Re: [Freesurfer] mri_segment error

[Z Hessam]

when i use first code for another data set, it sent me an error:

ERROR: /tmp/hessam91.tmp.decompressed.dcm.PV8Mal is not a dicom file

why this error happens?


On Thu, Feb 8, 2018 at 9:48 PM, Z Hessam  wrote:

> sure...
> with first code i convert *.dcm files.
> with second code i want to segment data:
>
> 1) recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid
> dyegmoh
> 2) recon-all -s dyegmoh -all
>
> and the log file is attached(recon-all_dyegmoh.log).
>
>
>
>
> On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl 
> wrote:
>
>> can you send us the complete command you ran, the entire screen output
>> and the recon-all.log file?
>>
>> cheers
>> Bruce
>>
>> On Thu, 8 Feb 2018, Z Hessam wrote:
>>
>> Hello FreeSurfer develpers
>>> I'm attempting to run " recon-all " command on a file of dicom data, and
>>> encounter with an error
>>> command:
>>>
>>> recon-all -s dyegmoh exited with ERRORS  at Thu Feb  8 17:08:16 +0330
>>> 2018
>>>
>>> how can i understand why this error happens  and what should i do to
>>> solve it?
>>>
>>>
>>>
>>>
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Cuda version > 5.0

[Melanie Ganz]

Dear FS list,

we just got a really nice graphics card (Quadro P6000) that we also 
would like to use to speed up recon-all, preferably for running high-res 
data with FS version 6. Now we know that in the precompiled FS version 6 
it still looks for cuda 5.0, but it seems like some people have gotten 
it to work with 8.0 (see e.g. here 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-May/052047.html).

Has anyone gotten FS version 6 compiled with cuda 9.1?

Cheers,

Melanie

-- 
Melanie Ganz-Benjaminsen, MSc, Ph.D.
Neurobiology Research Unit
University of Copenhagen
Rigshospitalet
Rockefeller Center
Juliane Maries Vej 28/30, 3.
DK-2100 Copenhagen
Denmark

phone:  +45 3545 6718
e-mail: melanie.g...@nru.dk
web: http://melanie.clausundmelanie.de/

___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cuda version > 5.0

[Melvin Robinson]

Yes, Freesurfer 6 works well with CUDA 9.1.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Melanie Ganz 

Sent: Thursday, February 8, 2018 10:54 AM
To: Freesurfer support list
Subject: [Freesurfer] Cuda version > 5.0

Dear FS list,

we just got a really nice graphics card (Quadro P6000) that we also
would like to use to speed up recon-all, preferably for running high-res
data with FS version 6. Now we know that in the precompiled FS version 6
it still looks for cuda 5.0, but it seems like some people have gotten
it to work with 8.0 (see e.g. here
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2017-2DMay_052047.html=DwIBAg=e7TYJBzRfB0YbjEn2u3vBA=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus=h70l-aJ2xIrLjRDQvds1wqaaNCl_-Fk7hd1I4Wkib9w=a-j4gSWmwY7hyzTLkGtyX0dK4e0hTeKoLpxWaTaNKVA=).

Has anyone gotten FS version 6 compiled with cuda 9.1?

Cheers,

Melanie

--
Melanie Ganz-Benjaminsen, MSc, Ph.D.
Neurobiology Research Unit
University of Copenhagen
Rigshospitalet
Rockefeller Center
Juliane Maries Vej 28/30, 3.
DK-2100 Copenhagen
Denmark

phone:  +45 3545 6718
e-mail: melanie.g...@nru.dk
web: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__melanie.clausundmelanie.de_=DwIBAg=e7TYJBzRfB0YbjEn2u3vBA=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus=h70l-aJ2xIrLjRDQvds1wqaaNCl_-Fk7hd1I4Wkib9w=Aac-cpBEykkyd5ztH6z2Zpl5xMPoZVSn2d9zVw28gdk=

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=e7TYJBzRfB0YbjEn2u3vBA=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus=h70l-aJ2xIrLjRDQvds1wqaaNCl_-Fk7hd1I4Wkib9w=j4hy0o25a7WNk41DzTF-4FPOqRtHBdKIkPKejz9eS30=


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 Partners Compliance HelpLine at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=DwIBAg=e7TYJBzRfB0YbjEn2u3vBA=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus=h70l-aJ2xIrLjRDQvds1wqaaNCl_-Fk7hd1I4Wkib9w=8BKGyw971u2vIXRZujMdS7YDoGLXpCSvthW7M1dN5cE=
 . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_segment error

[Bruce Fischl]

looks like the acquisition is not what you would need to run FreeSurfer 
on. Looking at the log I think your input is a T2-weighted image (we 
require a T1) with a slice thickness of 9mm (we require all voxel 
dimensions to be <=1.5mm or so)


cheers
Bruce



On Thu, 8 Feb 2018, Z Hessam wrote:


sure...
with first code i convert *.dcm files.
with second code i want to segment data:

1) recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid dyegmoh
2) recon-all -s dyegmoh -all

and the log file is attached(recon-all_dyegmoh.log).




On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl  wrote:
  can you send us the complete command you ran, the entire screen output 
and the
  recon-all.log file?

  cheers
  Bruce
  On Thu, 8 Feb 2018, Z Hessam wrote:

Hello FreeSurfer develpers
I'm attempting to run " recon-all " command on a file of dicom 
data, and
encounter with an error
command:

recon-all -s dyegmoh exited with ERRORS  at Thu Feb  8 17:08:16 
+0330 2018

how can i understand why this error happens  and what should i do 
to solve
it?




___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] smoothing command line- LGI

[Avideh Gharehgazlou]

Hi,

I am interested in looking at between-group differences in in LGI on Qdec (I 
will look at surface area as well later). I have a question regarding the 
smoothing stage. My recon-all for all subjects has completed, and I have LGI 
values for each subject. For smoothing, I was going to run the following 
command line:
Recon-all –s  -qcache

However, I saw in an archive post someone mentioning running the following line 
instead:
recon-all -s  -qcache -measure pial_lgi

Will you please tell me which command line I have to run?

Thanks so much,

Avi

CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.

AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y 
est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir 
des renseignements confidentiels et privilégiés. Toute lecture, utilisation, 
divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le 
destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et 
détruire toutes les copies du message original.
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

[m . bahri]

Dear Bruce,

Many thanks for you kind answer.
I sampled the perirhinal roi label into the volume using the suggested command 
line:
"mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o 
lh.perirhinal.volume.nii --hemi lh --identity".
 The obtained mask seems to cover well the perirhinal structure.

Now, I calculate the perirhinal volmue (mm3) based on the obtained mask but I 
found that the obtained value does not match the one obtained during the 
Freesurfer cortical reconstruction (values in the stat folder: files : 
rh/lh-BA_exvivo.stats).  did I messed something? 

Thank you very much in advance,

Best regards,

Mohamed

- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Lundi 22 Janvier 2018 16:12:10
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

oh, then I think you are just showing the surface-based label, which will 
only fill voxels that intersect with the white surface I believe. To 
sample it into the volume try mri_label2vol with the --fill-ribbon flag 
(the help is pretty extensive).

cheers
Bruce
On Mon, 22 Jan 2018, m.ba...@uliege.be 
wrote:

> Dear Bruce,
>
> Thank you for your answer!
>
> I just display the "T1.mgz" image (mri folder) using Freeview and then loaded 
> the "lh/rh.perirhinal_exvivo.label" rois (label folder).
>
> If this is not the good way to do it, please, could you explain more the 
> procedure? What do you mean by MT and PC?
>
> Thank you very much in advance,
>
> Best regards,
>
> Mohamed
>
>
> - Mail original -
> De: "Bruce Fischl" 
> À: "Freesurfer support list" 
> Envoyé: Vendredi 19 Janvier 2018 16:53:18
> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
>
> Hi Mohamed
>
> how are you visualizing the MT or PC ROIs. Did you sample them into the
> volume? If so, can you tell me where the file ROIs are in the data you
> sent me?
>
> cheers
> Bruce
> On Fri, 19 Jan 2018, m.ba...@uliege.be wrote:
>
>> Dear Bruce,
>>
>> Many thanks for your kind help!
>>
>> I put the subject data on your ftp site (s8201.tar).
>>
>> Best regards,
>>
>> Mohamed
>>
>>
>>
>> - Mail original -
>> De: "Bruce Fischl" 
>> À: "Freesurfer support list" 
>> Envoyé: Jeudi 18 Janvier 2018 16:37:10
>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
>>
>> Hi Mohamed
>>
>> if you tar, gzip and ftp this subject to our ftp site we will take a look
>> cheers
>> Bruce
>> On
>> Thu, 18 Jan 2018, m.ba...@uliege.be wrote:
>>
>>> Dear Bruce,
>>>
>>> Attached is the screen shot of the results of the segmentation of the 
>>> perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented 
>>> Roi does not cover the entire cortical thickness of the region. Is there 
>>> any other alternative to get a better segmentation of this region?
>>>
>>> Many thanks in advance,
>>>
>>> Best regards,
>>>
>>> Mohamed
>>>
>>> - Mail original -
>>> De: "Bruce Fischl" 
>>> À: "Freesurfer support list" 
>>> Envoyé: Mardi 9 Janvier 2018 14:50:16
>>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
>>>
>>> Hi Mohamed
>>>
>>> I'm pretty sure this was an issue with the ribbon-filling in V5 that is
>>> better in V6. Try using it and see if it is fixed.
>>>
>>> cheers
>>> Bruce
>>> On Tue, 9 Jan 2018,
>>> m.ba...@uliege.be wrote:
>>>
 Dear Freesurfer experts,

 We would like to use volume and cortical thickness measures obtained for 
 the perirhinal cortex in Freesurfer 5. When checking the region that has 
 been segmented (using lh/rh.perirhinal.label), we noticed that the ROI 
 does not seem to cover the entire cortical thickness of the region. On the 
 coronal slice shown in example (attached file), one can see that there are 
 still a few voxels of gray matter between the external border of the ROI 
 and the external boundary of the cortex. How reliable is this 
 segmentation? Is there a reason why the ROI appears so thin?

 Many thanks in advance,

 Best regards,



>>> ___
>>> 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 Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>> ___
>> Freesurfer 

Re: [Freesurfer] Wm.mgz editing

[Bruce Fischl]

Probably a topological defect but we would need the data to tell. Feel free to 
ftp it to us and we will take a look
Cheers
Bruce

> On Feb 8, 2018, at 12:19 PM, Emily Schwartz  
> wrote:
> 
> Hi FreeSurfer community,
> 
> I am relatively new to manually editing and am having some questions dealing 
> with editing the wm.mgz. Occasionally, white matter and grey matter are being 
> incorrectly cut out, but I cannot edit WM voxels in the area (lh postcentral) 
> because they are already considered WM in the heat map (but excluded from the 
> boundary). I have attached images. How would I go about fixing this? Would 
> control points work here?
> 
> And would the segmentation error in slices 79-81(lh postcentral) be edited by 
> adding wm voxels (I can't really add any to slice 79)?
> 
> (This is an elderly brain.)
> 
> Thank you,
> 
> Emily
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_segment error

[Z Hessam]

Hello FreeSurfer develpers
I'm attempting to run " recon-all " command on a file of dicom data, and
encounter with an error command:

recon-all -s dyegmoh exited with ERRORS  at Thu Feb  8 17:08:16 +0330 2018

how can i understand why this error happens  and what should i do to solve
it?
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Extending pial surface to include excluded cortex

[Bruce Fischl]

I agree that it looks like a topological defect that is fixed 
incorrectly. We can't tell from looking at the image of one slice though. 
If you gzip, tar and ftp the subject to us we will take a look


cheers
Bruce


On Thu, 8 Feb 2018, Arsenije Subotic 
wrote:




  Hi Doug,

  I’ve noticed that in my right hemisphere on top (I’m only using this 
hemisphere as the
  other hemisphere has tissue loss due to ischemia) there is also some 
atrophy. However,
  I’ve noticed that the surface can still probably be extended. It seems 
that there are
  some wm voxels which connect and disconnect after a couple of slices when 
I have wm.mgz
  on top of brain mask and when I use the heat colormap. In this case, is 
it ok to add wm
  voxels to connect them to the wm.mgz volume? This is what the tutorial 
says I should do,
  but I am worried since the wm intensity is sometimes 0 between these 
detached wm voxels
  and the main wm voxel. You can see it on the top left corner. And in 
general if there is
  no white matter sometimes and the pial surface does not extend and there 
is no defect,
  what is the general protocol? Thank you for your help!

  Arsenije



___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

[Bruce Fischl]

Hi Mohamed

it depends on how you computed it. I believe that the one in the 
exvivo.stats file computes it directly from the surfaces (i.e. sum of the 
volumes of the tetrahedra or something like that). If you sample it into 
the volume and add up voxels you will get discretization artifacts that 
will change the volume.


cheers
Bruce


On Thu, 8 Feb 2018, m.ba...@uliege.be 
wrote:



Dear Bruce,

Many thanks for you kind answer.
I sampled the perirhinal roi label into the volume using the suggested command 
line:
"mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o 
lh.perirhinal.volume.nii --hemi lh --identity".
The obtained mask seems to cover well the perirhinal structure.

Now, I calculate the perirhinal volmue (mm3) based on the obtained mask 
but I found that the obtained value does not match the one obtained 
during the Freesurfer cortical reconstruction (values in the stat folder: 
files : rh/lh-BA_exvivo.stats).  did I messed something?


Thank you very much in advance,

Best regards,

Mohamed

- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Lundi 22 Janvier 2018 16:12:10
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

oh, then I think you are just showing the surface-based label, which will
only fill voxels that intersect with the white surface I believe. To
sample it into the volume try mri_label2vol with the --fill-ribbon flag
(the help is pretty extensive).

cheers
Bruce
On Mon, 22 Jan 2018, m.ba...@uliege.be
wrote:


Dear Bruce,

Thank you for your answer!

I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the 
"lh/rh.perirhinal_exvivo.label" rois (label folder).

If this is not the good way to do it, please, could you explain more the 
procedure? What do you mean by MT and PC?

Thank you very much in advance,

Best regards,

Mohamed


- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Vendredi 19 Janvier 2018 16:53:18
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

how are you visualizing the MT or PC ROIs. Did you sample them into the
volume? If so, can you tell me where the file ROIs are in the data you
sent me?

cheers
Bruce
On Fri, 19 Jan 2018, m.ba...@uliege.be wrote:


Dear Bruce,

Many thanks for your kind help!

I put the subject data on your ftp site (s8201.tar).

Best regards,

Mohamed



- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Jeudi 18 Janvier 2018 16:37:10
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

if you tar, gzip and ftp this subject to our ftp site we will take a look
cheers
Bruce
On
Thu, 18 Jan 2018, m.ba...@uliege.be wrote:


Dear Bruce,

Attached is the screen shot of the results of the segmentation of the 
perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi 
does not cover the entire cortical thickness of the region. Is there any other 
alternative to get a better segmentation of this region?

Many thanks in advance,

Best regards,

Mohamed

- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Mardi 9 Janvier 2018 14:50:16
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

I'm pretty sure this was an issue with the ribbon-filling in V5 that is
better in V6. Try using it and see if it is fixed.

cheers
Bruce
On Tue, 9 Jan 2018,
m.ba...@uliege.be wrote:


Dear Freesurfer experts,

We would like to use volume and cortical thickness measures obtained for the 
perirhinal cortex in Freesurfer 5. When checking the region that has been 
segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem 
to cover the entire cortical thickness of the region. On the coronal slice 
shown in example (attached file), one can see that there are still a few voxels 
of gray matter between the external border of the ROI and the external boundary 
of the cortex. How reliable is this segmentation? Is there a reason why the ROI 
appears so thin?

Many thanks in advance,

Best regards,




___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


___

Re: [Freesurfer] mri_segment error

[Bruce Fischl]

can you send us the complete command you ran, the entire screen output 
and the recon-all.log file?


cheers
Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:


Hello FreeSurfer develpers
I'm attempting to run " recon-all " command on a file of dicom data, and 
encounter with an error
command:

recon-all -s dyegmoh exited with ERRORS  at Thu Feb  8 17:08:16 +0330 2018

how can i understand why this error happens  and what should i do to solve it?



___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.