Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

[Diamond, Bram Ryder]

Hi Xiaoqian,

We don't typically recommend this, but it looks like you will need to edit your 
brain.finalsurfs.mgz to account for the wm lesion. I tested this out by filling 
in the lesion with 110 and recreating the wm surface -- it seems to work quite 
well.

Once that is done, you can run the following command to finish your recon-all. 
I'm running it now to make sure the output is okay:
recon-all -s  -white -smooth2 -inflate2 -curvHK -curvstats 
-autorecon3

I also made some edits to the wm.mgz, but I'm not sure they were necessary. 
I'll send you copies of the edited files in a private email.

Best,
Bram


___
Bram R. Diamond, BSc
Sr. Clinical Research Coordinator
Laboratory for Computational Neuroimaging (LCN)
Laboratory for NeuroImaging of Coma and Consciousness (NICC)
Massachusetts General Hospital
(p): 617-726-6598

LCN: https://www.martinos.org/lab/lcn
NICC: https://www.massgeneral.org/nicc​


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Xiaoqian Yan 

Sent: Wednesday, October 16, 2019 12:11 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] imperfect segmentation in the occipital lobe in 
epilepsy patient


External Email - Use Caution

Dear Bruce,

Thanks for the reply. I have uploaded my data through the Martinos Center 
FileDrop, here is the link:
+ Data_Xiaoqian.zip (169.46 MiB) 


I explained my problems in that link, but still copy and past here:

'' I am having troubles doing a good segmentation in the right occipital lobe 
in a patient's brain. There is a thermal lesion in that region, a black whole, 
that could make the segmentations go wrong. I tried to edit the wm, but the 
results were not ideal.

The thermal lesion can be clearly seen from the axial slices 108 - 115, e.g. in 
RAS coordinate [40,-50,-4] on the axial slice 112. The bad segmentation (wm and 
pial surface) can be seen from the coronal slices 54 - 62, e.g. in coordinate 
[42, -52, -10] on the coronal slice 57. The wrong segmentation made it 
impossible to overlap the functional activations in the OFA (occipital face 
area) region on the surface.

In my uploaded data directory, I already edited the wm and brainmask, and I 
only reran 'recon-all -autorecon2-wm -subjid name' to save time. ''

Thanks in advance, and best wishes,

Xiaoqian





On Wed, 16 Oct 2019 at 15:07, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Xiaoqian

it's pretty hard to tell what's going on from these images. If you tar/gzip
your whole subject dir and upload it with an email telling us the specific
voxel coords that you want us to examine

cheers
Bruce


On Wed, 16 Oct 2019, Xiaoqian Yan wrote:

>
> External Email - Use Caution
>
> Dear Douglas,
> Thanks for your reply. I double checked my results. It was true that the
> rh.orig.nofix and rh.orig did not overlap over the region that I was
> interested in. I re-edit the wm, and only ran 'recon-all -autorecon2-wm
> -subjid patientname' to check the results, but the rh.orig.nofix and rh.orig
> were still not overlapped. Do you mind helping me check my wm edits? For me,
> the thermal lesion is a black hole that big enough to confuse the
> segmentation. Maybe there is a way to mark that region or add a label,
> before I run the recon-all?
>
> P.S. in the attached figures, pial is in green, rh.orig.nofix in red, and
> rh.orig in yellow.
>
> Thanks and have a nice day,
>
> Xiaoqian
>
>
>
> On Fri, 11 Oct 2019 at 00:47, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>   I think that the wm edits should have worked. Can you load the
>   rh.orig.nofix and rh.orig to see if they encompass your edits?
>   If not, then maybe your did not re-run it properly.
>
>   On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:
>
>   External Email - Use Caution
>
>   Dear Freesurfer experts,
> I am trying to do the segmentation on a patient's T1 image. I
> did not get error messages running the 'recon-all' (recon-all -i
> T1.nii -subjid PatientName -all), but the segmentation over the
> right occipital lobe was imperfect, which caused failures to map
> the functional activations in this region onto the surface.
>
> I tried to manually edit the wm.mgz several times, but the
> output did not change a lot (please see the attached image). The
> patient had depth EEG electrodes implanted in this region
> before, so there is a thermal lesion which I thought could have
> caused the bad segmentation.  Do you have any ideas about what I
> can do next, or it is possible for you to help me editing the
> data?
>
> Thanks in advance, best wishes
>
> Xiaoqian
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
> ___
> Freesurfer 

Re: [Freesurfer] recon-all error: Correcting defect

[Diamond, Bram Ryder]

Hi Miguel!

I'll be happy to help with your issue, but I'm having trouble finding your 
subject's directory on our server. Could you please try and upload the data via 
FTP, again? Also, have you tried either of Bruce's suggestions?

Thanks,
Bram

Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Wednesday, June 26, 2019 11:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error: Correcting defect

External Email - Use Caution

Hello Bruce,

Ok, I have sent to you the subject via FileDrop if you want to take a look. 
Thanks.

Best regards,

El mié., 26 jun. 2019 a las 17:04, Bruce Fischl 
(mailto:fis...@nmr.mgh.harvard.edu>>) escribió:
Hi Miguel

depending on the lesions it may not be fixable (since they may change the
topology of the cortex). If you upload the subject we will take a look, or
you can try manually filling in the lesion in the wm.mgz (or marking it as
lesion in the aseg.mgz) and seeing if that helps

cheers
Bruce
On Wed, 26 Jun 2019, Miguel Ángel Rivas
Fernández wrote:

>
> External Email - Use Caution
>
>
>  I ran the recon-all in one subject and and this process was stopped in the 
> topology correction. In
> particular during the
>
>  "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)".
>
> I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and 
> I noticed that the this
> error would be located in the lh.inflated.nofix file. I am not completely 
> sure but I suspect that
> this error may be due to the fact that there is a large amount of brain 
> lesion and this would
> difficult the topology correction. How can I fix this problem?
>
> Thanks in advance.
>
> Best regards,
>
> --
> Miguel Ángel Rivas Fernández
>
>___
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--
Miguel Ángel Rivas Fernández

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Re: [Freesurfer] MRISalloc error during automatic reconstruction

[Diamond, Bram Ryder]

Hi Julia,

I've taken a look at the data you sent us last week and it looks like the issue 
is stemming from the topology fixer. If you look through the input scan you've 
given us, you can see that the contrast between wm/gm is especially low in 
certain regions. This low contrast to noise ratio is making it hard for 
recon-all to produce a good wm segmentation which in turn gives the topology 
fixer trouble "cleaning up" the surfaces. This is causing your memory 
allocation error.

You may be able to improve the segmentation by including an expert.opts file 
with mri_segment adjustments (-wlo flag). Check out our resources on 
expert.opts files and the mri_segment option bellow:

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segment

I hope this helps.

Best,
Bram

Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Julia Ströhlein 

Sent: Tuesday, February 26, 2019 1:54 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] MRISalloc error during automatic reconstruction

External Email - Use Caution

Hi Bruce,
did you receive the link I sent you last week?
Best
Julia

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 19. Februar 2019 16:37
An: Freesurfer support list 
Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction

Hi Julia

did you upload the entire subject dir (gzipped and tarred)? And what
happened with ftp? We can help you get that working. I would think the whole
subject dir would be too big for the filedrop, but feel free to send me the
link

cheers
Bruce
On Tue, 19 Feb 2019, Julia Ströhlein wrote:

>External Email - Use Caution
>
> Hi Bruce,
>
> I created a link with the Martinos File Drop System, because ftp
> upload did not work.
> It's probably the best idea to send the links to your personal mail
address?
>
> Best
> Julia
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
> Fischl
> Gesendet: Montag, 18. Februar 2019 15:52
> An: Freesurfer support list 
> Betreff: Re: [Freesurfer] MRISalloc error during automatic
> reconstruction
>
> Hi Julia
>
> why don't you tar and gzip the subject directory and put it on our ftp
> site so we can take a look
>
> cheers
> Bruce
> On Mon, 18 Feb 2019, Julia Ströhlein wrote:
>
>>External Email - Use Caution
>>
>> Hi Bruce,
>> thanks for the advice. I ran the subject again with 4.5G, but it
>> ended with the same error. It only happens with this subject, the
>> stream worked fine for all the other subjects.
>> However, I tried running the subject with my Macbook, and it also
>> ended with an error (see the recon-all.log attached). I think it has
>> something to do with the MRI of the subject. Do you have any ideas?
>> Thanks for any help.
>> Best,
>> Julia
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
>> Fischl
>> Gesendet: Mittwoch, 13. Februar 2019 15:58
>> An: Freesurfer support list 
>> Betreff: Re: [Freesurfer] MRISalloc error during automatic
>> reconstruction
>>
>> Hi Julia
>>
>> I think you only have about 1.5G free memory at the beinning of
>> running recon-all, which is not enough for this subject. It looks
>> like some other process is using another 2G, which might be enough if
>> you can free it up. In general though you probably want a machine
>> with more ram
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 13 Feb
>> 2019, Julia Ströhlein wrote:
>>
>>>External Email - Use Caution
>>>
>>> Hi,
>>> of course.
>>>
>>> Julia
>>>
>>> -Ursprüngliche Nachricht-
>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
>>> Fischl
>>> Gesendet: Dienstag, 12. Februar 2019 16:12
>>> An: Freesurfer support list 
>>> Betreff: Re: [Freesurfer] MRISalloc error during automatic
>>> reconstruction
>>>
>>> Hi Julia
>>>
>>> can you send us the recon-all.log file?
>>>
>>> cheers
>>> Bruce
>>> On Tue, 12 Feb 2019,
>>> Julia Ströhlein wrote:
>>>

 External Email - Use Caution

 Dear experts,

 while running one of my subjects, I got this error:



 MRISalloc(732595, 480): could not allocate vertices

 Cannot allocate memory

 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10

 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux



 recon-all -s P_04 exited with ERRORS at Mon Feb  4 

Re: [Freesurfer] FreeSurfer: trouble processing subjects

[Diamond, Bram Ryder]

Hi Andrade,

I'm adding  the FreeSurfer support list so other can benefit.

To answer your question, you would use the first dicom from the diffusion 
scan... but since you don't have the dicoms that won't work. You can combine 
all of the DTI nifty files into one multi-frame diffusion 4d volume using 
mri_concat.

mri_concat /path/to/all/IXI025-Guys-0852-DTI-??.nii.gz --o /output/path/dti.mgz

Then run dt_recon using dti.mgz as your input.

cd /path/to/desired/subjects/dir
export SUBJECTS_DIR=$(pwd)
dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i /path/to/dti.mgz --s 
andrade --o /path/to/desired/diffusion/output

Let me know if this works.

Best,
Bram

Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: Renew Andrade 
Sent: Thursday, December 20, 2018 10:12:31 AM
To: Diamond, Bram Ryder
Subject: Re: FreeSurfer: trouble processing subjects

External Email - Use Caution

I don'tknow if I understand right. I don't have a dicom format file for 
dtrecons. What I have is nii.gz all that I gave you. In case I need to do 
dcmunpack either way I need to do dtrecons for each of those dcmunpack or just 
the first one?


Sent from my iPhone

> On 20 Dec 2018, at 15:46, Diamond, Bram Ryder  
> wrote:
>
> Hi Andrade,
>
> You should be submitting the IXI025-Guys-0852-T1.nii.gz for recon-all. This 
> seems to be working fine with freesurfer v6.0 on my machine.
>
> cd /path/to/desired/subjects/dir
> export SUBJECTS_DIR=$(pwd)
> recon-all -i /path/to/IXI025-Guys-0852-T1.nii.gz -s andrade -all
>
> For the diffusion scan, you will want to run it through dt_recon. If you have 
> the raw dcms, it would easiest to use one of those as input rather than 
> combine all of your directions into one multi-frame volume. You can run 
> unpacksdcmdir to get the first dcm of the diffusion scan.
>
> cd /path/to/desired/subjects/dir
> export SUBJECTS_DIR=$(pwd)
> unpacksdcmdir -src /path/to/dicom/dir -targ /path/to/desired/log/output/ 
> -scanonly unpack.log
> dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i 
> path/to/first/diffusion/dicom.dcm --s andrade --o 
> /path/to/desired/diffusion/output
>
> I hope this helps.
>
> Best,
> Bram
>
> Bram R. Diamond, BSc
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
>
> ________
> From: Renew Andrade 
> Sent: Wednesday, December 19, 2018 3:13:18 PM
> To: Diamond, Bram Ryder
> Subject: Re: FreeSurfer: trouble processing subjects
>
>External Email - Use Caution
>
> I sent you the whole information but the problem rises in processing with 
> recon-all the DTI files.
>
> Sent from my iPhone
>
>> On 19 Dec 2018, at 16:54, Diamond, Bram Ryder  
>> wrote:
>>
>> Good morning, Andrade.
>>
>> I received a message from Bruce that suggests you are having trouble 
>> processing a few of your subjects. We received the following file from you 
>> via the Martinos Center FileDrop:
>> IXI025-Guys-0852-DTI-16.nii.gz
>> IXI025-Guys-0852-DTI-14.nii.gz
>> IXI025-Guys-0852-DTI-15.nii.gz
>> IXI025-Guys-0852-DTI-13.nii.gz
>> IXI025-Guys-0852-DTI-12.nii.gz
>> IXI025-Guys-0852-DTI-10.nii.gz
>> IXI025-Guys-0852-DTI-09.nii.gz
>> IXI025-Guys-0852-DTI-11.nii.gz
>> IXI025-Guys-0852-DTI-08.nii.gz
>> IXI025-Guys-0852-DTI-07.nii.gz
>> IXI025-Guys-0852-DTI-05.nii.gz
>> IXI025-Guys-0852-DTI-06.nii.gz
>> IXI025-Guys-0852-DTI-04.nii.gz
>> IXI025-Guys-0852-DTI-03.nii.gz
>> IXI025-Guys-0852-DTI-02.nii.gz
>> IXI025-Guys-0852-DTI-01.nii.gz
>> IXI025-Guys-0852-DTI-00.nii.gz
>> bvecs.txt
>> bvals.txt
>> IXI025-Guys-0852-T1.nii.gz
>>
>> They seem to be a separated diffusion scan (along with bvec and bcal files), 
>> and a T1. In order for me to help you, I need to know what exactly you are 
>> having trouble with.
>>
>> Thanks,
>> Bram
>>
>>
>> Bram R. Diamond, BSc
>> Research Technician II
>> Laboratory for Computational Neuroimaging
>> Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> 149 13th Street
>> Charlestown, MA 02129
>> (p): 617-726-6598
>>
>>
>>
>> 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.
>>
>
>



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Re: [Freesurfer] When no control points are needed...

[Diamond, Bram Ryder]

Hi Rosalia,


Within the FTP interface, you need to write "put two_different_problems.txt". 
It seems like you only wrote the file name. Also, the example we provide is 
"filename.txt", make sure you write your file name - only include ".txt" if 
your file has that extension.


Let me know if you have any additional questions.


Best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rosalia Dacosta Aguayo 

Sent: Monday, December 3, 2018 10:54:53 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] When no control points are needed...


External Email - Use Caution

Hi Bruce,

This is the directory where I have the data:

/home/rosalia/Desktop/transfer

And I changed the directory before doing FTP...and then asked again for the 
directory and I wrote the same directory  and then when asked me for the name 
of the file, I provided the name of the file.txt

Thank you,
Rosalia

On Mon, Dec 3, 2018 at 4:51 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
is that the right directory/path on your end?

On Mon, 3 Dec 2018, Rosalia Dacosta
Aguayo wrote:

>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thank you for your reply.
> I am having problems when trying to upload the two files with FTP, it seems
> the problem is with the directory.
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
?? ?
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd home/rosalia/Desktop/transfer
> 550 Failed to change directory.
> ftp>
>
>
> On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>>
> wrote:
>   Hi Rosalia
>
>   you always have to run autorecon3 every time autorecon2 is run
>
>   cheers
>   Bruce
>
>
>   On Mon, 3 Dec 2018, Rosalia
>   Dacosta Aguayo wrote:
>
>   >
>   > External Email - Use Caution
>   >
>   > Dear Bruce and Bram,
>   >
>   > After improving the pial surface for my participants, I have
>   seen that some of them do not need
>   > control points. My question is: for those ones, should I run
>   -autorecon2 and -autorecon3 or only
>   > -autorecon3.
>   >
>   > Hi Bruce and Bram, I will try to upload two problematic files.
>   When I told you that I have been
>   > editing all my participants I was referring that some of them
>   need more editing than others, and the
>   > ones that needed the less I just tried to improve the pial
>   surface not too much, but now the results
>   > are better than before.
>   >
>   > Thank you in advance for your help.Yours sincerely,
>   > Rosalia
>   >
>   >___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu
>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

I'm not sure why there is no error with the mri_convert function, but it 
somehow took in your BE2_T1.nii and creating a corrupted 001.mgz. The 
rawavg.mgz is just a copy of the 001.mgz, so it's no surprise that it has the 
same issues. You only get an error when recon-all attempts to run mri_convert 
on the rawavg.mgz.


The corrupted 001.mgz is only 8K - it should be more like 12M. I can't open it 
in Matlab with MRIread to see what might have gone wrong. I'm not sure what the 
problem is, but it is definitely local to whatever machine you are using to run 
recon-all. I've run the nifty you uploaded through recon-all using freesurfer 
5.3 without an issue on my machine.


Please let me know if downloading freesurfer again fixes the issue.


Best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Batuhan Erkat 

Sent: Saturday, December 1, 2018 9:52:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

I will ask our admin to do so. I also don't have any problems on my personal 
computer, so my T1 image should be fine, but the problem starts at mri_convert 
function, which surprisingly gives no error. Is it possible for you to look at 
the 001.mgz and rawavg.mgz files and see what could be the problem with the 
mri_convert function?

Best,
Batuhan

On Sat, Dec 1, 2018 at 12:54 AM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

It's strange, but I'm not having the same issue. Can you try downloading 5.3 
again and see if that fixes your issue?


Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Friday, November 30, 2018 12:49:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Can you please upload the BE2_T1.nii?


Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Thursday, November 29, 2018 12:35:06 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I finally did it, thank you for your help, and sorry about my noobity!

ftp> put BE2.tar.xz
local: BE2.tar.xz remote: BE2.tar.xz
200 PORT command successful. Consider using PASV.
150 Ok to send data.
226 Transfer complete.
61572 bytes sent in 0.15 secs (402.3777 kB/s)

Best regards,
Batuhan

On Thu, Nov 29, 2018 at 5:36 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

I can't see any of your data. The problem is likely that you are feeding the 
full file path. Try using just the file name without the path. First cd to your 
data directory, then log on to the freesurfer FTP file exchange and follow the 
instructions on our wiki.

Thanks for your patience! I'll be updating our wiki documentation to be more 
clear.

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

It's strange, but I'm not having the same issue. Can you try downloading 5.3 
again and see if that fixes your issue?


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Batuhan Erkat 

Sent: Friday, November 30, 2018 12:49:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Can you please upload the BE2_T1.nii?


Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Thursday, November 29, 2018 12:35:06 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I finally did it, thank you for your help, and sorry about my noobity!

ftp> put BE2.tar.xz
local: BE2.tar.xz remote: BE2.tar.xz
200 PORT command successful. Consider using PASV.
150 Ok to send data.
226 Transfer complete.
61572 bytes sent in 0.15 secs (402.3777 kB/s)

Best regards,
Batuhan

On Thu, Nov 29, 2018 at 5:36 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

I can't see any of your data. The problem is likely that you are feeding the 
full file path. Try using just the file name without the path. First cd to your 
data directory, then log on to the freesurfer FTP file exchange and follow the 
instructions on our wiki.

Thanks for your patience! I'll be updating our wiki documentation to be more 
clear.

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

I tried to put the subject folder in tar.xz format for ease, this is what I get:

ftp> put /home/gorkem/output/BE2.tar.xz
local: /home/gorkem/output/BE2.tar.xz remote: /home/gorkem/output/BE2.tar.xz
200 PORT command successful. Consider using PASV.
553 Could not create file.

Best,
Batuhan

On Tue, Nov 27, 2018 at 12:47 PM Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>> wrote:
Hello Bram,

I just followed the guideline at FTPFileExchange, put them to transfer/incoming.

Files I put are:
001.mgz
rawavg.mgz
build-stamp.txt
recon-all-status.log
recon-all.cmd
recon-all.env
recon-all.error
recon-all.local-copy
recon-all.log
error.log

I tried to create a folder, but of course I don't have permission. If you can 
open a folder named Batuhan, or something like that, I can put them there. 
Also, I tried and couldn't put my subject folder directly via Filezilla or the 
terminal.

Best,
Batuhan

On Mon, Nov 26, 2018 at 10:23 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Hi Batuhan,


I'm trying to access the files now.  What is the name of the files/directory 
you uploaded? I'm not sure they transferred.


Thanks,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Wednesday, November 21, 2018 12:01:53 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

Can you please upload the BE2_T1.nii?


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Batuhan Erkat 

Sent: Thursday, November 29, 2018 12:35:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I finally did it, thank you for your help, and sorry about my noobity!

ftp> put BE2.tar.xz
local: BE2.tar.xz remote: BE2.tar.xz
200 PORT command successful. Consider using PASV.
150 Ok to send data.
226 Transfer complete.
61572 bytes sent in 0.15 secs (402.3777 kB/s)

Best regards,
Batuhan

On Thu, Nov 29, 2018 at 5:36 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

I can't see any of your data. The problem is likely that you are feeding the 
full file path. Try using just the file name without the path. First cd to your 
data directory, then log on to the freesurfer FTP file exchange and follow the 
instructions on our wiki.

Thanks for your patience! I'll be updating our wiki documentation to be more 
clear.

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

I tried to put the subject folder in tar.xz format for ease, this is what I get:

ftp> put /home/gorkem/output/BE2.tar.xz
local: /home/gorkem/output/BE2.tar.xz remote: /home/gorkem/output/BE2.tar.xz
200 PORT command successful. Consider using PASV.
553 Could not create file.

Best,
Batuhan

On Tue, Nov 27, 2018 at 12:47 PM Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>> wrote:
Hello Bram,

I just followed the guideline at FTPFileExchange, put them to transfer/incoming.

Files I put are:
001.mgz
rawavg.mgz
build-stamp.txt
recon-all-status.log
recon-all.cmd
recon-all.env
recon-all.error
recon-all.local-copy
recon-all.log
error.log

I tried to create a folder, but of course I don't have permission. If you can 
open a folder named Batuhan, or something like that, I can put them there. 
Also, I tried and couldn't put my subject folder directly via Filezilla or the 
terminal.

Best,
Batuhan

On Mon, Nov 26, 2018 at 10:23 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Hi Batuhan,


I'm trying to access the files now.  What is the name of the files/directory 
you uploaded? I'm not sure they transferred.


Thanks,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Wednesday, November 21, 2018 12:01:53 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I uploaded all the files, including my input image and recon-all scripts. As 
you can see, there are no errors for mri_convert, but there is for mghRead(). 
If you inspect the 001.mgz and rawavg.mgz files, you'll realize that they are 
corrupted and probably that's why mghRead fails to read rawavg.mgz.

Can you see the files, did I do the file transmission correctly?

Best,
Batuhan

On Wed, Nov 21, 2018 at 7:32 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Hi Batuhan,

Can you please upload the BE2 subject data using our ftp file exchange and let 
me know the exact command and terminal output when you ran mri_convert?

Info on our ftp file exchange: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Bio

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

I can't see any of your data. The problem is likely that you are feeding the 
full file path. Try using just the file name without the path. First cd to your 
data directory, then log on to the freesurfer FTP file exchange and follow the 
instructions on our wiki.

Thanks for your patience! I'll be updating our wiki documentation to be more 
clear.

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Batuhan Erkat 

Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

I tried to put the subject folder in tar.xz format for ease, this is what I get:

ftp> put /home/gorkem/output/BE2.tar.xz
local: /home/gorkem/output/BE2.tar.xz remote: /home/gorkem/output/BE2.tar.xz
200 PORT command successful. Consider using PASV.
553 Could not create file.

Best,
Batuhan

On Tue, Nov 27, 2018 at 12:47 PM Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>> wrote:
Hello Bram,

I just followed the guideline at FTPFileExchange, put them to transfer/incoming.

Files I put are:
001.mgz
rawavg.mgz
build-stamp.txt
recon-all-status.log
recon-all.cmd
recon-all.env
recon-all.error
recon-all.local-copy
recon-all.log
error.log

I tried to create a folder, but of course I don't have permission. If you can 
open a folder named Batuhan, or something like that, I can put them there. 
Also, I tried and couldn't put my subject folder directly via Filezilla or the 
terminal.

Best,
Batuhan

On Mon, Nov 26, 2018 at 10:23 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Hi Batuhan,


I'm trying to access the files now.  What is the name of the files/directory 
you uploaded? I'm not sure they transferred.


Thanks,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Wednesday, November 21, 2018 12:01:53 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I uploaded all the files, including my input image and recon-all scripts. As 
you can see, there are no errors for mri_convert, but there is for mghRead(). 
If you inspect the 001.mgz and rawavg.mgz files, you'll realize that they are 
corrupted and probably that's why mghRead fails to read rawavg.mgz.

Can you see the files, did I do the file transmission correctly?

Best,
Batuhan

On Wed, Nov 21, 2018 at 7:32 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Hi Batuhan,

Can you please upload the BE2 subject data using our ftp file exchange and let 
me know the exact command and terminal output when you ran mri_convert?

Info on our ftp file exchange: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--

MSc Candidate

Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--

MSc Candidate

Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey


--

MSc Candidate

Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey
___
Freesu

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

Hi Batuhan,


I'm trying to access the files now.  What is the name of the files/directory 
you uploaded? I'm not sure they transferred.


Thanks,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Batuhan Erkat 

Sent: Wednesday, November 21, 2018 12:01:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I uploaded all the files, including my input image and recon-all scripts. As 
you can see, there are no errors for mri_convert, but there is for mghRead(). 
If you inspect the 001.mgz and rawavg.mgz files, you'll realize that they are 
corrupted and probably that's why mghRead fails to read rawavg.mgz.

Can you see the files, did I do the file transmission correctly?

Best,
Batuhan

On Wed, Nov 21, 2018 at 7:32 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Hi Batuhan,

Can you please upload the BE2 subject data using our ftp file exchange and let 
me know the exact command and terminal output when you ran mri_convert?

Info on our ftp file exchange: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--

MSc Candidate

Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

Hi Batuhan,

Can you please upload the BE2 subject data using our ftp file exchange and let 
me know the exact command and terminal output when you ran mri_convert?

Info on our ftp file exchange: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Possibly - I would definitely start there. The surfaces are following the 
corpus callosum into the right hemisphere because the aseg labeling is off.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:48:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled 
too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think 
that can fix the middle line?
​

Thanks,
Maxime



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Diamond, Bram Ryder 

Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline


Hi Maxime,


What did you edit in the aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Sorry. Here are the good links :

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t

Maxime

On Oct 16, 2018, at 2:22 PM, Maxime Perron 
mailto:maxime.perro...@ulaval.ca>> wrote:


External Email - Use Caution

Hi Bram,

No worries.

Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h

Thanks,
Maxime

On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:


Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime,

I'll take a look at your data and the issue you're having and get back to you 
after the weekend.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on th

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,


What did you edit in the aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Sorry. Here are the good links :

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t

Maxime

On Oct 16, 2018, at 2:22 PM, Maxime Perron 
mailto:maxime.perro...@ulaval.ca>> wrote:


External Email - Use Caution

Hi Bram,

No worries.

Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h

Thanks,
Maxime

On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:


Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime,

I'll take a look at your data and the issue you're having and get back to you 
after the weekend.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation 

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Diamond, Bram Ryder 

Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline


Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you 
after the weekend.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
>>>>External Email - Use Caution
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
>>>> midline cutting error, that
>>>> is the midline does not go through exactly the center of the brain in 
>>>> coronal cut. For example, the
>>>> midline is a little bit fuzzy and goes through an hemisphere than the 
>>>> other (see attachment). I've
>>>> searched in the mail list and ​I don't find the way to fix it. Does anyone 
>>>> have any idea to fix it?
>>>> Thank you,
>>>> Maxime Perron
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you 
after the weekend.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
External Email - Use Caution
 Hello FreeSurfer Developers,

 I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
 midline cutting error, that
 is the midline does not go through exactly the center of the brain in 
 coronal cut. For example, the
 midline is a little bit fuzzy and goes through an hemisphere than the 
 other (see attachment). I've
 searched in the mail list and ​I don't find the way to fix it. Does anyone 
 have any idea to fix it?
 Thank you,
 Maxime Perron
>>> ___
>>> 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
>>
>>
> ___
> 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] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

Yes - if you've used the -bigventricles flag, you should always include it with 
the recon-all command.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Matthieu Vanhoutte 

Sent: Tuesday, September 18, 2018 12:45:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed


External Email - Use Caution

Ok I will test it on normal subjects.

Do I have to put this -bigventricles flag on all recon-all commands following 
manual editing of brainmask, white matter,...etc or just once at the first 
recon-all -all command ?

Best,
Matthieu

Le mar. 18 sept. 2018 à 18:03, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> a écrit :
I think it should be ok. It will be a bit slower, but shouldn't reduce
accuracy I don't think. Try it and see
Bruce
On Tue, 18 Sep 2018, Matthieu
Vanhoutte wrote:

>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thanks, but in this case will recon-all with -bigventricles flag work well on 
> normal patients
> without big ventricles ?
>
> Best,
> Matthieu
>
> 2018-09-18 15:56 GMT+00:00 Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>>:
>   Hi Matthieu
>
>   yes, you will want to run all of your subjects with it
>
>   cheers
>   Bruce
>   On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
>
>
> External Email - Use Caution
>
> Dear Bram,
>
> It looks like the -bigventricles flag fixed my problem with my 
> specific
> subject. Not only, this took
> into account large ventricles but also corrected grey matter 
> segmentation
> from extra Dura tissue
> that was erroneously segmented in GM.
>
> I understand the first point of amelioration allowed by the flag 
> but don't
> understand where the
> second point come from ?
>
> If I used the -bigventricles flag for all my atrophied and large 
> ventricles
> patients and not for my
> healthy patients, wouldn't it introduce a bias when further 
> statistically
>     comparing groups between
> them ?
>
> Best,
> Matthieu
>
> 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder 
> mailto:brdiam...@mgh.harvard.edu>>:
>   If you haven't already, you may want to run the subject 
> through
> recon-all with the
>   -bigventricles flag since it looks like the lateral 
> ventricle was
> significantly
>   mislabeled in the aseg. If using the -bigventricles flag 
> doesn't fix
> your problem, you
>   can edit the aseg.mgz manually by following the directions 
> in this
> tutorial. Then run
>   the following command (again, substituting  for 
> your
> subject's id):
> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>
> I would try this before doing the wm.mgz edits I suggested in my 
> previous
> email.
>
> Best,
> Bram
>
> _______
> _
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> 
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  on
> behalf of Diamond, Bram Ryder 
> mailto:brdiam...@mgh.harvard.edu>>
> Sent: Friday, September 14, 2018 11:07:42 AM
> To: 
> matthieuvanhou...@gmail.com<mailto:matthieuvanhou...@gmail.com>
> Cc: 
> freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; 
> astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Troubles to determine the type of recon 
> editing needed
>
>
> Hi Matthieu,
>
>
> I've taken a look through the files you shared with us and I see 
> the poor
> surfaces in the
> posterior right hemisphere you were referring to in your message. 
> It looks
> like your subject
> has a combination of abnormally large ventricles and significant 
> wm
> abnormalities, so I'm
> surprised FreeSurfer did as well as it did.
>
>
> As for the recon editing - I would recommend editing the wm.mgz 
> to more
> accurately represent
> the wm from slice 84 to 39. You

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

Hi Matthieu,


The initial estimate for surfaces is based off the wm.mgz. Since you're wm.mgz 
is incorrect (due to the large ventricles and wm abnormalities) the first pass 
at a surface reconstruction is way off. The wm.mgz is created in-part from the 
aseg.mgz, so it is important that you ensure your aseg.mgz is accurate. 
Additionally, it will be useful to have an accurate aseg.mgz for subcortical 
analyses.


I hope that answers your question.


Bram


From: Matthieu Vanhoutte 
Sent: Friday, September 14, 2018 4:48:36 PM
To: Diamond, Bram Ryder
Cc: Freesurfer support list
Subject: Re: Troubles to determine the type of recon editing needed


External Email - Use Caution

Dear Bram,

Thank you for your answer. As soon as possible I will run recon-all with the 
-bigventricles flag.

Concerning the manual editing I don't understand well the aim of editing 
aseg.mgz since it seems to most concern subcortical structures and statistics 
and not have an impact on surfaces computed ?

Best,
Matthieu

Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> a écrit :
If you haven't already, you may want to run the subject through recon-all with 
the -bigventricles flag since it looks like the lateral ventricle was 
significantly mislabeled in the aseg. If using the -bigventricles flag doesn't 
fix your problem, you can edit the aseg.mgz manually by following the 
directions in this 
tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations>.
 Then run the following command (again, substituting  for your 
subject's id):

recon-all -autorecon2-noaseg -autorecon3 -subjid 

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com<mailto:matthieuvanhou...@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; 
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Troubles to determine the type of recon editing needed


Hi Matthieu,


I've taken a look through the files you shared with us and I see the poor 
surfaces in the posterior right hemisphere you were referring to in your 
message. It looks like your subject has a combination of abnormally large 
ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as 
well as it did.


As for the recon editing - I would recommend editing the wm.mgz to more 
accurately represent the wm from slice 84 to 39. You can take a look at the 
white matter edits 
tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0>
 for details on how to do that. Then run the following command (substituting 
 for your subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


The surface reconstruction may also benefit from labeling the right lateral 
ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since 
you didn't send us the surfaces for the left hemisphere. Before you do that, 
edit the wm.mgz as explained in the tutorial and tell us how that goes.


All the best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


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Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

If you haven't already, you may want to run the subject through recon-all with 
the -bigventricles flag since it looks like the lateral ventricle was 
significantly mislabeled in the aseg. If using the -bigventricles flag doesn't 
fix your problem, you can edit the aseg.mgz manually by following the 
directions in this 
tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations>.
 Then run the following command (again, substituting  for your 
subject's id):

recon-all -autorecon2-noaseg -autorecon3 -subjid 

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best,
Bram

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Diamond, Bram Ryder 

Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type of recon editing needed


Hi Matthieu,


I've taken a look through the files you shared with us and I see the poor 
surfaces in the posterior right hemisphere you were referring to in your 
message. It looks like your subject has a combination of abnormally large 
ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as 
well as it did.


As for the recon editing - I would recommend editing the wm.mgz to more 
accurately represent the wm from slice 84 to 39. You can take a look at the 
white matter edits 
tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0>
 for details on how to do that. Then run the following command (substituting 
 for your subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


The surface reconstruction may also benefit from labeling the right lateral 
ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since 
you didn't send us the surfaces for the left hemisphere. Before you do that, 
edit the wm.mgz as explained in the tutorial and tell us how that goes.


All the best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598

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[Freesurfer] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

Hi Matthieu,


I've taken a look through the files you shared with us and I see the poor 
surfaces in the posterior right hemisphere you were referring to in your 
message. It looks like your subject has a combination of abnormally large 
ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as 
well as it did.


As for the recon editing - I would recommend editing the wm.mgz to more 
accurately represent the wm from slice 84 to 39. You can take a look at the 
white matter edits 
tutorial
 for details on how to do that. Then run the following command (substituting 
 for your subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


The surface reconstruction may also benefit from labeling the right lateral 
ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since 
you didn't send us the surfaces for the left hemisphere. Before you do that, 
edit the wm.mgz as explained in the tutorial and tell us how that goes.


All the best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598

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Re: [Freesurfer] Manually editing location of surface

[Diamond, Bram Ryder]

Hi Elena,


I've taken a look through the files you shared with us and can only find the 
complete subject directories for sub-90188_run-01_T1w and sub-90310. The 
subject directory for sub-01262 (and 209 other subjects) is empty. Could you 
please send another link with the subject directory for sub-01262?


Thanks,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Elena Nicole Dominguez 

Sent: Wednesday, August 22, 2018 3:01:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manually editing location of surface


External Email - Use Caution

The subject in particular is in their 90's. I have been seeing a similar 
occurrence in many of my other subjects as well. I will be attaching a link 
through google drive to share the subject I recently sent. 
(https://drive.google.com/a/uci.edu/file/d/1ZuekNGyEJ7gPbM3Yl3S8HeNMVLL60l0_/view?usp=sharing)

Thank you for your help in looking into this and please let me know what else 
is needed on my behalf.

[https://drive-thirdparty.googleusercontent.com/16/type/application/x-gzip] 
sub-01262.tar.gz


On Wed, Aug 22, 2018 at 8:44 AM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
wow, looks like a pretty serious failure (which we rarely see). If you
tar, gzip and ftp the entire subject dir for this subject we will take a
look

cheers
Bruce
On Tue, 21 Aug 2018, Elena Nicole Dominguez wrote:

>
> External Email - Use Caution
>
> Thank you for getting back to me. I am attaching an example of one of the 
> problems I am encountering.
>
> On Tue, Aug 21, 2018 at 8:57 AM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>   Hi Elena
>
>   can you send us an image to show us what the issue is? The correct
>   intervention depends on why the surface is not correct.
>
>   cheers
>   Bruce
>   On Fri, 17 Aug 2018,
>   Elena Nicole Dominguez wrote:
>
>   >
>   > External Email - Use Caution
>   >
>   > Hello FreeSurfer Developers,
>   > On the tutorial it states that it is not possible to directly edit 
> the location of a surface.
>   > However, on the corresponding video posted onto the website the 
> gentleman mentions being able to
>   > accomplish this. I have been trying to locate the literature on how 
> to do this and have not been
>   > successful. I am using 
> 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c'
>   >
>   > I would kindly appreciate some help on locating any tutorials or 
> information available.
>   >
>   > Thank you for your help.
>   >
>   >___
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>   contains patient information, please contact the Partners Compliance 
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> properly
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Re: [Freesurfer] Lookup Table

[Diamond, Bram Ryder]

Hi Jason,


You can use mri_binarize to extract a wm-hypointensities.mgz volume and view 
that over the orig.mgz.  The following will make a binary volume called 
wm-hypointensities.mgz from all voxels in the aseg.mgz with an intensity of 77 
- all voxels labeled wm-hypointensities:


mri_binarize --i mri/aseg.mgz --o mri/wm-hypointensities.mgz --match 77


Then view the new wm-hypointensities volume over the orig.mgz like this:


freeview mri/orig.mgz mri/wm-hypointensities.mgz:colormap=heat


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ledesma, Jason 

Sent: Wednesday, February 21, 2018 1:53:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Lookup Table


Hi,


When viewing MRI mgz images in Freeview, is it possible to only look at certain 
structures specified in the look up table?  That is, to only view colorization 
of one structure to view it more concisely?  Specifically, we want to look at 
wm-hypointensities to see lesion approximations. Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



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Re: [Freesurfer] external WM and GM masks as input to recon-all?

[Diamond, Bram Ryder]

Hi Shadia,


How did you make the externally-derived ribbons?  Can you please send us your 
recon-all.log and your subject directory so we can take a look? 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange


Thanks,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of MIKHAEL Shadia 

Sent: Sunday, January 21, 2018 1:58:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] external WM and GM masks as input to recon-all?

Dear Bruce,

Thank you for your reply at 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055512.html 
regarding the use of grey and white matter masks.

Since you were suggesting that this may be difficult, I have instead tried to 
introduce external masks at a later stage (ribbons) in the process as follows:
running recon-all once (run1), all the way through, then replacing 
?h.ribbon.nii and ?h.ribbon.mgz with externally-derived ribbons, before calling 
recon-all a second time (run2) in FreeSurfer 6.0 as follows:

recon-all -autorecon-pial -parcstats -cortparc2 -parcstats2 -cortparc3 
-parcstats3 -subjid s1-freesurfer60-run2-external_ribbon

I have experimented with the following 2 setups for this 2nd run of recon-all:
1. run2-setup1: keeping all the files in the 'mri' directory generated by run 
1, except for ?h.ribbon.nii and ?h.ribbon.mgz which I'm replacing by the 
externally-derived ones
2. run2-setup2: keeping only the files in the 'mri' directory generated by run 
1  before ?h.ribbon.nii and ?h.ribbon.mgz. Files generated after those 2 were 
deleted, and the ribbons were replaced by the externally-derived ones

I have found that in both cases, the ?h.ribbon.mgz are getting modified by the 
recon-all process, and the stats file is identical to that of run 1, which is 
not what I was hoping for. Altering the ribbons did not alter the parcellation 
& corresponding stats.

Could you please advise on the steps that I've missed/done wrongly in order for 
the ribbon changes to get incorporated? Should I be clearing the 'stats' 
directory? And is the 2nd run of recon-all correct? Any tips would be greatly 
appreciated.

Thank you in advance.

Shadia



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


-Original Message-
From: MIKHAEL Shadia
Sent: 12 January 2018 18:43
To: freesurfer@nmr.mgh.harvard.edu
Subject: external WM and GM masks as input to recon-all?

Dear FreeSurfer experts,

Could you please advise on whether it would be possible to run recon-all in 
FreeSurfer 6.0 using externally-derived probabilistic white matter and grey 
matter masks, both of which include the cerebellum but not the ventricles, and 
if so, how? Would the flag -autorecon2-pial suffice?

Thank you in advance.

Shadia


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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Diamond, Bram Ryder]

Hi Martin,


I will have to defer to Bruce or Doug regarding the validity of analyzing 
FreeSurfer output for your subject - although I would not recommend any 
analysis on the current state of your subject's surfaces.  After glancing at 
your data, I have a few recommendations:


  1.  You seem to be using an excessive number of control points.  Control 
points are designed for diffuse intensity normalize - using too many control 
points is unnecessary and possibly counterproductive.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0?highlight=%28control%29%7C%28point%29
 for more information on control points.
  2.  I've noticed that your brainmask.mgz is missing a large portion of your 
subject's cerebellum.  This most likely caused some issues down the recon-all 
pipeline so you should address this issue first.  You can change the watershed 
value to adjust the brain extraction.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 for 
information of fixing a bad skull strip.
  3.  Since the wm.mgz has done such a poor job of identifying white matter, I 
would suggest directly editing the wm.mgz.  Of course, only edit the wm.mgz 
after first attempting to use (fewer) control points on a better skull-stripped 
brainmask.mgz.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for 
information on editing the wm.mgz.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Loeffler, Martin 
<martin.loeff...@zi-mannheim.de>
Sent: Saturday, December 23, 2017 4:26:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst


Dear Bruce,

Dear Bram,



Thanks a lot for having a look. Unfortunately the left hemisphere is equally 
important as the right one for our question of interest. With a lot of patience 
the recon-all has finished and the result looks surprisingly ok. I have 
additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after 
setting control points to correct errors in the wm.mgz. Some errors were 
corrected, but not all. Next I would like to correct the surfaces.

My questions:

-  I know that recon-all is not designed for such a subject. But is 
there any argument against continuing the analysis now?

-  What can I do for those errors where the wm.mgz is still false, 
despite control points?

I have uploaded the respective files.



Best,

Martin





Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram 
Ryder
Gesendet: Mittwoch, 13. Dezember 2017 23:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst



Hi Martin,



We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.



Best,

Bram



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Loeffler, Martin 
<martin.loeff...@zi-mannheim.de<mailto:martin.loeff...@zi-mannheim.de>>
Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst



Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harv

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Diamond, Bram Ryder]

Hi Martin,


We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loeffler, Martin 

Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von
> Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura
> attached, etc...). Try looking at the ?h.orig.nofix and/or the
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to
>> advance.
>>
>> Following this post:
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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