[Freesurfer] mri_segstats for lobar intensity values

[Julie Ottoy]

External Email - Use Caution

Hi Freesurfer team,

I want to calculate the average PET intensity values per lobe. I want to
use the lobar annotations as outlined here in 'lobe mapping':
https://secure-web.cisco.com/1Opn2TyIP5_MF5tP6PRtaju8QtoITdCtzrmIlxZvYGO1bUWJFDMXcyGSrhgGeBk9csj3wKUttG0FvjSCUnYPwpYyF6cPOba2CehkcXo3W1q_XkX7oMenhvOgoqQ3XiXHW2TvCdINaa-Rxg6qRomLJnfwNkYJVCdMWZakmu7NJdQavpI_rUfC6Jq02CbfxAI_BgyW_J4yECTW1nc6J4qDBLKib1ZAfIaJhkM-e1XEdj6Rh88hcjzYY47DXy0icnzxd8uKcj8wW4OA_vUKn4Gv3CYN1nPsZpQndeoV2PcMn8DKTzIf9b4oO4U2metVlkguYGTeez7Y-1ZnLHFt9U1PWNQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCorticalParcellation

My PET images are volumetric in T1w MRI space.

I have successfully created my lobes following this command:

mri_annotation2label --subject $session --hemi lh --lobesStrict lobes

However I'm getting an error with my next command:

mri_segstats --annot $session/label/lh.lobes.annot --i
$session/pet_surf/SUVR/SUVR_T1space.nii.gz --sum lh.pet_lobar.sum


It is reading in the white surface, because I get this error: error:
MRISread($path/$session/label/rh.lobes.annot/surf/--i.white): could not
open file


How should I run this command when reading from the volumetric PET image?


Thank you,

Julie
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[Freesurfer] Segment the centrum semiovale

[Julie Ottoy]

External Email - Use Caution

Dear Freesurfer team,

I was wondering if FS has a way to segment the centrum semiovale?
The freesurfer colorLUT table mentions "Centrum semiovale is also labled
with 5001 (left) and 5002 (right)." (see
https://secure-web.cisco.com/16ntnqYurxLXfYvZCsM5evs9fxRFquoTnxIkD0H4vCmJ3wyz1ILXajrnEbC8QyD23IXTjhznWNEd6JY41T_1i4pFiAhYAmIiof9tTBS1o1Uv6Xe0jQ8zZK9BhCaaj7eG9eskRi7K2wraMBF5F1EQuFvn37XsurmsDLZ0IDBk02St-7AjIKjoN_btWKXbQQ_GjGriTaQKWn4oNTTT1J4WJiO73HLMdnC4N3JLqbQ0M7Rv8LV2WSnPMBUXHQA8R1nK869ZmYnfSz43n0gGUGW4dwGx6BqLbae0K35hubuWgxRFxCSpAMGc4xDZWv753Hyn8XTc1jpc5Dq57MVQ-eWsDRQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROI%2FFreeSurferColorLUT
)

What does the "also" refer to in this description?

Do the following rois represent the centrum semiovale ? :

5001Left-UnsegmentedWhiteMatter 20  30  40  0
5002Right-UnsegmentedWhiteMatter20  30  40  0

Thank you for your help!
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[Freesurfer] --pv flag in mri_segstats

[Julie Ottoy]

External Email - Use Caution

Hello FS team,

If I want to calculate the average diffusion-weighted signal from a DWI
image within WM regions using mri_segstats, would it be beneficial to use
the --pv flag for "partial volume correction" , or would this only have an
influence on the Volume calculation?

mri_segstats --seg ${whitemattermask} --i ${DTI_image} --sum ${
whitematter_stats} --excludeid 0

or

norm=${subject}/mri/norm.mgz
mri_segstats --seg ${whitemattermask} --i ${DTI_image} --sum ${
whitematter_stats} --pv ${norm} --excludeid 0


Thanks,
Julie
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[Freesurfer] Longitudinal FS: does ordering of time points matter in the command

[Julie Ottoy]

External Email - Use Caution

Hi FS team,

I just wanted to double check if, for the longitudinal pipeline, it matters
which time point is being read first? For example, in the command below,
should -tp  -tp  in the order of the scans being acquired?

recon-all -base  -tp  -tp  ... -all

Thank you for the information.
Best wishes
Julie
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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:
>>
>>
>>
>> 
>>
>>
>>
>> __

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

[Julie Ottoy]

External Email - Use Caution

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:
>
>
>
> 
>
>
>
> ___
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> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, p

Re: [Freesurfer] Spatial distance between regions

[Julie Ottoy]

External Email - Use Caution

Hi Doug

Thank you, worked as a charm!

I was wondering if I can apply this code on other atlases, for example I
have the schaefer atlas (in MNI152) space. Can I just run the
mri_segcentroids on the schaefer as input to extract the centroid
coordinates of the schaefer parcels? (My final goal is to calculate the
distances between each of the centroids)

Thank you! Best wishes for the new year.
Julie

On Sun, 2 Jan 2022 at 16:11, Douglas N. Greve 
wrote:

> Try mri_segcentroids. Run it with --help to get docs
>
> On 12/20/2021 3:34 AM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug,
>
> Just checking in with the question below. Does Freesurfer have such an
> option?
>
> Thanks,
> Julie
>
> On Tue, 14 Dec 2021 at 18:38, Julie Ottoy 
> wrote:
>
>> Hello FreeSurfer team,
>>
>> I was wondering if there is a way to calculate a distance matrix between
>> atlas-based regions (e.g. between their centers of mass) in volumetric
>> space (MNI152) space?
>>
>> Thank you for the information!
>> Best regards
>> Julie
>>
>
> ___
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>
>
> ___
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> The information in this e-mail is intended only for the person to whom it
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> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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Re: [Freesurfer] Spatial distance between regions

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

Just checking in with the question below. Does Freesurfer have such an
option?

Thanks,
Julie

On Tue, 14 Dec 2021 at 18:38, Julie Ottoy  wrote:

> Hello FreeSurfer team,
>
> I was wondering if there is a way to calculate a distance matrix between
> atlas-based regions (e.g. between their centers of mass) in volumetric
> space (MNI152) space?
>
> Thank you for the information!
> Best regards
> Julie
>
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[Freesurfer] Fwd: Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

Did you have a chance to look at this subject ?

Thanks a lot,
Julie

-- Forwarded message -
From: Julie Ottoy 
Date: Thu, 18 Mar 2021 at 13:08
Subject: Re: [Freesurfer] Failed tissue type check {Disarmed}
To: Freesurfer support list 


Hi Doug

I upload the files on the server, see subject_ottoy.tar.gz

thanks a lot!
Julie

On Tue, 16 Mar 2021 at 12:03, Douglas N. Greve 
wrote:

> I don't know. Can you upload the data so I can take a look? Instructions
> are below. I'd need both the anatomical data (output of recon-all) and
> input.nii.gz and PET.lta
>
> From the linux command line,
> Create the file you want to upload, eg,
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
>
> On 3/8/2021 11:47 AM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug,
>
> Any other suggestions I could try? It seems to be only an issue with the
> non-pvc data.
>
> Thanks
> Julie
>
> On Tue, 2 Feb 2021 at 11:10, Julie Ottoy  wrote:
>
>> Hi Doug,
>>
>> I tried these fixes but they still give me the error message below. I did
>> replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab
>> in the aux folder ?
>>
>> Thanks,
>> Julie
>>
>> On Tue, 12 Jan 2021 at 10:37, Julie Ottoy 
>> wrote:
>>
>>> Hi Doug
>>>
>>> I tried that as well but getting the same error as with --replace 29 3.
>>>
>>> ERROR: CTABpruneCTab(): ctab does not have segid 2
>>>
>>>
>>> Thanks,
>>> julie
>>>
>>> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>>
>>>> Try using --replace 29 2
>>>>
>>>>
>>>> On 12/29/2020 12:48 PM, Julie Ottoy wrote:
>>>>
>>>> External Email - Use Caution
>>>> Hi Doug
>>>>
>>>> Thanks for your reply. I tried both your suggestions, but it seems as
>>>> though they both ran into an error.
>>>>
>>>> For your first suggestion, i.e. adding --replace 29 3 to the command
>>>> line of gtmpvc, I get the error:
>>>>
>>>> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
>>>>
>>>> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
>>>>
>>>> Reading 057_S_5295re/mri/gtmseg.lta
>>>>
>>>> Replacing 19
>>>>
>>>> Pruning ctab
>>>>
>>>> ERROR: CTABpruneCTab(): ctab does not have segid 3
>>>>
>>>>
>>>> For your second suggestion, i.e. I replaced the following line in the
>>>> ctab:
>>>>
>>>>   29  Left-undetermined   135 206 2350  -1
>>>>
>>>> ==> replaced by:  29  Left-undetermined   135 206 2350
>>>> 3
>>>>
>>>>
>>>> I get the error:
>>>>
>>>> Computing Seg in input space
>>>>
>>>> Building GTM DoVoxFracCor=0
>>>>
>>>> ERROR: creating region for nthseg=12, segid=29, Left-undetermined
>>>>
>>>> It may be that there are no voxels for this seg when mapped into the
>>>> input space.
>>>>
>>>> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
>>>> registration
>>>>
>>>>  Build time 5.9690, err = 1
>>>>
>>>>
>>>> Thank you,
>>>>
>>>> Julie
>>>>
>>>> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
>>>> dgr...@mgh.harvard.edu> wrote:
>>>>
>>>>> You can use the fix from my previous email or you can add the
>>>>> following line any were into the gtmseg.ctab file:
>>>>>  29  Left-undetermined   135 206 235 0 3
>>>>>
>>>>>
>>>>> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>>>>>
>>>>> External Email - Use Caution
>>>>> Sorry I would like to correct my previous post. The subject also
>>>>> failed with PVC.
>>>

Re: [Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

Any other suggestions I could try? It seems to be only an issue with the
non-pvc data.

Thanks
Julie

On Tue, 2 Feb 2021 at 11:10, Julie Ottoy  wrote:

> Hi Doug,
>
> I tried these fixes but they still give me the error message below. I did
> replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab
> in the aux folder ?
>
> Thanks,
> Julie
>
> On Tue, 12 Jan 2021 at 10:37, Julie Ottoy 
> wrote:
>
>> Hi Doug
>>
>> I tried that as well but getting the same error as with --replace 29 3.
>>
>> ERROR: CTABpruneCTab(): ctab does not have segid 2
>>
>>
>> Thanks,
>> julie
>>
>> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> Try using --replace 29 2
>>>
>>>
>>> On 12/29/2020 12:48 PM, Julie Ottoy wrote:
>>>
>>> External Email - Use Caution
>>> Hi Doug
>>>
>>> Thanks for your reply. I tried both your suggestions, but it seems as
>>> though they both ran into an error.
>>>
>>> For your first suggestion, i.e. adding --replace 29 3 to the command
>>> line of gtmpvc, I get the error:
>>>
>>> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
>>>
>>> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
>>>
>>> Reading 057_S_5295re/mri/gtmseg.lta
>>>
>>> Replacing 19
>>>
>>> Pruning ctab
>>>
>>> ERROR: CTABpruneCTab(): ctab does not have segid 3
>>>
>>>
>>> For your second suggestion, i.e. I replaced the following line in the
>>> ctab:
>>>
>>>   29  Left-undetermined   135 206 2350  -1
>>>
>>> ==> replaced by:  29  Left-undetermined   135 206 2350  3
>>>
>>>
>>> I get the error:
>>>
>>> Computing Seg in input space
>>>
>>> Building GTM DoVoxFracCor=0
>>>
>>> ERROR: creating region for nthseg=12, segid=29, Left-undetermined
>>>
>>> It may be that there are no voxels for this seg when mapped into the
>>> input space.
>>>
>>> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
>>> registration
>>>
>>>  Build time 5.9690, err = 1
>>>
>>>
>>> Thank you,
>>>
>>> Julie
>>>
>>> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>>
>>>> You can use the fix from my previous email or you can add the following
>>>> line any were into the gtmseg.ctab file:
>>>>  29  Left-undetermined   135 206 235 0 3
>>>>
>>>>
>>>> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>>>>
>>>> External Email - Use Caution
>>>> Sorry I would like to correct my previous post. The subject also failed
>>>> with PVC.
>>>> I see now that the issue is happening during the gtm seg stage where it
>>>> gives the error: WARNING: segid   29 Left-undetermined tissue type is not
>>>> set.
>>>> For your information: I ran the standard FS and petsurfer pipeline as
>>>> outlined on the wiki. I tried two gtm seg commands:
>>>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
>>>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
>>>> --subseg-cblum-wm
>>>>
>>>> Thank you for your help,
>>>> Julie
>>>>
>>>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
>>>> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>> Dear Doug,
>>>>>
>>>>> I have the same issue as the people below. I was wondering if this was
>>>>> solved in the meantime.
>>>>>
>>>>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC
>>>>> and got the following error in only one of my subjects. When I ran the 
>>>>> same
>>>>> subject with PVC and specified psf, it did run fine.
>>>>>
>>>>> $Id: mri_gtmpvc.c,-
>>>>> setenv -
>>>>> cd -
>>>>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
>>>>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
>>>>> /g

Re: [Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

I tried these fixes but they still give me the error message below. I did
replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab
in the aux folder ?

Thanks,
Julie

On Tue, 12 Jan 2021 at 10:37, Julie Ottoy  wrote:

> Hi Doug
>
> I tried that as well but getting the same error as with --replace 29 3.
>
> ERROR: CTABpruneCTab(): ctab does not have segid 2
>
>
> Thanks,
> julie
>
> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Try using --replace 29 2
>>
>>
>> On 12/29/2020 12:48 PM, Julie Ottoy wrote:
>>
>> External Email - Use Caution
>> Hi Doug
>>
>> Thanks for your reply. I tried both your suggestions, but it seems as
>> though they both ran into an error.
>>
>> For your first suggestion, i.e. adding --replace 29 3 to the command line
>> of gtmpvc, I get the error:
>>
>> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
>>
>> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
>>
>> Reading 057_S_5295re/mri/gtmseg.lta
>>
>> Replacing 19
>>
>> Pruning ctab
>>
>> ERROR: CTABpruneCTab(): ctab does not have segid 3
>>
>>
>> For your second suggestion, i.e. I replaced the following line in the
>> ctab:
>>
>>   29  Left-undetermined   135 206 2350  -1
>>
>> ==> replaced by:  29  Left-undetermined   135 206 2350  3
>>
>>
>> I get the error:
>>
>> Computing Seg in input space
>>
>> Building GTM DoVoxFracCor=0
>>
>> ERROR: creating region for nthseg=12, segid=29, Left-undetermined
>>
>> It may be that there are no voxels for this seg when mapped into the
>> input space.
>>
>> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
>> registration
>>
>>  Build time 5.9690, err = 1
>>
>>
>> Thank you,
>>
>> Julie
>>
>> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> You can use the fix from my previous email or you can add the following
>>> line any were into the gtmseg.ctab file:
>>>  29  Left-undetermined   135 206 235 0 3
>>>
>>>
>>> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>>>
>>> External Email - Use Caution
>>> Sorry I would like to correct my previous post. The subject also failed
>>> with PVC.
>>> I see now that the issue is happening during the gtm seg stage where it
>>> gives the error: WARNING: segid   29 Left-undetermined tissue type is not
>>> set.
>>> For your information: I ran the standard FS and petsurfer pipeline as
>>> outlined on the wiki. I tried two gtm seg commands:
>>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
>>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
>>> --subseg-cblum-wm
>>>
>>> Thank you for your help,
>>> Julie
>>>
>>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>> Dear Doug,
>>>>
>>>> I have the same issue as the people below. I was wondering if this was
>>>> solved in the meantime.
>>>>
>>>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC
>>>> and got the following error in only one of my subjects. When I ran the same
>>>> subject with PVC and specified psf, it did run fine.
>>>>
>>>> $Id: mri_gtmpvc.c,-
>>>> setenv -
>>>> cd -
>>>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
>>>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
>>>> /gtmnopvc.output.ceregrey --rescale 8 47
>>>> sysname  Linux
>>>> hostname -
>>>> machine  -
>>>> user -
>>>> vgthresh   0.001000
>>>> nReplace   18
>>>> 0. 0. 0. 0. 0. 0.
>>>> 24 avail.processors, using 1
>>>> Creating output directory /gtmnopvc.output.ceregrey
>>>> Loading seg for gtm /ID/mri/gtmseg.mgz
>>>> Loading seg ctab /ID/mri/gtmseg.ctab
>>>> Reading /ID/mri/gtmseg.lta
>>>> Replacing 18
>>>> Pruning ctab
>>>> Checking tissue type
>>>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined

Re: [Freesurfer] almost empty mask.mgh with glmfit

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

Thanks. Yeah I am sure. I went through all my subjects with the time button.
Could it potentially be an internal rounding issue (almost all my pet
values are between 0 and 1, so they are put to 0?) Most likely not, but
still not sure what's happening!

On Fri, 15 Jan 2021 at 09:27, Douglas N. Greve 
wrote:

> Are you sure that there is not one subject that has a bunch of 0s? All it
> would take is one. You can also look at a "time course" of your subjects by
> clicking on the time course button in freeview
>
> On 1/14/2021 11:38 AM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug, thank you for your reply!
> When I look at my surface-projected non-pvc data per subject, initially it
> seemed as there were a lot of values zero, but when I go to configure > and
> replace the threshold to 0, the whole surface is  covered with non-zero pet
> values, as would be expected. Hence, I do not understand why the stacking
> of these images over all subjects gives me an almost empty mask.mgh (only
> about 1500 vertices with a pet value left) and thus an almost empty stacked
> 4D pet file.
>
> This is my command for projection of the non-pvc data:
> mri_vol2surf --mov
> ${in_dir}/${session}.gtmnopvc.output.pons/mgx.ctxgm.nii.gz --reg
> ${in_dir}/${session}.gtmnopvc.output.pons/aux/bbpet2anat.lta --hemi lh
> --projfrac 0.5 \
> --o ${in_dir}/lh.mgx.ctxgm.${session}.fsaverage.sm00.nopvc.pons.nii.gz
> --cortex --trgsubject fsaverage
>
> for the stacking, I am using:
> mri_concat --f "$lhmgxctxgm" --prune --o
> ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nopvc.pons.nii.gz
>
> When I omit the prune flag with the mri_concat, I get a good result.
>
> Do you recognize any issues here?
> Thank you!
> best regards
> Julie
>
> On Thu, 14 Jan 2021 at 10:57, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> A 0 value usually indicates a bad or uninterpretable voxel which you
>> would not want to include in your analysis. You can, of course, by not
>> pruning. But I think you need to answer the question as to why the values
>> are 0. Is 0 interpretable in this case?
>>
>> On 1/11/2021 6:15 PM, Julie Ottoy wrote:
>>
>> External Email - Use Caution
>> Dear Doug,
>>
>> I was wondering why the flag --prune is recommended (petsurfer website)
>> when creating a stacked pet file and during surface-smoothing. If I
>> understood correctly, this would set all vertices that are 0 in at least
>> one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my
>> non-pvc data, it seems as though a lot of the surface-projected values are
>> 0. Hence, when I perform a surface-based regression between PET and a
>> regressor and I use the --prune flag during mri_concat, I don't get any
>> results.
>>
>> Thank you!
>> best regards
>> Julie
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1Fmpo3Zkmb4lhiUruZyYmxV7lfxE-QIX9IW-FnljeiFwesCcYI7h_rM9OOJeBBnEr8GcpNHkqvHjKrM0CgFTIXbzov8x2IdYV2fiZASeyFhPvDaljNcw8az4WVfTgA6cRy4o01dYVlk0EQUjVL93ArPEZYHNLZE2Ir7KS3NKkFQXWUgdsVM3JNavnutFqP7rm7UJZrEoCKyEZDZi1USd1aTFSAtv_BvFold4YFuvRxHf8WNWXBQtuBmcpEz982ajN2OSarM7Q5PF8uXRacAHrGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1Fmpo3Zkmb4lhiUruZyYmxV7lfxE-QIX9IW-FnljeiFwesCcYI7h_rM9OOJeBBnEr8GcpNHkqvHjKrM0CgFTIXbzov8x2IdYV2fiZASeyFhPvDaljNcw8az4WVfTgA6cRy4o01dYVlk0EQUjVL93ArPEZYHNLZE2Ir7KS3NKkFQXWUgdsVM3JNavnutFqP7rm7UJZrEoCKyEZDZi1USd1aTFSAtv_BvFold4YFuvRxHf8WNWXBQtuBmcpEz982ajN2OSarM7Q5PF8uXRacAHrGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Re: [Freesurfer] almost empty mask.mgh with glmfit

[Julie Ottoy]

External Email - Use Caution

Hi Doug, thank you for your reply!
When I look at my surface-projected non-pvc data per subject, initially it
seemed as there were a lot of values zero, but when I go to configure > and
replace the threshold to 0, the whole surface is  covered with non-zero pet
values, as would be expected. Hence, I do not understand why the stacking
of these images over all subjects gives me an almost empty mask.mgh (only
about 1500 vertices with a pet value left) and thus an almost empty stacked
4D pet file.

This is my command for projection of the non-pvc data:
mri_vol2surf --mov
${in_dir}/${session}.gtmnopvc.output.pons/mgx.ctxgm.nii.gz --reg
${in_dir}/${session}.gtmnopvc.output.pons/aux/bbpet2anat.lta --hemi lh
--projfrac 0.5 \
--o ${in_dir}/lh.mgx.ctxgm.${session}.fsaverage.sm00.nopvc.pons.nii.gz
--cortex --trgsubject fsaverage

for the stacking, I am using:
mri_concat --f "$lhmgxctxgm" --prune --o
${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nopvc.pons.nii.gz

When I omit the prune flag with the mri_concat, I get a good result.

Do you recognize any issues here?
Thank you!
best regards
Julie

On Thu, 14 Jan 2021 at 10:57, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> A 0 value usually indicates a bad or uninterpretable voxel which you would
> not want to include in your analysis. You can, of course, by not pruning.
> But I think you need to answer the question as to why the values are 0. Is
> 0 interpretable in this case?
>
> On 1/11/2021 6:15 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Dear Doug,
>
> I was wondering why the flag --prune is recommended (petsurfer website)
> when creating a stacked pet file and during surface-smoothing. If I
> understood correctly, this would set all vertices that are 0 in at least
> one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my
> non-pvc data, it seems as though a lot of the surface-projected values are
> 0. Hence, when I perform a surface-based regression between PET and a
> regressor and I use the --prune flag during mri_concat, I don't get any
> results.
>
> Thank you!
> best regards
> Julie
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Non-uniform voxel size

[Julie Ottoy]

External Email - Use Caution

Thank you Doug, this is great!


On Wed, 13 Jan 2021 at 10:41, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I've just created a new version of gtmstats2table (attached). This will
> take a --volume flag to report the volume of the ROIs instead of the uptake
>
>
> On 1/6/2021 6:00 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Thank you Doug!
> I have another question related to voxel size.
>
> In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels.
> However, is there a way to easily retrieve the volume (instead of NVoxels)
> for each ROI within the gtm.stats file? I know that you should rescale by
> the pet voxel size; however, I have a multi-site study with all different
> voxel sizes.
> Or is there perhaps a way to apply the "aparcstats2table -meas volume"
> command but get the same ROIs outputted as those in the gtm.stats file?
>
> Thank you for the info!
> Julie
>
> On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> No, not a problem.
>>
>>
>> On 12/21/2020 12:52 PM, Julie Ottoy wrote:
>>
>> External Email - Use Caution
>> Dear freesurfer team,
>>
>> I am dealing with PET scans that were acquired at different sites. They
>> do not have uniform voxel size and dimensions. I was wondering if this
>> would be an issue for the sGTM and MG PETSurfer-PVC and/or for the
>> "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I
>> resample to a uniform voxelsize prior to these steps or does freesurfer
>> take care of this issue internally?
>>
>> Thank you for the information.
>> Best regards
>> Julie
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
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>>
>>
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[Freesurfer] matrix is ill-conditioned or badly scaled

[Julie Ottoy]

External Email - Use Caution

Hi freesurfer experts,

I am trying to run a GLM fit between cortical thickness and some other
continuous marker. My cortical thickness were stacked before using the
mris_preproc and surf2surf commands.
I have an FSGD file with the same subjects as used during the stacking of
the thickness maps, but I added a new continuous regressor (my independent
variable of interest). However, some subjects have a missing value for this
regressor, so I added NaN. This makes me run into the following error. When
I replace the NaN values by random numbers in the FSGD, it all runs fine.

M = [ ...
 1.0  0.99577  0.70711  0.98278  0.97547 -0.97111  nan
 0.99577  1.0  0.70628  0.97775  0.97819 -0.95833  nan
 0.70711  0.70628  1.0  0.68252  0.70488 -0.70032  nan
 0.98278  0.97775  0.68252  1.0  0.95399 -0.96466  nan
 0.97547  0.97819  0.70488  0.95399  1.0 -0.92863  nan
-0.97111 -0.95833 -0.70032 -0.96466 -0.92863  1.0  nan
 nan  nan  nan  nan  nan  nan  nan  ]
Normalized matrix condition is 1e+08
Design matrix --

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.


I made sure that my FSGD file does not have any weird characters, so i
applied the cat fsgd.txt | sed 's/\r/\n/g' > new.fsgd.txt, but this also
didn't help.

Thank you for your help,
Julie
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Re: [Freesurfer] Transform rescaled non-pvc PET to surface

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

Thank you!
Is that the same output as using mri_gtmpvc with --psf 0 --no-tfe and look
at the mgx.ctxgm.nii.gz ?

Thanks
Julie

On Tue, 12 Jan 2021 at 10:39, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> If you've run mri_gtmpvc already, you can add --save-input and it will
> save a file called input.rescaled.nii.gz which will be rescaled to your
> reference region
>
> On 12/29/2020 4:19 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Dear Freesurfer team,
>
> I have a question related to petsurfer. On the website, it is stated that "If
> you are not using PVC, you can use the template.reg.lta to sample the PET
> volume onto the surface using mri_vol2surf, then apply standard
> surface-based analysis."
>
> However, I was wondering how to do this for PET data that I first want to
> normalize to a reference region (to perform group-wise glm analyses
> afterwards). For example, I want to transform the "non-pvc and
> pons-rescaled PET volume" to the surface. Is there a way to easily do this?
> Or should I use the --scale flag with vol2surf and input the non-pvc
> reference region value for each subject reading from the gtm.stats.dat
> file, which I got from the mri_gtmpvc with --psf 0 --no-tfe --no-rescale?
>
> Thank you for the help!
> Best regards
> Julie
>
>
> ___
> Freesurfer mailing 
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>
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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug

I tried that as well but getting the same error as with --replace 29 3.

ERROR: CTABpruneCTab(): ctab does not have segid 2


Thanks,
julie

On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Try using --replace 29 2
>
>
> On 12/29/2020 12:48 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug
>
> Thanks for your reply. I tried both your suggestions, but it seems as
> though they both ran into an error.
>
> For your first suggestion, i.e. adding --replace 29 3 to the command line
> of gtmpvc, I get the error:
>
> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
>
> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
>
> Reading 057_S_5295re/mri/gtmseg.lta
>
> Replacing 19
>
> Pruning ctab
>
> ERROR: CTABpruneCTab(): ctab does not have segid 3
>
>
> For your second suggestion, i.e. I replaced the following line in the ctab:
>
>   29  Left-undetermined   135 206 2350  -1
>
> ==> replaced by:  29  Left-undetermined   135 206 2350  3
>
>
> I get the error:
>
> Computing Seg in input space
>
> Building GTM DoVoxFracCor=0
>
> ERROR: creating region for nthseg=12, segid=29, Left-undetermined
>
> It may be that there are no voxels for this seg when mapped into the input
> space.
>
> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
> registration
>
>  Build time 5.9690, err = 1
>
>
> Thank you,
>
> Julie
>
> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> You can use the fix from my previous email or you can add the following
>> line any were into the gtmseg.ctab file:
>>  29  Left-undetermined   135 206 235 0 3
>>
>>
>> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>>
>> External Email - Use Caution
>> Sorry I would like to correct my previous post. The subject also failed
>> with PVC.
>> I see now that the issue is happening during the gtm seg stage where it
>> gives the error: WARNING: segid   29 Left-undetermined tissue type is not
>> set.
>> For your information: I ran the standard FS and petsurfer pipeline as
>> outlined on the wiki. I tried two gtm seg commands:
>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
>> --subseg-cblum-wm
>>
>> Thank you for your help,
>> Julie
>>
>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
>> wrote:
>>
>>> External Email - Use Caution
>>> Dear Doug,
>>>
>>> I have the same issue as the people below. I was wondering if this was
>>> solved in the meantime.
>>>
>>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and
>>> got the following error in only one of my subjects. When I ran the same
>>> subject with PVC and specified psf, it did run fine.
>>>
>>> $Id: mri_gtmpvc.c,-
>>> setenv -
>>> cd -
>>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
>>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
>>> /gtmnopvc.output.ceregrey --rescale 8 47
>>> sysname  Linux
>>> hostname -
>>> machine  -
>>> user -
>>> vgthresh   0.001000
>>> nReplace   18
>>> 0. 0. 0. 0. 0. 0.
>>> 24 avail.processors, using 1
>>> Creating output directory /gtmnopvc.output.ceregrey
>>> Loading seg for gtm /ID/mri/gtmseg.mgz
>>> Loading seg ctab /ID/mri/gtmseg.ctab
>>> Reading /ID/mri/gtmseg.lta
>>> Replacing 18
>>> Pruning ctab
>>> Checking tissue type
>>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not
>>> set
>>> Failed tissue type check
>>>
>>> Any suggestions would be appreciated!
>>> Thank you,
>>> Julie
>>>
>>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
>>> <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGDCYbw1nr7Bymh0JNbA3Nr4M_m3-TZzftvlgMiJh7YiC6aUDW4Al3Wj4Kuy-05sd4QjU4E_RzWvbOfb_BTd5VaY6BPCSTWz6zWkEU0xuqeLNwwPRnm1yANvQkKZrMAWw2Gw7xnEbbIx95EqXWVkcRYx-x2scLfRIy4vfC9Cwn0nm4LrwA7h_KSoSDmXwnNLtLoWCfmI3LlkSE6EtVO2bwfNHaGn2-d6rSu0cljwjoiw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg55983.html>
>>> 2017-11-25
>>> <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaL

[Freesurfer] almost empty mask.mgh with glmfit

[Julie Ottoy]

External Email - Use Caution

Dear Doug,

I was wondering why the flag --prune is recommended (petsurfer website)
when creating a stacked pet file and during surface-smoothing. If I
understood correctly, this would set all vertices that are 0 in at least
one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my
non-pvc data, it seems as though a lot of the surface-projected values are
0. Hence, when I perform a surface-based regression between PET and a
regressor and I use the --prune flag during mri_concat, I don't get any
results.

Thank you!
best regards
Julie
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Re: [Freesurfer] Non-uniform voxel size

[Julie Ottoy]

External Email - Use Caution

Thank you Doug!
I have another question related to voxel size.

In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels.
However, is there a way to easily retrieve the volume (instead of NVoxels)
for each ROI within the gtm.stats file? I know that you should rescale by
the pet voxel size; however, I have a multi-site study with all different
voxel sizes.
Or is there perhaps a way to apply the "aparcstats2table -meas volume"
command but get the same ROIs outputted as those in the gtm.stats file?

Thank you for the info!
Julie

On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> No, not a problem.
>
>
> On 12/21/2020 12:52 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Dear freesurfer team,
>
> I am dealing with PET scans that were acquired at different sites. They do
> not have uniform voxel size and dimensions. I was wondering if this would
> be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf
> --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a
> uniform voxelsize prior to these steps or does freesurfer take care of this
> issue internally?
>
> Thank you for the information.
> Best regards
> Julie
>
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[Freesurfer] Transform rescaled non-pvc PET to surface

[Julie Ottoy]

External Email - Use Caution

Dear Freesurfer team,

I have a question related to petsurfer. On the website, it is stated that "If
you are not using PVC, you can use the template.reg.lta to sample the PET
volume onto the surface using mri_vol2surf, then apply standard
surface-based analysis."

However, I was wondering how to do this for PET data that I first want to
normalize to a reference region (to perform group-wise glm analyses
afterwards). For example, I want to transform the "non-pvc and
pons-rescaled PET volume" to the surface. Is there a way to easily do this?
Or should I use the --scale flag with vol2surf and input the non-pvc
reference region value for each subject reading from the gtm.stats.dat
file, which I got from the mri_gtmpvc with --psf 0 --no-tfe --no-rescale?

Thank you for the help!
Best regards
Julie
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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug

Thanks for your reply. I tried both your suggestions, but it seems as
though they both ran into an error.

For your first suggestion, i.e. adding --replace 29 3 to the command line
of gtmpvc, I get the error:

Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz

Loading seg ctab 057_S_5295re/mri/gtmseg.ctab

Reading 057_S_5295re/mri/gtmseg.lta

Replacing 19

Pruning ctab

ERROR: CTABpruneCTab(): ctab does not have segid 3


For your second suggestion, i.e. I replaced the following line in the ctab:

  29  Left-undetermined   135 206 2350  -1

==> replaced by:  29  Left-undetermined   135 206 2350  3


I get the error:

Computing Seg in input space

Building GTM DoVoxFracCor=0

ERROR: creating region for nthseg=12, segid=29, Left-undetermined

It may be that there are no voxels for this seg when mapped into the input
space.

Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
registration

 Build time 5.9690, err = 1


Thank you,

Julie

On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You can use the fix from my previous email or you can add the following
> line any were into the gtmseg.ctab file:
>  29  Left-undetermined   135 206 235 0 3
>
>
> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Sorry I would like to correct my previous post. The subject also failed
> with PVC.
> I see now that the issue is happening during the gtm seg stage where it
> gives the error: WARNING: segid   29 Left-undetermined tissue type is not
> set.
> For your information: I ran the standard FS and petsurfer pipeline as
> outlined on the wiki. I tried two gtm seg commands:
> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
> --subseg-cblum-wm
>
> Thank you for your help,
> Julie
>
> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
> wrote:
>
>> External Email - Use Caution
>> Dear Doug,
>>
>> I have the same issue as the people below. I was wondering if this was
>> solved in the meantime.
>>
>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and
>> got the following error in only one of my subjects. When I ran the same
>> subject with PVC and specified psf, it did run fine.
>>
>> $Id: mri_gtmpvc.c,-
>> setenv -
>> cd -
>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
>> /gtmnopvc.output.ceregrey --rescale 8 47
>> sysname  Linux
>> hostname -
>> machine  -
>> user -
>> vgthresh   0.001000
>> nReplace   18
>> 0. 0. 0. 0. 0. 0.
>> 24 avail.processors, using 1
>> Creating output directory /gtmnopvc.output.ceregrey
>> Loading seg for gtm /ID/mri/gtmseg.mgz
>> Loading seg ctab /ID/mri/gtmseg.ctab
>> Reading /ID/mri/gtmseg.lta
>> Replacing 18
>> Pruning ctab
>> Checking tissue type
>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not
>> set
>> Failed tissue type check
>>
>> Any suggestions would be appreciated!
>> Thank you,
>> Julie
>>
>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
>> <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGDCYbw1nr7Bymh0JNbA3Nr4M_m3-TZzftvlgMiJh7YiC6aUDW4Al3Wj4Kuy-05sd4QjU4E_RzWvbOfb_BTd5VaY6BPCSTWz6zWkEU0xuqeLNwwPRnm1yANvQkKZrMAWw2Gw7xnEbbIx95EqXWVkcRYx-x2scLfRIy4vfC9Cwn0nm4LrwA7h_KSoSDmXwnNLtLoWCfmI3LlkSE6EtVO2bwfNHaGn2-d6rSu0cljwjoiw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg55983.html>
>> 2017-11-25
>> <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8hnIkonyOL9FxrLNrp4Bj2WuN0PTQlUGm_PJQva6MLutv6BMWs-SO763W-gwW1nAT6N4vj217JzAEoSXtBbWL5JUyfL-O7BWGLfrj_ULjoLxBYnq2LcSNQgj9kva8w0E0bdnIFYTLoXYkJqjYbk7i-67h2LWjuOMCsdK3wV31zmywpixGXpXL85YXKxMmEETIQFPv9cZG3dAO4WLNFtjdVE1ZXCWD0o5zbpJqBYb5A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20171125%26o%3Dnewest%26f%3D1>
>>  Thread
>> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.ed

[Freesurfer] No extracerebral CSF in sGTM

[Julie Ottoy]

External Email - Use Caution

Dear Petsurfer team

Does the sGTM PVC correct for the uptake in extra cerebral CSF?
If not, how would this affect the reliability of the cortical PVC measures,
considering the spill-out of grey matter uptake to csf is being ignored?

Thank you!
Best regards
Julie
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[Freesurfer] Non-uniform voxel size

[Julie Ottoy]

External Email - Use Caution

Dear freesurfer team,

I am dealing with PET scans that were acquired at different sites. They do
not have uniform voxel size and dimensions. I was wondering if this would
be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf
--projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a
uniform voxelsize prior to these steps or does freesurfer take care of this
issue internally?

Thank you for the information.
Best regards
Julie
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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Sorry I would like to correct my previous post. The subject also failed
with PVC.
I see now that the issue is happening during the gtm seg stage where it
gives the error: WARNING: segid   29 Left-undetermined tissue type is not
set.
For your information: I ran the standard FS and petsurfer pipeline as
outlined on the wiki. I tried two gtm seg commands:
gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
--subseg-cblum-wm

Thank you for your help,
Julie

On Fri, 18 Dec 2020 at 00:09, Julie Ottoy  wrote:

> External Email - Use Caution
>
> Dear Doug,
>
> I have the same issue as the people below. I was wondering if this was
> solved in the meantime.
>
> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and
> got the following error in only one of my subjects. When I ran the same
> subject with PVC and specified psf, it did run fine.
>
> $Id: mri_gtmpvc.c,-
> setenv -
> cd -
> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
> /gtmnopvc.output.ceregrey --rescale 8 47
> sysname  Linux
> hostname -
> machine  -
> user -
> vgthresh   0.001000
> nReplace   18
> 0. 0. 0. 0. 0. 0.
> 24 avail.processors, using 1
> Creating output directory /gtmnopvc.output.ceregrey
> Loading seg for gtm /ID/mri/gtmseg.mgz
> Loading seg ctab /ID/mri/gtmseg.ctab
> Reading /ID/mri/gtmseg.lta
> Replacing 18
> Pruning ctab
> Checking tissue type
> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not
> set
> Failed tissue type check
>
> Any suggestions would be appreciated!
> Thank you,
> Julie
>
> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
> <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGDCYbw1nr7Bymh0JNbA3Nr4M_m3-TZzftvlgMiJh7YiC6aUDW4Al3Wj4Kuy-05sd4QjU4E_RzWvbOfb_BTd5VaY6BPCSTWz6zWkEU0xuqeLNwwPRnm1yANvQkKZrMAWw2Gw7xnEbbIx95EqXWVkcRYx-x2scLfRIy4vfC9Cwn0nm4LrwA7h_KSoSDmXwnNLtLoWCfmI3LlkSE6EtVO2bwfNHaGn2-d6rSu0cljwjoiw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg55983.html>
> 2017-11-25
> <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8hnIkonyOL9FxrLNrp4Bj2WuN0PTQlUGm_PJQva6MLutv6BMWs-SO763W-gwW1nAT6N4vj217JzAEoSXtBbWL5JUyfL-O7BWGLfrj_ULjoLxBYnq2LcSNQgj9kva8w0E0bdnIFYTLoXYkJqjYbk7i-67h2LWjuOMCsdK3wV31zmywpixGXpXL85YXKxMmEETIQFPv9cZG3dAO4WLNFtjdVE1ZXCWD0o5zbpJqBYb5A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20171125%26o%3Dnewest%26f%3D1>
>  Thread
> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1>
>  Douglas Greve
> <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV4jNz4fwyUMZPIMoCVdt9d_bUFEK6r8QndJ4GnxUzSJ5nFbTzLdgAE-xzB-cDHXFlDfjsbfBplG7gX0td56lZUCF6RZPQS86X8fx38fzgpoQ3ODino_OhrbrTLu_vxfi-hx0Kk2lh3HyNlKDTzyXnTgdkp2Aal7nkVZSeRuXTLXG3JF5hoKLtnmjEillAunhi3_Opx8m7CSxBHkkUEndRqMO7hLRg4xySjrREex2pQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BGreve%2522%26o%3Dnewest%26f%3D1>
>
> sorry, can you send me the details again?
>
>
> On 11/21/17 10:24 AM, Klein, Gregory wrote:
>
> Hello Donatas and Douglas,
>
> Did you ever find a cause and solution for this problem? I too
> occasionally get this error message, and cannot get the results of
> mri_gtmpvc for certain subjects.
>
>
> Any suggestions are welcome.
> Thanks,
> Greg
>
> --
> Gregory Klein, PhD
> Principal Scientist, Biomarker Experimental Medicine Leader
> F. Hoffmann-La Roche Ltd.
> Bldg 01, Floor 16, N445
> Grenazacherstrasse 170,
> 4070 Basel, Switzerland
> Mobile: +41 79 572 97 89
> Office Phone: +41 61 682 07 59
> email: gregory.kl...@roche.com
>
> Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City,
> AL7 1TW Registration No:100674
>
>
> Confidentiality note: This message is intended for the use of the
> named recipient(s) only and may contain confidential and / or
> privileged information. If you are not the intended recipient, please
> contact the sender and delete this message. A

[Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Dear Doug,

I have the same issue as the people below. I was wondering if this was
solved in the meantime.

I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and
got the following error in only one of my subjects. When I ran the same
subject with PVC and specified psf, it did run fine.

$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
/gtmnopvc.output.ceregrey --rescale 8 47
sysname  Linux
hostname -
machine  -
user -
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ceregrey
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Any suggestions would be appreciated!
Thank you,
Julie

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

2017-11-25

 Thread

 Douglas Greve


sorry, can you send me the details again?


On 11/21/17 10:24 AM, Klein, Gregory wrote:

Hello Donatas and Douglas,

Did you ever find a cause and solution for this problem? I too
occasionally get this error message, and cannot get the results of
mri_gtmpvc for certain subjects.


Any suggestions are welcome.
Thanks,
Greg

--
Gregory Klein, PhD
Principal Scientist, Biomarker Experimental Medicine Leader
F. Hoffmann-La Roche Ltd.
Bldg 01, Floor 16, N445
Grenazacherstrasse 170,
4070 Basel, Switzerland
Mobile: +41 79 572 97 89
Office Phone: +41 61 682 07 59
email: gregory.kl...@roche.com

Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City,
AL7 1TW Registration No:100674


Confidentiality note: This message is intended for the use of the
named recipient(s) only and may contain confidential and / or
privileged information. If you are not the intended recipient, please
contact the sender and delete this message. Any unauthorized use of
the information contained in this message is prohibited.


___
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

[Freesurfer] PVE correction tool Petsurfer {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Dear FreeSurfer Team,

I am interested in the answer to the question of Subin below. I don't think
this question was answered -- at least I cannot find the reply.
If the PET images are already smoothed to 8mm (which is the case with the
post-processed ADNI images), does it make any sense to apply PVC with --psf
8 at all on them?

The issue is that ADNI data does not provide the PSF of their scanner/recon
method. As such, I am unsure what to do in this case.

Thank you for your help!
Best regards
Julie

Re: [Freesurfer] PVE correction tool on Freesurfer 6


Lee Subin Kristine

 Wed, 20 Jul 2016 02:29:17 -0700


Hi Doug,

Thanks for your help!

For your response to question #1 from my previous email(copied below), then if
all PET images were smoothed so that they all have a uniform resolution of 8mm
FWHM, would I put 8 for the psf flag?


> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the
> point-spread function of the scanner or would a default value of 6
> work for all? I am using PET images from multiple centers and thus
> each image are from different scanners, and I'm not sure how I would
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change
depending upon recon method and parameters and even the ligand used. If
you get it about right, probably it will be close enough.


Also, for the second question (copied below), then does setting it to .01 mean
maximum sensitivity to gray matter in each PET voxel, and thus this is the
recommended threshold for the most accurate resutls?


> (b) For the mgx flag, is the GM threshold .01 an optimal threshold
> referring to the p-value?(am new to PVEcorrection and asking out of
> curiosity) What is the difference if I enter .01 versus I don't enter it?
>
You must enter a threshold. When Muller-Gartner is implemented, there
are two stages: (1) orthogonalization (subtracting out non-GM) and (2)
rescaling. In the rescaling step, each voxel is divided by the fraction
of GM in that voxel. If that fraction is 0, then you will get an error.
If it is close to 0, you can get extreme noise amplification in that
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be
rescaled, otherwise the voxel is set to 0.



Best,

Subin


보낸 사람: Douglas Greve  대신
freesurfer-boun...@nmr.mgh.harvard.edu

보낸 날짜: 2016년 7월 19일 화요일 오전 10:28:42
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6


the response is in the body f the mail

On 7/18/16 9:27 PM, Lee Subin Kristine wrote:

Hi Doug,

It seems that the email reply you just sent to me was empty. Could you please
check your email message again?


Thank you as always,

Subin



보낸 사람: Douglas N Greve
 대신
freesurfer-boun...@nmr.mgh.harvard.edu


보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6



On 07/12/2016 11:03 PM, Lee Subin Kristine wrote:
>
> Hi Doug,
>
>
> Thanks a lot for the page! It was very helpful.
>
>
> I have a few questions about one of the commands and a question for
> one of the output files.
>
>
> 1)*mri_gtmpvc --i pet.nii.gz --reg templat

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Dear Bruce and Douglas,

Thanks for the help, I have now uploaded the data. This is called
subject_FS_upload.zip

Please refer to the antsdn.brain.mgz (for T1) and the pial surface.
As described below, the freesurfer output did not delineate some parts of
the frontal lobe and medial temporal lobe correctly and this was not fixed
by putting control points (as there is no white matter in this area). Also
adapting the skull stripping did not help.
For my dataset with a lot of atrophic brains, the issue particularly in the
medial temporal lobe is very common (about 15% of my dataset)

Any tips / help would be appreciated!
Julie

On Thu, 5 Nov 2020 at 09:42, Douglas N. Greve 
wrote:

> Try these instructions
>
> From the linux command line,
> Create the file you want to upload, eg,
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
> On 11/3/2020 12:38 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Bruce,
>
> Thanks for your answer and cc'ing Rob.
> I did use anonymous as the username.
>
> Thanks,
> Julie
>
> On Tue, 3 Nov 2020 at 11:44, Fischl, Bruce 
> wrote:
>
>> Hmmm, did you log in as anonymous? I’ll cc Rob who should be able to help
>>
>>
>>
>> Cheers
>>
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
>> *Sent:* Tuesday, November 3, 2020 11:12 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Fixing error with pial surface {Disarmed}
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Bruce
>>
>>
>>
>> Thank you!
>>
>> Meanwhile, I tried to upload the subject on the server but I always get
>> the following error:
>>
>>
>>
>> 230 Login successful.
>> Remote system type is UNIX.
>> Using binary mode to transfer files.
>> ftp> cd transfer/incoming
>> 250 Directory successfully changed.
>> ftp> put subject_FS_upload.zip
>> local: subject_FS_upload.zip remote: subject_FS_upload.zip
>> 421 Service not available, remote server has closed connection
>>
>>
>>
>> Could you help me out with this?
>>
>> Thanks
>>
>> Julie
>>
>>
>>
>> On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce 
>> wrote:
>>
>> Hi Julie
>>
>>
>>
>> It’s really hard to diagnose this way. Are you able to upload the
>> subject? If so, please send us the coordinates of the region where you
>> think things are going wrong
>>
>>
>>
>> Cheers
>>
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
>> *Sent:* Monday, October 12, 2020 3:42 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Fixing error with pial surface
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Bruce,
>>
>>
>>
>> Thanks for your answer. I have checked the wm.mgz but it does not seem to
>> be a topological error I think.
>>
>> I have added coronal, axial, and sag views in attachment (see the red
>> cursor). Also I have added the first (coronal) slice that starts to show
>> white matter (couple slices later).
>>
>>
>>
>> Let me know if you still would like me to upload the data.
>>
>>
>>
>> Best
>>
>> Julie
>>
>>
>>
>> On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce 
>> wrote:
>>
>> Hi Julie
>>
>>
>>
>> It’s hard to tell from the single slice. Is there white matter in the
>> wm.mgz that doesn’t have surface (?h.white) covering it? That would
>> indicate a topological defect.
>>
>>
>> If you upload the entire gzipped and tarred subject’s directory we will
>> take a look
>>
>>
>>
>> Cheers
>>
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
>&

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Bruce,

Thanks for your answer and cc'ing Rob.
I did use anonymous as the username.

Thanks,
Julie

On Tue, 3 Nov 2020 at 11:44, Fischl, Bruce  wrote:

> Hmmm, did you log in as anonymous? I’ll cc Rob who should be able to help
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
> *Sent:* Tuesday, November 3, 2020 11:12 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Fixing error with pial surface {Disarmed}
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce
>
>
>
> Thank you!
>
> Meanwhile, I tried to upload the subject on the server but I always get
> the following error:
>
>
>
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> put subject_FS_upload.zip
> local: subject_FS_upload.zip remote: subject_FS_upload.zip
> 421 Service not available, remote server has closed connection
>
>
>
> Could you help me out with this?
>
> Thanks
>
> Julie
>
>
>
> On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce 
> wrote:
>
> Hi Julie
>
>
>
> It’s really hard to diagnose this way. Are you able to upload the subject?
> If so, please send us the coordinates of the region where you think things
> are going wrong
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
> *Sent:* Monday, October 12, 2020 3:42 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Fixing error with pial surface
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Thanks for your answer. I have checked the wm.mgz but it does not seem to
> be a topological error I think.
>
> I have added coronal, axial, and sag views in attachment (see the red
> cursor). Also I have added the first (coronal) slice that starts to show
> white matter (couple slices later).
>
>
>
> Let me know if you still would like me to upload the data.
>
>
>
> Best
>
> Julie
>
>
>
> On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce 
> wrote:
>
> Hi Julie
>
>
>
> It’s hard to tell from the single slice. Is there white matter in the
> wm.mgz that doesn’t have surface (?h.white) covering it? That would
> indicate a topological defect.
>
>
> If you upload the entire gzipped and tarred subject’s directory we will
> take a look
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
> *Sent:* Sunday, October 11, 2020 3:51 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Fixing error with pial surface
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer team,
>
>
>
> I have a question related to fixing the pial surface when a part was
> missed (see attachment). On the freesurfer website, I only found how to
> erase the pial when there was too much (see *MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1POCEML4QLGqdTfIf8StL0SUvgpIg3DncxT_ePZTsjRJHXGuGaY7K6NgEjwtHaDFZ04Yf1bbiarRLoActM_yTUXYdF6UU8f0_ZT5aTEgEXb2dCKc0omWAizj7NVEJF-Ih_MBLD513Nx8uDT4x6pRJ__v2mrGOOqfGOKtaQSLwVB2QjVAY7MYLqZbZ5cqIEYBIxkGV1_BTRJy8ktBMJnX-0g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEditsV6.0
> <https://secure-web.cisco.com/1gpx46tpa8CTIUNay0UrrJ-gxsIj8Mag4YGO8J8nyhFBk_vUGzoIRj4Mcbd6QhCbXxxACP5NekTgpkwy1i_7hReP5AFQqNeKWbPlOKFgTdD71o6FOQEC25-2mLI9VIZ3DCCUILUIjSEHeA8PQm-jSQuf2Q35SRlvA0gE74LLqJnkql0Rs2lM9RWexhSh3jGixx7QPZFpX0y4nDvIsDFmhtQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEditsV6.0>
> ), but I could not find what to do when there was too little.
>
> As there is no white matter in this particular area, it is also not an
> option to place control points. Also the skull stripping did not change
> anything: I tried both the freesurfer skull stripping and an in-house skull
> stripping algorithm.
>
>
>
> Thank you for your help.
>
> Best regards
>
> Julie
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secu

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Bruce

Thank you!
Meanwhile, I tried to upload the subject on the server but I always get the
following error:

230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put subject_FS_upload.zip
local: subject_FS_upload.zip remote: subject_FS_upload.zip
421 Service not available, remote server has closed connection

Could you help me out with this?
Thanks
Julie

On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce  wrote:

> Hi Julie
>
>
>
> It’s really hard to diagnose this way. Are you able to upload the subject?
> If so, please send us the coordinates of the region where you think things
> are going wrong
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
> *Sent:* Monday, October 12, 2020 3:42 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Fixing error with pial surface
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Thanks for your answer. I have checked the wm.mgz but it does not seem to
> be a topological error I think.
>
> I have added coronal, axial, and sag views in attachment (see the red
> cursor). Also I have added the first (coronal) slice that starts to show
> white matter (couple slices later).
>
>
>
> Let me know if you still would like me to upload the data.
>
>
>
> Best
>
> Julie
>
>
>
> On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce 
> wrote:
>
> Hi Julie
>
>
>
> It’s hard to tell from the single slice. Is there white matter in the
> wm.mgz that doesn’t have surface (?h.white) covering it? That would
> indicate a topological defect.
>
>
> If you upload the entire gzipped and tarred subject’s directory we will
> take a look
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
> *Sent:* Sunday, October 11, 2020 3:51 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Fixing error with pial surface
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer team,
>
>
>
> I have a question related to fixing the pial surface when a part was
> missed (see attachment). On the freesurfer website, I only found how to
> erase the pial when there was too much (see
> https://secure-web.cisco.com/1gpx46tpa8CTIUNay0UrrJ-gxsIj8Mag4YGO8J8nyhFBk_vUGzoIRj4Mcbd6QhCbXxxACP5NekTgpkwy1i_7hReP5AFQqNeKWbPlOKFgTdD71o6FOQEC25-2mLI9VIZ3DCCUILUIjSEHeA8PQm-jSQuf2Q35SRlvA0gE74LLqJnkql0Rs2lM9RWexhSh3jGixx7QPZFpX0y4nDvIsDFmhtQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEditsV6.0
>  ), but
> I could not find what to do when there was too little.
>
> As there is no white matter in this particular area, it is also not an
> option to place control points. Also the skull stripping did not change
> anything: I tried both the freesurfer skull stripping and an in-house skull
> stripping algorithm.
>
>
>
> Thank you for your help.
>
> Best regards
>
> Julie
>
>
>
>
>
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[Freesurfer] Skull strip t1 in recon-all

[Julie Ottoy]

External Email - Use Caution

Dear freesurfer team

I'm trying to use my own skull stripped T1 when running recon-all. For
this, I'm doing following steps:
1) run recon-all with -autorecon-1 -noskullstrip
2) mri_convert --in_type nii --out_type mgz -rl
./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz
./FreeSurfer/ID/mri/brainmask.mgz
3) run recon-all with -autorecon-2 and autorecon-3

My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore,
when transforming to the size of brainmask.mgz (256x256x256), it deforms. I
tried nearest, cubic, and interpolate, but none of them gives actually a
good result in terms of retaining the contrast. I was wondering if it is
important to keep a good contrast for brainmask.mgz , or whether this
brainmask.mgz is just used to determine the brain borders for segmentation.
(ie.: in which steps of recon-all is the brainmask.mgz actually used and
for what?)

Any recommendations?

Thank you!
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[Freesurfer] Fwd: using own skull stripped t1

[Julie Ottoy]

External Email - Use Caution

Hi Freesurfer team

I was wondering if you’d have some time to take a look at question below.
Thanks!

-- Forwarded message -
From: Julie Ottoy 
Date: Thu, 30 Jul 2020 at 13:22
Subject: using own skull stripped t1
To: Freesurfer support list 


Dear freesurfer team

I'm trying to use my own skull stripped T1 when running recon-all. For
this, I'm doing following steps:
1) run recon-all with -autorecon-1 -noskullstrip
2) mri_convert --in_type nii --out_type mgz -rl
./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz
./FreeSurfer/ID/mri/brainmask.mgz
3) run recon-all with -autorecon-2 and autorecon-3

My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore,
when transforming to the size of brainmask.mgz (256x256x256), it deforms. I
tried nearest, cubic, and interpolate, but none of them gives actually a
good result in terms of retaining the contrast. I was wondering if it is
important to keep a good contrast for brainmask.mgz , or whether this
brainmask.mgz is just used to determine the brain borders for segmentation.
(ie.: in which steps of recon-all is the brainmask.mgz actually used?)

Any recommendations?

Thank you!
Julie
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[Freesurfer] using own skull stripped t1

[Julie Ottoy]

External Email - Use Caution

Dear freesurfer team

I'm trying to use my own skull stripped T1 when running recon-all. For
this, I'm doing following steps:
1) run recon-all with -autorecon-1 -noskullstrip
2) mri_convert --in_type nii --out_type mgz -rl
./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz
./FreeSurfer/ID/mri/brainmask.mgz
3) run recon-all with -autorecon-2 and autorecon-3

My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore,
when transforming to the size of brainmask.mgz (256x256x256), it deforms. I
tried nearest, cubic, and interpolate, but none of them gives actually a
good result in terms of retaining the contrast. I was wondering if it is
important to keep a good contrast for brainmask.mgz , or whether this
brainmask.mgz is just used to determine the brain borders for segmentation.
(ie.: in which steps of recon-all is the brainmask.mgz actually used?)

Any recommendations?

Thank you!
Julie
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[Freesurfer] Fwd: Fwd: question regarding mri_vol2label

[Julie Ottoy]

External Email - Use Caution

Hi FS team,

I was wondering if you could take a look at the question below. Thanks!

-- Forwarded message -
From: Julie Ottoy 
Date: Fri, 10 Jul 2020 at 20:49
Subject: Re: [Freesurfer] Fwd: question regarding mri_vol2label
To: Freesurfer support list 


Thank you for your reply. It worked to convert to surface label :)
When i overlay the surface labels on the pial surface, I can view a
histogram showing the number of vertices versus the numbers of labels i
have. As a follow-up question, do you know how I could extract a txt file
that gives me the vertices with their corresponding label number. For
example, for 10,000 vertices and 100 labels, I'd like to get a txt file
with 10,000 rows and each row has a label value between 1 and 100.

Thank you for your help!

On Fri, 10 Jul 2020 at 16:28, Douglas N. Greve 
wrote:

> That will create a volume label, not a surface label (but it should not
> have been empty -- look in the label (it is just a text file)). To get a
> surface label, first map the volume to the surface with something like
> mri_vol2surf --mov parcellationvolumes.nii.gz --projfrac-max -.5 1 .1
> --hemi lh --o lh.parcellationvolumes.mgz --regheader subject
>  mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf subject lh
> --l lh.20.label
>
>
> On 7/10/2020 3:46 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Freesurfer team
>
> I am trying to convert parcellation (cortical) volumes that I acquired
> through another platform into surface labels using freesurfer. I tried
> following code to convert the volume with ID 20 from the
> parcellationvolumes.nii.gz file into a label
>
> mri_cor2label  --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label
>
> Although the code runs fine and finishes successfully, whenever I try to
> open the created label in freeview, it says that the label is empty.
>
> Any idea what I am doing wrong? Do you have an easier way to project all
> ROI volumes onto the surface?
>
> A second related question: I have run the recon-all for T1 of the subject
> and it creates rh.pial and lh.pial. I was wondering whether the
> transformation to go from T1 volume to the surface is saved somewhere and
> whether I can apply this transformation to convert my cortical volume
> parcellations into surface parcellations?
>
> Thank you for your help!
> Best regards
> Julie
>
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>
>
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Re: [Freesurfer] Fwd: question regarding mri_vol2label

[Julie Ottoy]

External Email - Use Caution

Thank you for your reply. It worked to convert to surface label :)
When i overlay the surface labels on the pial surface, I can view a
histogram showing the number of vertices versus the numbers of labels i
have. As a follow-up question, do you know how I could extract a txt file
that gives me the vertices with their corresponding label number. For
example, for 10,000 vertices and 100 labels, I'd like to get a txt file
with 10,000 rows and each row has a label value between 1 and 100.

Thank you for your help!

On Fri, 10 Jul 2020 at 16:28, Douglas N. Greve 
wrote:

> That will create a volume label, not a surface label (but it should not
> have been empty -- look in the label (it is just a text file)). To get a
> surface label, first map the volume to the surface with something like
> mri_vol2surf --mov parcellationvolumes.nii.gz --projfrac-max -.5 1 .1
> --hemi lh --o lh.parcellationvolumes.mgz --regheader subject
>  mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf subject lh
> --l lh.20.label
>
>
> On 7/10/2020 3:46 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Freesurfer team
>
> I am trying to convert parcellation (cortical) volumes that I acquired
> through another platform into surface labels using freesurfer. I tried
> following code to convert the volume with ID 20 from the
> parcellationvolumes.nii.gz file into a label
>
> mri_cor2label  --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label
>
> Although the code runs fine and finishes successfully, whenever I try to
> open the created label in freeview, it says that the label is empty.
>
> Any idea what I am doing wrong? Do you have an easier way to project all
> ROI volumes onto the surface?
>
> A second related question: I have run the recon-all for T1 of the subject
> and it creates rh.pial and lh.pial. I was wondering whether the
> transformation to go from T1 volume to the surface is saved somewhere and
> whether I can apply this transformation to convert my cortical volume
> parcellations into surface parcellations?
>
> Thank you for your help!
> Best regards
> Julie
>
> ___
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>
>
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[Freesurfer] combining left and right pial surface

[Julie Ottoy]

External Email - Use Caution

Hi Freesurfer team,

I am trying to combine the left and right pial surfaces into one surface. I
tried to use the following code:

mris_convert --combinesurfs lh.pial rh.pial rh+lh.pial

But the outcome is not correct (it has a lot of gaps in the combined pial).

Thank you.
Best regards,
Julie
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[Freesurfer] Fwd: question regarding mri_vol2label

[Julie Ottoy]

External Email - Use Caution

Hi Freesurfer team

I am trying to convert parcellation (cortical) volumes that I acquired
through another platform into surface labels using freesurfer. I tried
following code to convert the volume with ID 20 from the
parcellationvolumes.nii.gz file into a label

mri_cor2label  --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label

Although the code runs fine and finishes successfully, whenever I try to
open the created label in freeview, it says that the label is empty.

Any idea what I am doing wrong? Do you have an easier way to project all
ROI volumes onto the surface?

A second related question: I have run the recon-all for T1 of the subject
and it creates rh.pial and lh.pial. I was wondering whether the
transformation to go from T1 volume to the surface is saved somewhere and
whether I can apply this transformation to convert my cortical volume
parcellations into surface parcellations?

Thank you for your help!
Best regards
Julie
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[Freesurfer] PETsurfer: --usf in gtmseg

[Julie Ottoy]

External Email - Use Caution

Hi,

In PETsurfer gtmseg, there is the --usf (upsampling factor) which is by
default 2, corresponding to 0.5 mm voxelsize. I was wondering if the usf is
recommended to be chosen depending on your mri voxelsize (eg, usf 1 for 1mm
voxelsize of the mri), or will it just depend on how "accurate" you want
your segmentation to be? Can you safely use --usf 2 for an mri with 1mm
voxelsize?

Thank you!
best regards
Julie
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