0=4192)
XL defect detected...
...

After exiting with Ctrl-C, brain.finalsurfs.mgz include cerebellum, and the 
pial surfaces include cerebellum. I guess the "defect" FS is trying to correct 
is the cerebellum that was mislabeled.

My manual edits to brain.finalsurfs.mgz consisted of removing cerebellum by 
painting with brush value = 1 (freeview voxel edit tool). Thereafter, I 
recomputed autorecon 3:

recon-all -autorecon3 -s $SUBJECT -no-isrunning

With this, recon-all finishes "without error" but the recomputed aparc+aseg.mgz 
still thinks cerebellum is cerebral white matter and the pial surfaces again 
include cerebellum.

This is with Martinos Center stable version 6.

Any suggestions would be greatly appreciated! Also happy to send a link to the 
original T1 and recon-all results if you would like.

Bests,

Tommi

---
Tommi Raij, MD, PhD
MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th st
Charlestown, MA 02129
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[Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

[Drucker, Daniel]

Hi,

If I do:
$ freeview -v myfile.nii.gz

If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview 
window pops up, the loading bar gets to 99%, then then nothing else happens. 
I'm not sure what to do to debug this further.




--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School

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 .
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Re: [Freesurfer] Recon-all in post stroke aphasic patients.

[Huang, Yujing]

Hi Steve,

You can use ‘-hemi ’ to select which hemisphere to process. If you are 
interested in right hemisphere only, pass ‘-hemi rh’ to recon-all along with 
other flags.

I don’t have answers to your first question.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Steve Petersen
Sent: Tuesday, November 15, 2022 11:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all in post stroke aphasic patients.


External Email - Use Caution

Dear FreeSurfer experts,

I would like to run the recon-all command in MRI images of post-stroke aphasic 
patients. Should I use a particular flag in the recon-all command to avoid 
important errors during cortical reconstruction?. We are only interested in the 
right hemisphere (where there is no brain injury), can I conduct the recon-all 
only in the right hemisphere?.

Any help would be appreciated.

Thank you very much in advance.

Best regards,

Steve.
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 .
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Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

[Julie Ottoy]

External Email - Use Caution

Hi,

I just wanted to check in with my questions below? Thanks!
Julie

On Thu, 10 Nov 2022 at 17:03, Julie Ottoy  wrote:

> Hi,
>
> Yes you are right! Taking out the -parallel solved the issue! Does this
> mean v7 longitudinal recon-all does not support this flag?
> I have one other question, any help would be appreciated. I ran the
> baseline recon-all with the -bv (big ventricles) flag. Should I add this
> flag for longitudinal processing as well, or will it not matter?
>
> Thanks again for your support,
> Best wishes
> Julie
>
>
> On Wed, 9 Nov 2022 at 15:36, Huang, Yujing 
> wrote:
>
>> Hi Julie,
>>
>>
>>
>> I noticed that you were running recon-all with ‘-parallel’ flag. It is
>> causing the error.
>>
>>
>>
>> The process should work if you remove ‘-parallel’ from recon-all command.
>>
>>
>>
>> Best,
>>
>>
>>
>> Yujing
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
>> *Sent:* Tuesday, November 8, 2022 9:27 AM
>> *To:* Freesurfer support list ; fsbuild <
>> fsbu...@contbay.com>
>> *Subject:* [Freesurfer] Fwd: Longitudinal FS pipeline consistently
>> interrupts at -Sphere for all participants
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi FS team,
>>
>>
>>
>> Just wanted to follow up with my question below. Thanks!
>>
>> Julie
>>
>> -- Forwarded message -
>> From: *Julie Ottoy* 
>> Date: Fri, 4 Nov 2022 at 00:11
>> Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently
>> interrupts at -Sphere for all participants
>> To: fsbuild 
>>
>>
>>
>> Hi Fsbuild team,
>>
>>
>>
>> Thank you for your reply. Sorry for the confusion, my system was actually
>> Linux, not Windows. It did *not* run on top of Windows (sorry again for
>> the confusion).
>>
>> In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2
>> consistently on Linux. I also used two different machines (our institute
>> server as well as ComputeCanada, hence I do not believe it's a memory
>> issue). Each run got stuck at the -Sphere x.long.x step as indicated in my
>> previous email. Interestingly, I tried today with the longitudinal FS
>> v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug
>> in the v7 series for longitudinal processing that was not present in the v6
>> series? I tried on two different types of input T1w data acquired from
>> different centers and they point to the same issue => -Sphere error in
>> x.long.x for v7 , while it runs fine for v6. Please see attached log files
>> and screenshots for both.
>>
>>
>>
>> I am also thinking if it would be ok to run the longitudinal with v6
>> since we ran the baseline data with v7.2. Could you please advise on this?
>>
>>
>>
>> Last, I was wondering if there is a way to receive more detailed
>> log/error files? As indicated from my previous email and screenshots, the
>> code just exited at Sphere but did not indicate why it went wrong there.
>>
>>
>>
>> Thank you for your help!
>>
>> Best regards
>>
>> Julie
>>
>>
>>
>> On Wed, 2 Nov 2022 at 17:02, fsbuild  wrote:
>>
>> One way we’ve seen recon-all eventually fail running on Linux hosted on
>> Windows is whatever is virtualizing Linux to run on top of the Windows OS -
>> simply runs out of memory at some point in the processing pipeline.  That
>> can result in a message in the recon-all.log like a file was not found,
>> i.e., a computation fails and the results are not saved in a file that
>> later on is expected to be found, opened and read.  I don’t see messages
>> like that in your log.
>>
>>
>>
>> It might be helpful to know more about how you are running Linux on
>> windows, e.g., if you are using the built-in Windows Subsystem for Linux
>> (WSL) or using a VM running on something like VirtualBox.
>>
>>
>>
>> You could also send along the output in the linux terminal from:
>>
>> $ cat /etc/os-release
>>
>> $ cat $FREESURFER_HOME/build-stamp.txt
>>
>>
>>
>> - R.
>>
>>
>>
>> On Nov 2, 2022, at 15:03, Julie Ottoy  wrote:
>>
>>
>>
>> 
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>> The information in this e-mail is intended only for the person to whom it
>> is addressed.  If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at
>> 

[Freesurfer] Recon-all in post stroke aphasic patients.

[Steve Petersen]

External Email - Use Caution

Dear FreeSurfer experts,

I would like to run the recon-all command in MRI images of post-stroke
aphasic patients. Should I use a particular flag in the recon-all command
to avoid important errors during cortical reconstruction?. We are only
interested in the right hemisphere (where there is no brain injury), can I
conduct the recon-all only in the right hemisphere?.

Any help would be appreciated.

Thank you very much in advance.

Best regards,

Steve.
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contains patient information, please contact the Mass General Brigham 
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 .
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[Freesurfer] Freesurfer Passcode

[Nadeem Schwen]

External Email - Use Caution

Hi! I am trying to 3D print my child's recent brain MRI. Can I please have
the passcode to unzip the Virtualbox image for Freesurfer? Thanks in
advance!
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 .
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Re: [Freesurfer] aseg.mgz not created

[Fischl, Bruce R.,PHD]

Hi Sarah

I think you didn't give it any flags other than the subject and input. You need 
to specify -all if you want it to run all the steps it knows how to

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of O'Dor, Sarah,PhD
Sent: Tuesday, November 15, 2022 9:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aseg.mgz not created

Good morning,
Recon-all finished without error, but no aseg.mgz file was created. I cannot 
find any errors in the recon-all.log (attached) to indicate what may have 
happened. Any suggestions on how to troublshoot this?
Thank you,
Sarah
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Re: [Freesurfer] aseg.mgz not created

[Huang, Yujing]

Hi Sarah,

It doesn't look like your recon-all is done processing yet from the attached 
recon-all.log.

You should also have these two files:
recon-all-status.log
recon-all.done

What did they report?

Thanks.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of O'Dor, Sarah,PhD
Sent: Tuesday, November 15, 2022 9:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aseg.mgz not created

Good morning,
Recon-all finished without error, but no aseg.mgz file was created. I cannot 
find any errors in the recon-all.log (attached) to indicate what may have 
happened. Any suggestions on how to troublshoot this?
Thank you,
Sarah
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.